Is there a plant genome project similar to the human genome project?
1000 Plant Genomes Project
While the 1000 Genomes Project has been initially estimated to cost up to $50 million USD, the 1000 Plant Genomes Project will likely not be as expensive; the difference in cost comes from the target sequence in the genomes. Since the 1000 Plant Genomes Project will only be sequencing the transcriptome, whereas the human project will sequence as much of the genome as is decided feasible, there is a much lower amount of sequencing effort needed in this more specific approach. While this means that there will be less overall sequence output relative to the 1000 Genomes Project, the non-coding portions of the genomes excluded in the 1000 Plant Genomes Project are not important to its goals like they are to the human project. So then the more focused approach of the 1000 Plant Genomes Project minimizes cost while still achieving its goals.
Exposome
The idea of a Human Exposome Project, analogous to the Human Genome Project, has been proposed and discussed in numerous scientific meetings, but as of 2017, no such project exists. Given the lack of clarity on how science would go about pursuing such a project, support has been lacking. Reports on the issue include:The concept of the exposome has contributed to the 2010 proposal of a new paradigm in disease phenotype, "the unique disease principle": Every individual has a unique disease process different from any other individual, considering uniqueness of the exposome and its unique influence on molecular pathologic processes including alterations in the interactome. This principle was first described in neoplastic diseases as "the unique tumor principle". Based on this unique disease principle, the interdisciplinary field of molecular pathological epidemiology (MPE) integrates molecular pathology and epidemiology.
Whole genome sequencing
In 1999, the entire DNA sequence of human chromosome 22, the shortest human autosome, was published. By the year 2000, the second animal and second invertebrate (yet first insect) genome was sequenced - that of the fruit fly "Drosophila melanogaster" - a popular choice of model organism in experimental research. The first plant genome - that of the model organism "Arabidopsis thaliana" - was also fully sequenced by 2000. By 2001, a draft of the entire human genome sequence was published. The genome of the laboratory mouse "Mus musculus" was completed in 2002.
Human Genome Project
Due to widespread international cooperation and advances in the field of genomics (especially in sequence analysis), as well as major advances in computing technology, a 'rough draft' of the genome was finished in 2000 (announced jointly by U.S. President Bill Clinton and the British Prime Minister Tony Blair on June 26, 2000). This first available rough draft assembly of the genome was completed by the Genome Bioinformatics Group at the University of California, Santa Cruz, primarily led by then graduate student Jim Kent. Ongoing sequencing led to the announcement of the essentially complete genome on April 14, 2003, two years earlier than planned. In May 2006, another milestone was passed on the way to completion of the project, when the sequence of the last chromosome was published in "Nature".
Oak
Beginning November 1, 2011, a project began to sequence the entire oak genome. The goal of the project is to create a high resolution sequence of the Quercus robur genome, and to study genetic diversity by comparison of the genomes of different species. Current research has compiled genomic data from many different sources and techniques to create a genome map with 89% coverage of the genome. The project is still in the process of annotating this genome.
Evolutionary history of plants
Genome doubling is a relatively common occurrence in plant evolution and results in polyploidy, which is consequently a common feature in plants. It is estimated that at least half (and probably all) plants have seen genome doubling in their history. Genome doubling entails gene duplication, thus generating functional redundancy in most genes. The duplicated genes may attain new function, either by changes in expression pattern or changes in activity. Polyploidy and gene duplication are believed to be among the most powerful forces in evolution of plant form; though it is not known why genome doubling is such a frequent process in plants. One probable reason is the production of large amounts of secondary metabolites in plant cells. Some of them might interfere in the normal process of chromosomal segregation, causing genome duplication.
In recent times, plants have been shown to possess significant microRNA families, which are conserved across many plant lineages. In comparison to animals, while the number of plant miRNA families are lesser than animals, the size of each family is much larger. The miRNA genes are also much more spread out in the genome than those in animals, where they are more clustered. It has been proposed that these miRNA families have expanded by duplications of chromosomal regions. Many miRNA genes involved in regulation of plant development have been found to be quite conserved between plants studied.
Walter Gilbert
Gilbert was an early proponent of sequencing the human genome. At a March 1986 meeting in Santa Fe New Mexico he proclaimed "The total human sequence is the grail of human genetics". In 1987, he proposed starting a company called Genome Corporation to sequence the genome and sell access to the information. In an opinion piece in Nature in 1991, he envisioned completion of the human genome sequence transforming biology into a field in which computer databases would be as essential as laboratory reagents
Cognitive genomics
In 2003, the Human Genome Project produced the first complete human genome. Despite the project’s success, very little is known about cognitive gene expression. Prior to 2003, any evidence concerning human brain connectivity was based on post-mortem observations. Due to ethical concerns, no invasive in vivo genomics studies have been performed on live humans.
Chimpanzee genome project
Human and chimpanzee chromosomes are very similar. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. Humans have 23 pairs of chromosomes and other great apes have 24 pairs of chromosomes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres, producing human chromosome 2. There are nine other major chromosomal differences between chimpanzees and humans: chromosome segment inversions on human chromosomes 1, 4, 5, 9, 12, 15, 16, 17, and 18. After the completion of the Human genome project, a common chimpanzee genome project was initiated. In December 2003, a preliminary analysis of 7600 genes shared between the two genomes confirmed that certain genes such as the forkhead-box P2 transcription factor, which is involved in speech development, are different in the human lineage. Several genes involved in hearing were also found to have changed during human evolution, suggesting selection involving human language-related behavior. Differences between individual humans and common chimpanzees are estimated to be about 10 times the typical difference between pairs of humans.
Plant genome assembly
In general, for sequencing and assembling large and complex genomes like plants, different strategies are used, based on the technologies available at that time when the project started.
1000 Plant Genomes Project
Many plant species (especially agriculturally manipulated ones) are known to have undergone large genome-wide changes through duplication of the whole genome. The rice and the wheat genomes, for example, can have 4-6 copies of whole genomes (wheat) whereas animals typically only have 2 (diploidy). These duplicated genes may pose a problem for the "de novo" assembly of sequence fragments, because repeat sequences confuse the computer programs when trying to put the fragments together, and they can be difficult to track through evolution.
History of research on Arabidopsis thaliana
An international consortium began sequencing and assembly of a draft genome for "A. thaliana" in 1990. 
This work paralleled the Human Genome Project
and related projects for other model organisms,
and built on efforts to sequence expressed sequence tags
from "A. thaliana".
Descriptions of the sequences of chromosomes 4 and 2 were published in 1999,
and the project was completed in 2000.
This represented the first reference genome for a flowering plant and facilitated comparative genomics.
Fiocruz Genome Comparison Project
The Fiocruz Genome Comparison Project is a collaborative effort involving Brazil's Oswaldo Cruz Institute and IBM's World Community Grid, designed to produce a database comparing the genes from many genomes with each other using SSEARCH. The program SSEARCH performs a rigorous Smith–Waterman alignment between a protein sequence and another protein sequence, a protein database, a DNA or a DNA library.
The nature of the computation in the project allows it to easily take advantage of distributed computing. This, along with the likely humanitarian benefits of the research, has led the World Community Grid (a distributed computing grid that uses idle computer clock time) to run the Fiocruz project. All products are in the public domain by contract with WCG.
Copidosoma floridanum
A cosmopolitan species, "Copidosoma floridanum" is distributed worldwide. Because of its significance to agriculture as pest control and its phylogenic relationship with other important species, the wasp's genome is being sequenced by the Human Genome Sequencing Center as part of the i5K project, which aims to sequence the genomes of 5,000 arthropods.
Earth BioGenome Project
The initiative was inspired by Human Genome Project, and emerged during November 2015 meeting between Harris Lewin (UCD), Gene E. Robinson (IGB) and W. John Kress (Smithsonian Institution's National Museum of Natural History). In February 2017, at major conference on genomics and biodiversity organized by the Smithsonian Institution and BGI in Washington, D.C. was supported project's 10-year plan and organizational structure.
Plant Proteome Database
The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants. It includes data for two plants that are widely studied in molecular biology, Arabidopsis thaliana and maize (Zea mays). Initially the project was limited to plant plastids, under the name of the Plastid PDB, but was expanded and renamed Plant PDB in November 2007.
Human Genome Project
Although the working draft was announced in June 2000, it was not until February 2001 that Celera and the HGP scientists published details of their drafts. Special issues of "Nature" (which published the publicly funded project's scientific paper) and "Science" (which published Celera's paper) described the methods used to produce the draft sequence and offered analysis of the sequence. These drafts covered about 83% of the genome (90% of the euchromatic regions with 150,000 gaps and the order and orientation of many segments not yet established). In February 2001, at the time of the joint publications, press releases announced that the project had been completed by both groups. Improved drafts were announced in 2003 and 2005, filling in to approximately 92% of the sequence currently.
Genome project
Genome assembly is a very difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as repeats. These repeats can be thousands of nucleotides long, and some occur in thousands of different locations, especially in the large genomes of plants and animals.
Michael Smith (chemist)
Throughout the 1980s, Smith and his colleagues at the Canadian Institute for Advanced Research advocated for the establishment of a facility that would enable Canada to play a part in what had become known as the Human Genome Project. Eventually, funding was secured from the BC Cancer Agency and in 1999 the Genome Sequence Centre was established with a mandate to develop and deploy genomics technologies in support of the life sciences, and in particular cancer research. The Genome Sciences Centre also provided technology to Genome Canada and Genome BC projects in the areas of human health, the environment, forestry, agriculture, and aquaculture.
Social history of viruses
The Human Genome Project has revealed the presence of numerous viral DNA sequences scattered throughout the human genome. These sequences make up around eight per cent of human DNA, and appear to be the remains of ancient retrovirus infections of human ancestors. These pieces of DNA have firmly established themselves in human DNA. Most of this DNA is no longer functional, but some of these friendly viruses have brought with them novel genes that are important in human development. Viruses have transferred important genes to plants. About ten per cent of all photosynthesis uses the products of genes that have been transferred to plants from blue-green algae by viruses.
List of drugs by year of discovery
21st century begins with the first complete sequences of individual human genomes by Human Genome Project, on February 12, 2001, this allowed a switch in drug development and research from the traditional way of drug discovery that was isolating molecules from plants or animals or create new molecules and see if they could be useful in treatment of illness in humans, to pharmacogenomics, that is the study and knowledge of how genes respond to drugs. Another field beneficed by Human Genome Project is pharmacogenetics, that is the study of inherited genetic differences in drug metabolic pathways which can affect individual responses to drugs, both in terms of therapeutic effect as well as adverse effects.
Human genome
The human genome is the complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome, and the mitochondrial genome. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees (approximately 4%) and bonobos.
1000 Plant Genomes Project
Rather than sequencing the entire genome (all DNA sequence) of the various plant species, the project will sequence only those regions of the genome that produce a protein product (coding genes); the transcriptome. This approach is justified by the focus on biochemical pathways where only the genes producing the involved proteins are required to understand the synthetic mechanism, and because these thousands of sequences would represent adequate sequence detail to construct very robust evolutionary relationships through sequence comparison. The numbers of coding genes in plant species can vary considerably, but all have tens of thousands or more making the transcriptome a large collection of information. However, non-coding sequence makes up the majority (>90%) of the genome content. Although this approach is similar conceptually to expressed sequence tags (ESTs), it is fundamentally different in that the entire sequence of each gene will be acquired with high coverage rather than just a small portion of the gene sequence with an EST. To distinguish the two, the non-EST method is known as “shotgun transcriptome sequencing”.
ENCODE
The pilot phase tested and compared existing methods to rigorously analyze a defined portion of the human genome sequence. It was organized as an open consortium and brought together investigators with diverse backgrounds and expertise to evaluate the relative merits of each of a diverse set of techniques, technologies and strategies. The concurrent technology development phase of the project aimed to develop new high throughput methods to identify functional elements. The goal of these efforts was to identify a suite of approaches that would allow the comprehensive identification of all the functional elements in the human genome. Through the ENCODE pilot project, National Human Genome Research Institute (NHGRI) assessed the abilities of different approaches to be scaled up for an effort to analyse the entire human genome and to find gaps in the ability to identify functional elements in genomic sequence.
Plant evolutionary developmental biology
Since the past few years, researchers have indeed begun looking at non-model, "non-conventional" organisms using modern genetic tools. One example of this is the Floral Genome Project, which envisages to study the evolution of the current patterns in the genetic architecture of the flower through comparative genetic analyses, with a focus on EST sequences. Like the FGP, there are several such ongoing projects that aim to find out conserved and diverse patterns in evolution of the plant shape. Expressed sequence tag (EST) sequences of quite a few non-model plants like sugarcane, apple, lotus, barley, cycas, coffee, to name a few, are available freely online. The Cycad Genomics Project, for example, aims to understand the differences in structure and function of genes between gymnosperms and angiosperms through sampling in the order Cycadales. In the process, it intends to make available information for the study of evolution of seeds, cones and evolution of life cycle patterns. Presently the most important sequenced genomes from an evo-devo point of view include those of "A. thaliana" (a flowering plant), poplar (a woody plant), "Physcomitrella patens" (a bryophyte), Maize (extensive genetic information), and "Chlamydomonas reinhardtii" (a green alga). The impact of such a vast amount of information on understanding common underlying developmental mechanisms can easily be realised.
Human proteome project
The structure and goals of a larger project that would parallel the Human Genome Project has been debated in the scientific literature. The results of this debate and a series of meetings at the World Congresses of the Human Proteome Organization in 2009, 2010 and 2011 has been the decision to define the Human Proteome Project as being composed of two sub-projects, C-HPP and B/D-HPP. The C-HPP will be organized into 25 groups, one per human chromosome. The B/D-HPP will be organized into groups by the biological and disease relevance of proteins.
Human Genome Project
The process of identifying the boundaries between genes and other features in a raw DNA sequence is called genome annotation and is in the domain of bioinformatics. While expert biologists make the best annotators, their work proceeds slowly, and computer programs are increasingly used to meet the high-throughput demands of genome sequencing projects. Beginning in 2008, a new technology known as RNA-seq was introduced that allowed scientists to directly sequence the messenger RNA in cells. This replaced previous methods of annotation, which relied on inherent properties of the DNA sequence, with direct measurement, which was much more accurate. Today, annotation of the human genome and other genomes relies primarily on deep sequencing of the transcripts in every human tissue using RNA-seq. These experiments have revealed that over 90% of genes contain at least one and usually several alternative splice variants, in which the exons are combined in different ways to produce 2 or more gene products from the same locus.
Human Genome Diversity Project
The study of human populations has been at the forefront of genomic and clinical research since the Human Genome Project (HGP) was completed. Projects similar to HGDP are the 1000 Genomes Project and the HapMap Project. Each has its own specificities and each has been used by scientists to a large extent for overlapping purposes.
Genomic library
Genome-wide association studies are general applications to find specific gene targets and polymorphisms within the human race. In fact, the International HapMap project was created through a partnership of scientists and agencies from several countries to catalog and utilize this data. The goal of this project is to compare genetic sequences of different individuals to elucidate similarities and differences within chromosomal regions. Scientists from all of the participating nations are cataloging these attributes with data from populations of African, Asian, and European ancestry. Such genome-wide assessments may lead to further diagnostic and drug therapies while also helping future teams focus on orchestrating therapeutics with genetic features in mind. These concepts are already being exploited in genetic engineering. For example, a research team has actually constructed a PAC shuttle vector that creates a library representing two-fold coverage of the human genome. This could serve as an incredible resource to identify genes, or sets of genes, causing disease. Moreover, these studies can serve as a powerful way to investigate transcriptional regulation as it has been seen in the study of baculoviruses. Overall, advances in genome library construction and DNA sequencing has allowed for efficient discovery of different molecular targets. Assimilation of these features through such efficient methods can hasten the employment of novel drug candidates.
Solanaceae
Many of the species belonging to this family, among them tobacco and the tomato, are model organisms that are used for research into fundamental biological questions. One of the aspects of the solanaceas’ genomics is an international project that is trying to understand how the same collection of genes and proteins can give rise to a group of organisms that are so morphologically and ecologically different. The first objective of this project was to sequence the genome of the tomato. In order to achieve this each of the 12 chromosomes of the tomato’s haploid genome was assigned to different sequencing centres in different countries. So chromosomes 1 and 10 were sequenced in the United States, 3 and 11 in China, 2 in Korea, 4 in Britain, 5 in India, 7 in France, 8 in Japan, 9 in Spain and 12 in Italy. The sequencing of the mitochondrial genome was carried out in Argentina and the chloroplast genome was sequenced in the European Union.
George M. Church
With Walter Gilbert, Church published the first direct genomic sequencing method in 1984. Described in that publication were the cyclic application of fluids to a solid phase alternating with imaging, plus avoidance of bacterial cloning, strategies that are still used in current dominant Next-Generation Sequencing technologies. These technologies began to affect genome-scale sequencing in 2005. Church also helped initiate the Human Genome Project in 1984. He invented the broadly applied concepts of molecular multiplexing and barcode tags. Technology transfer from his Harvard laboratory of automated sequencing and software to Genome Therapeutics Corp. resulted in the first bacterial genome sequence and first commercial genome (the human pathogen "Helicobacter pylori") in 1994. Church was also co-inventor of nanopore sequencing in 1995, which are now commercially available (e.g. Oxford Nanopore Technologies), but not in the form embodied in Church's contribution to the original patents.
Neanderthal genome project
It was initiated by 454 Life Sciences, a biotechnology company based in Branford, Connecticut in the United States and is coordinated by the Max Planck Institute for Evolutionary Anthropology in Germany. In May 2010 the project published their initial draft of the Neanderthal genome based on the analysis of four billion base remain in modern humans outside Africa.
Human interactome
The human interactome is the set of protein–protein interactions (the interactome) that occur in human cells. The sequencing of reference genomes, in particular the Human Genome Project, has revolutionized human genetics, molecular biology, and clinical medicine. Genome-wide association study results have led to the association of genes with most Mendelian disorders, and over 140 000 germline mutations have been associated with at least one genetic disease. However, it became apparent that inherent to these studies is an emphasis on clinical outcome rather than a comprehensive understanding of human disease; indeed to date the most significant contributions of GWAS have been restricted to the “low-hanging fruit” of direct single mutation disorders, prompting a systems biology approach to genomic analysis. The connection between genotype and phenotype (how variation in genotype affects the disease or normal functioning of the cell and the human body) remain elusive, especially in the context of multigenic complex traits and cancer. To assign functional context to genotypic changes, much of recent research efforts have been devoted to the mapping of the networks formed by interactions of cellular and genetic components in humans, as well as how these networks are altered by genetic and somatic disease.
List of sequenced plant genomes
This list of sequenced plant genomes contains plant species known to have publicly available complete genome sequences that have been assembled, annotated and published. Unassembled genomes are not included, nor are organelle only sequences. For all kingdoms, see the list of sequenced genomes.
Tag SNP
Because whole genome sequencing of individuals is still cost prohibitive, the international HapMap Project was constructed with a goal to map the human genome to haplotype groupings (haplotype blocks) that can describe common patterns of human genetic variation. By mapping the entire genome to haplotypes, tag SNPs can be identified to represent the haplotype blocks examined by genetic studies. An important factor to consider when planning a genetic study is the frequency and risk incurred by specific alleles. These factors can vary in different populations so the HapMap project used a variety of sequencing techniques to discover and catalog SNPs from different sets of populations. Initially the project sequenced individuals from Yoruba population of African origin (YRI), residents of Utah with western European ancestry (CEU), unrelated individuals from Tokyo, Japan (JPT) and unrelated Han Chinese individuals from Beijing, China (CHB). Recently their datasets have been expanded to include other populations (11 groups)
Gerd Jürgens
During his postdoctoral years in the 1980s he worked with Nobel prize winners Christiane Nüsslein-Volhard and Eric Wieschaus at the European Molecular Biology Laboratory (EMBL) in Heidelberg on the topic of "Drosophila melanogaster" embryogenesis.
At the age of 37 he made the switch from animal to plant research and became one of the first researchers to work on what was later to become the model plant organism: "Arabidopsis thaliana".
He was responsible for pioneering research in the genetic dissection of plant embryogenesis. Using the genetically-tractable plant "Arabidopsis thaliana" he conducted the first forward genetic screen (using mutagenesis with 0.3% ethyl methane sulfonate(EMS)) looking for embryonic defects.
His laboratory discovered and characterized the protein KNOLLE, which is required for cytokinesis and was the first protein known to exclusively target the cell plate in plant cells. 
Prof Gerd Jürgens also worked extensively on the ARF-GEF GNOM. Both "knolle" and "gnom" were first discovered in his embryonic mutant screens.
Earth BioGenome Project
The project is projected to cost US$4.7 billion. It includes already ongoing projects such as i5K (insects), B10K (birds) and the Darwin Tree of Life, which aim to sequence the estimated 66,000 eukaryotic species in the United Kingdom. The project is aiming to sequence and annotate the roughly 1.5 million known eukaryotic species in three phases, with first to create "annotated chromosome-scale reference assemblies for at least one representative species of each of the ∼9,000 eukaryotic taxonomic families".
1000 Genomes Project
The 1000 Genomes Project (abbreviated as 1KGP), launched in January 2008, was an international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists planned to sequence the genomes of at least one thousand anonymous participants from a number of different ethnic groups within the following three years, using newly developed technologies which were faster and less expensive. In 2010, the project finished its pilot phase, which was described in detail in a publication in the journal "Nature". In 2012, the sequencing of 1092 genomes was announced in a "Nature" publication. In 2015, two papers in "Nature" reported results and the completion of the project and opportunities for future research. Many rare variations, restricted to closely related groups, were identified, and eight structural-variation classes were analyzed.
Computational biology
Computational genomics is a field within genomics which studies the genomes of cells and organisms. It is sometimes referred to as Computational and Statistical Genetics and encompasses much of Bioinformatics. The Human Genome Project is one example of computational genomics. This project looks to sequence the entire human genome into a set of data. Once fully implemented, this could allow for doctors to analyze the genome of an individual patient. This opens the possibility of personalized medicine, prescribing treatments based on an individual’s pre-existing genetic patterns. This project has created many similar programs. Researchers are looking to sequence the genomes of animals, plants, bacteria, and all other types of life.
Genographic Project
Shortly after the announcement of the project in April 2005, the Indigenous Peoples Council on Biocolonialism (IPCB), based in Nevada, released a statement criticizing the project: spokespersons noted its connections to controversial issues (such as concern among some tribes that the results of genetic human migration studies might indicate that Native Americans are not indigenous to North America) raised by the Human Genome Diversity Project, which had government overview, unlike the privately-funded Genographic Project. The IPCB recommended against indigenous people participating. It also recommended that indigenous peoples boycott IBM, Gateway Computers, and National Geographic, which at that time were collaborating on the Genographic Project.
Cooperative Human Linkage Center
CHLC (or Cooperative Human Linkage Center) was a NIH project to map a large number of human genome markers, prior to the completion of the Human Genome Project. The project was stopped in 1999
GENCODE
The Human Genome Project was an international research effort to determine the sequence of the human genome and identify the genes that it contains. The Project was coordinated by the National Institutes of Health and the U.S. Department of Energy. Additional contributors included universities across the United States and international partners in the United Kingdom, France, Germany, Japan, and China. The Human Genome Project formally began in 1990 and was completed in 2003, 2 years ahead of its original schedule.
Following the release of the completed human genome sequence in April 2003, the scientific community intensified its efforts to mine the data for clues about how the body works in health and in disease. A basic requirement for this understanding of human biology is the ability to identify and characterize sequence-based functional elements through experimentation and computational analysis. In September 2003, the NHGRI introduced the ENCODE project to facilitate the identification and analysis of the complete set of functional elements in the human genome sequence.
Personal Genome Project
The Personal Genome Project (PGP) is a long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personal genomics and personalized medicine. It was initiated by Harvard University's George M. Church in 2005. As of November 2017, more than 10,000 volunteers had joined the project. Volunteers were accepted initially if they were permanent residents of the US and were able to submit tissue and/or genetic samples. Later the project was expanded to other countries.
Human Genome Project
The genome was broken into smaller pieces; approximately 150,000 base pairs in length. These pieces were then ligated into a type of vector known as "bacterial artificial chromosomes", or BACs, which are derived from bacterial chromosomes which have been genetically engineered. The vectors containing the genes can be inserted into bacteria where they are copied by the bacterial DNA replication machinery. Each of these pieces was then sequenced separately as a small "shotgun" project and then assembled. The larger, 150,000 base pairs go together to create chromosomes. This is known as the "hierarchical shotgun" approach, because the genome is first broken into relatively large chunks, which are then mapped to chromosomes before being selected for sequencing.
Genome diversity and karyotype evolution of mammals
The first step of the Human Genome Project took place when Tjio and Levan, in 1956, reported the accurate diploid number of human chromosomes as 2n = 46.
Animal Genome Size Database
The Animal Genome Size Database is a catalogue of published genome size estimates for vertebrate and invertebrate animals. It was created in 2001 by Dr. T. Ryan Gregory of the University of Guelph in Canada. As of September 2005, the database contains data for over 4,000 species of animals. A similar database, the Plant DNA C-values Database ("C-value" being analogous to "genome size" in diploid organisms) was created by researchers at the Royal Botanic Gardens, Kew, in 1997.
Honey Bee Genome Sequencing Consortium
The Honey Bee Genome Sequencing Consortium is an international collaborative group of genomics scientists, scientific organisations and universities trying to decipher the genome sequences of the honey bee ("Apis mellifera"). It was formed in 2001 by American scientists. In the US, the project is funded by the National Human Genome Research Institute (a division of the National Institutes of Health (NIH)), the United States Department of Agriculture (USDA), the Texas Agricultural Experiment Station, the University of Illinois Sociogenomics Initiative, and various beekeepers association and the bee industry.
Plant genome assembly
Due to its relatively cheap cost in comparison to previous methods, most of the recent plant genomes were sequenced and assembled using data from NGS (next-generation- sequencing) technology. In general the NGS data are used in combination with Sanger Sequencing technology or long-reads obtained from the third generation sequencing.
The genome of the cucumber, (Cucumis sativus), was one of the plant genomes that used the NGS Illumina reads in combination with Sanger sequences. 72.2-fold genome coverage high quality base pairs were generated from which 3.9-fold coverage was provided from Sanger and the Illumina GA reads provided 68.3-fold coverage. From this two assemblies were produced based on the sequencing technology. The resulting contigs were compared between them, resulting in a total length of the assembled genome of 243.5 Mb. The result is about 30% smaller than the genome size estimated by flow cytometry of isolated nuclei stained with propidium iodide (367 Mb). A genetic map was constructed to anchor the assembled genome. 72.8% of the assembled sequences were successfully anchored onto the seven chromosomes.
Another plant genome that combined NGS with Sanger sequencing was the genome of Theobroma cacao, 2010, an economically important tropical fruit tree crop. The genome was sequenced in a consortium, “The International Cocoa Genome Sequencing consortium (ICGS) “ and produced a total of 17.6 million 454 single end reads, 8.8 million 454 paired-end reads, 398.0 million Illumina paired-end reads and about 88,000 Sanger BAC reads. First by using genome assembly software, Newbler, an assembly was produced with 25,912 contigs and 4,792 scaffolds from the reads obtained from Roche/454 and Sanger raw data. This had a total length of 326.9 Mb, which represents 76% of the estimated genome size.
The Illumina reads were used to complement the 454 assembly, by aligning the short reads on the cocoa genome assembly using the SOAP software.
A similar strategy that combined NGS reads and Sanger Sequencing was used for other important plant species like the first published apple genome (Malus domestica), cotton (Gossypium Raimond), draft genome of sweet orange (Citrus sinensis) and the domesticated tomato (Solanum lycopersicum) genome
Human genome
There are several important points concerning the human reference genome:Most studies of human genetic variation have focused on single-nucleotide polymorphisms (SNPs), which are substitutions in individual bases along a chromosome. Most analyses estimate that SNPs occur 1 in 1000 base pairs, on average, in the euchromatic human genome, although they do not occur at a uniform density. Thus follows the popular statement that "we are all, regardless of race, genetically 99.9% the same", although this would be somewhat qualified by most geneticists. For example, a much larger fraction of the genome is now thought to be involved in copy number variation. A large-scale collaborative effort to catalog SNP variations in the human genome is being undertaken by the International HapMap Project.
David Haussler
As a collaborator on the international Human Genome Project, his team posted the first publicly available computational assembly of the human genome sequence on the Internet on July 7, 2000. Following this, his team developed the UCSC Genome Browser, a web-based tool that is used extensively in biomedical research and serves as the platform for several large-scale genomics projects. These include NHGRI’s ENCODE project to use omics methods to explore the function of every base in the human genome (for which UCSC serves as the Data Coordination Center), NIH’s Mammalian Gene Collection, NHGRI’s 1000 genomes project to explore human genetic variation, and NCI’s Cancer Genome Atlas project to explore the genomic changes in cancer.
Floral Genome Project
The Floral Genome Project is a collaborative research cooperation primarily between Penn State University, University of Florida, and Cornell University. The initial funding came from a grant of $7.4 million from the National Science Foundation. The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. According to the website, the following are the aims of the project:
The Art Genome Project
The Art Genome Project has often been compared to Pandora's Music Genome Project, and was originally developed in consultation with Pandora's Joe Kennedy. Both aim to create comprehensive (though by no means exhaustive) analyses of types of art by identifying a set of criteria, which both call "genes". These are both broadly applicable to their respective art forms, as well as useful for generating interesting connections for users. Importantly, while The Art Genome is currently one extensive list of genes for all works of art, Pandora has separate genomes (lists of genes) for each genre of music.
Genomics of domestication
Historically genomic studies have been focused on select organisms for which there is funding to study. Initially, when sequencing costs were prohibitive, this was limited to organisms with small genomes, such as viruses and bacteria, and then in eukaryotes, model organisms of importance to the scientific community for research. These included the "Mus musculus" (the house mouse), "Drosophila melanogaster" (fruit fly) and "Arabidopsis thaliana" ("Arabidopsis") genomes. One of the most prominent publicly funded genome projects was the Human Genome Project which helped to refine existing sequencing techniques as well as develop additional ones. Following these model organisms, agriculturally important species were next emphasized. As of 2009, there are more than 50 plant species whose genomes are being sequenced. However, the most important agricultural crops, including those in the grass and legume families such as rice, wheat and maize, have received the most attention and funding. As of 2005, a full sequence of the rice genome has been published. These domesticated species and in some cases, their wild ancestors, have received focus due to their agricultural and economic importance and the benefits that having a sequenced genome for these species confers such as the ability to easily identify targets for selective breeding programs to increase yield, facilitate drought tolerance, or select a variety of desirable traits.
Plant DNA C-values Database
The Plant DNA C-values Database is a comprehensive catalogue of C-value (nuclear DNA content, or in diploids, genome size) data for land plants and algae. The database was created by Prof. Michael D. Bennett and Dr. Ilia J. Leitch of the Royal Botanic Gardens, Kew, UK. The database was originally launched as the "Angiosperm DNA C-values Database" in April 1997, essentially as an online version of collected data lists that had been published by Prof. Bennett and colleagues since the 1970s. Release 1.0 of the more inclusive Plant DNA C-values Database was launched in 2001, with subsequent releases 2.0 in January 2003 and 3.0 in December 2004. In addition to the angiosperm dataset made available in 1997, the database has been expanded taxonomically several times and now includes data from pteridophytes (since 2000), gymnosperms (since 2001), bryophytes (since 2001), and algae (since 2004) (see (1) for update history). (Note that each of these subset databases is cited individually as they may contain different sets of authors). As of September 2005, the database as a whole contains data for over 4,800 species of plants in these various taxa. A similar Animal Genome Size Database was created in 2001 by Dr. T. Ryan Gregory of the University of Guelph, Canada.
Plant genome assembly
The initiative for sequencing the genome of rice ("Oryza sativa"), began in September 1997, when scientists from many nations agreed to an international collaboration to sequence the rice genome, forming “The International Rice Genome Sequencing Project” (IRGSP). At an estimated size between 400-430 Mb, approximatively four times larger in dimensions than "A. thaliana", rice has the smallest of the major cereal crop genomes.
1000 Genomes Project
The project unites multidisciplinary research teams from institutes around the world, including China, Italy, Japan, Kenya, Nigeria, Peru, the United Kingdom, and the United States. Each will contribute to the enormous sequence dataset and to a refined human genome map, which will be freely accessible through public databases to the scientific community and the general public alike.
By providing an overview of all human genetic variation, the consortium will generate a valuable tool for all fields of biological science, especially in the disciplines of genetics, medicine, pharmacology, biochemistry, and bioinformatics.
David Haussler
David Haussler (born 1953) is an American bioinformatician known for his work leading the team that assembled the first human genome sequence in the race to complete the Human Genome Project and subsequently for comparative genome analysis that deepens understanding the molecular function and evolution of the genome. He is a Howard Hughes Medical Institute Investigator, professor of biomolecular engineering and director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz, director of the California Institute for Quantitative Biosciences (QB3) on the UC Santa Cruz campus, and a consulting professor at the Stanford University School of Medicine and the UC San Francisco Biopharmaceutical Sciences Department.
Michael Stratton
At the announcement of the completion of the Human Genome Project in 2000, Stratton discussed using genome sequences to revolutionise cancer treatment. He and Andy Futreal had already initiated the Cancer Genome Project at the Sanger Centre, as it was then known, to use genome-wide analysis to find somatic mutations in human cancers. According to fellow cancer researcher Chris Marshall, doing so prior to the completion of the human genome sequence was an "audacious idea." The aims of the project are to identify new cancer genes, to understand how cancers develop and to study how the structure of genomes influence cancer. In 2002 and 2004, Stratton's team discovered mutations in the BRAF and ERBB2 genes in approximately 60 per cent of malignant melanomas and 4 per cent of non-small-cell lung cancers respectively.
Jute genome
It all began in February 2008, when Maqsudul Alam approached Professor Ahmad Shamsul Islam, Coordinator of GNOBB (Global Network of Bangladeshi Biotechnologists) regarding the possibility of sequencing the jute genome. The Bangladeshi science community, which was already looking into the possibility of getting the jute genome sequenced, responded to this offer, which started the process. The whole process began with many long conference calls between Dr. Alam and plant molecular biologists, Professors Haseena Khan and Zeba Islam Seraj of the Department of Biochemistry and Molecular Biology, University of Dhaka. They established connection with University of Hawaii, USA and University of Science Malaysia for technical support and prepared a project proposal to collect fund from different institutions. At the beginning there were many assurance but the reality was different. In the primary stage Genome Research Center USA and University of Science Malaysia gave some technical help to collect research data about jute from all over the world. To analyze huge amount of data there arose a need for a super computer. There was still need of funding for field research. "Swapnajatra" team become frustrated by not getting proper support. It became difficult to keep engage the team members. In 2009, The Daily Prothom Alo published an article about the research that changed everything. Agriculture Minister Matia Chowdhury introduced Dr. Maqsudul Alam to prime minister Sheikh Hasina and assured about further support. Thus team "Swapnajatra" regained their confidence and continued their work.
Plant genome assembly
The genome of plants can vary in their structure and complexity from small genomes like green algae (15 Mbp). to very large and complex genomes that have typically much higher ploidy, higher rates of heterozygosity and repetitive elements than species from other kingdoms. One of the most complex plant genome assemblies available is that of loblolly pine (22 Gbp). Due to their complexity, the plants’ genome sequences can't be assembled back into chromosomes using only short reads provided by next-generation- sequencing technologies (NGS), and therefore most plant genome assemblies available that used NGS alone are highly fragmented, contain large numbers of contigs, and genome regions are not finished. Highly repetitive sequences, often larger than 10kbp, are the main challenge in plants. Most of the chromosomal sequences are produced by the activity of mobile genetic elements (MGEs) in the plant genomes. MGEs are divided into two classes: class I or retrotransposons, and class II or DNA transposons. In plants, long- terminal repeat (LTR) retrotransposons are predominant and constitute from 15% to 90% of the genome. Polyploidy is another challenge in assembling a plant genome, and it is estimated that ~80% of plants are polyploids.
Human genetic variation
Human genome projects are scientific endeavors that determine or study the structure of the human genome. The Human Genome Project was a landmark genome project.Regional:
Projects:
1000 Plant Genomes Project
The project is funded by Alberta Innovates - Technology Futures (merger of iCORE , the Alberta Agricultural Research Institute (AARI), Genome Alberta, the University of Alberta, the Beijing Genomics Institute (BGI), and Musea Ventures (a USA-based private investment firm). To date, the project has received $1.5 million CAD from the Alberta Government and another $0.5 million from Musea Ventures. An additional $2.5 million CAD will be contributed by the Alberta government over the next 3 years. In January 2010, BGI announced that it would be contributing $100 million to large-scale sequencing projects of plants and animals (including the 1000 Plant Genomes Project).
Craig Venter
Venter viewed the slow pace of progress in the Human Genome project as an opportunity to continue his interest in patenting genes, so he sought funding from the private sector to birth Celera Genomics. The company planned to profit from their work by creating genomic data to which users could subscribe for a fee. The goal consequently put pressure on the public genome program and spurred several groups to redouble their efforts to produce the full sequence. Venter's effort won him renown as he and his team at Celera Corporation shared credit for sequencing the first draft human genome with the publicly funded Human Genome Project.
Cotton
There is a public effort to sequence the genome of cotton. It was started in 2007 by a consortium of public researchers. Their aim is to sequence the genome of cultivated, tetraploid cotton. "Tetraploid" means that its nucleus has two separate genomes, called A and D. The consortium agreed to first sequence the D-genome wild relative of cultivated cotton ("G. raimondii", a Central American species) because it is small and has few repetitive elements. It has nearly one-third of the bases of tetraploid cotton, and each chromosome occurs only once. Then, the A genome of "G. arboreum" would be sequenced. Its genome is roughly twice that of "G. raimondii". Part of the difference in size is due the amplification of "retrotransposons" (GORGE). After both diploid genomes are assembled, they would be used as models for sequencing the genomes of tetraploid cultivated species. Without knowing the diploid genomes, the euchromatic DNA sequences of AD genomes would co-assemble, and their repetitive elements would assemble independently into A and D sequences respectively. There would be no way to untangle the mess of AD sequences without comparing them to their diploid counterparts.
Vivian Lee
Early in her tenure at the University of Utah, Lee announced the Utah Genome Project as a cornerstone of the University of Utah's biomedical research strategy. The Utah Genome Project is "a large-scale genome sequence and analysis initiative to discover new disease-causing genes," and is unique among genome initiatives because it uncovers genetic signatures of disease and drug response in large families. The University, one of the few sites selected to conduct large scale mapping for the Human Genome Project and the International HapMap Project, had previously identified important disease-causing genes such as BRCA1, breast and ovarian cancer gene, APC colon cancer gene, and KCNH2 cardiac arrhythmia gene, among more than 30 others. Among the industry partnerships developed to advance genomic research as part of the Utah Genome Project included Regeneron, Omicia, and Janssen Research and Development.
Human Epigenome Project
Human Epigenome Project (HEP) is a multinational science project, with the stated aim to "identify, catalog, and interpret genome-wide DNA methylation patterns of all human genes in all major tissues". It is financed by government funds as well as private investment, via a consortium of genetic research organisations.
Human Genome Project
The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). The "genome" of any given individual is unique; mapping the "human genome" involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual.
Leroy Hood
The DNA sequencer was a critical technology for the Human Genome Project.
Hood was involved with the Human Genome Project from its first meeting, held at the University of California, Santa Cruz, in 1985. Hood became an enthusiastic advocate for The Human Genome Project and its potential. Hood directed the Human Genome Center’s sequencing of portions of human chromosomes 14 and 15.
Human evolutionary genetics
, the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed a total of 324 million variants found in sequenced human genomes.
Nucleotide diversity, the average proportion of nucleotides that differ between two individuals, is estimated at between 0.1% and 0.4% for contemporary humans (compared to 2% between humans and chimpanzees).
This corresponds to genome differences at a few million sites; the 1000 Genomes Project similarly found 
that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence."
Comparative genomics
Comparative genomics has a root in the comparison of virus genomes in the early 1980s. For example, small RNA viruses infecting animals (picornaviruses) and those infecting plants (cowpea mosaic virus) were compared and turned out to share significant sequence similarity and, in part, the order of their genes. In 1986, the first comparative genomic study at a larger scale was published, comparing the genomes of varicella-zoster virus and Epstein-Barr virus that contained more than 100 genes each.
Chimpanzee genome project
The results of the chimpanzee genome project suggest that when ancestral chromosomes 2A and 2B fused to produce human chromosome 2, no genes were lost from the fused ends of 2A and 2B. At the site of fusion, there are approximately 150,000 base pairs of sequence not found in chimpanzee chromosomes 2A and 2B. Additional linked copies of the PGML/FOXD/CBWD genes exist elsewhere in the human genome, particularly near the p end of chromosome 9. This suggests that a copy of these genes may have been added to the end of the ancestral 2A or 2B prior to the fusion event. It remains to be determined if these inserted genes confer a selective advantage.
Wang Jun (scientist)
While studying as a PhD student at Peking University, in 1999 Wang founded the bioinformatics group at BGI, which lead China's contribution to sequencing 1% of the Human Genome Project. His team was subsequently involved in efforts to genetically sequence the first Asian person, the rice plant, SARS, the giant panda, silkworms, pigs, chickens, goats, and the human gut microbiome, amongst other organisms.
1000 Plant Genomes Project
There have been efforts to determine the evolutionary relationships between the known plant species, but phylogenies (or phylogenetic trees) created solely using morphological data, cellular structures, single enzymes, or on only a few sequences (like rRNA) can be prone to error; morphological features are especially vulnerable when two species look physically similar though they are not closely related (as a result of convergent evolution for example) or homology, or when two species closely related look very different because, for example, they are able to change in response to their environment very well. These situations are very common in the plant kingdom. An alternative method for constructing evolutionary relationships is through changes in DNA sequence of many genes between the different species which is often more robust to problems of similar-appearing species. With the amount of genomic sequence produced by this project, many predicted evolutionary relationships can be better tested by sequence alignment (figure 1) to improve their certainty.
Genome project
In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism. Such projects may also include gene prediction to find out where the genes are in a genome, and what those genes do. There may also be related projects to sequence ESTs or mRNAs to help find out where the genes actually are.
Applied Biosystems
Also in 1990, the U.S. government approved financing to support the Human Genome Project. Dr. James D. Watson, who founded the consortium, forecast that the project could be completed in 15 years from its 1990 starting date, at a cost of cost US$3 billion. Over the next couple years, Japan began a project to sequence the rice genome, and other laboratories initiated programs to sequence the mouse, fruit fly, and yeast genomes.
Plant genome assembly
One of the most important crops in the world, maize (Zea mays), is the last plant genome project primarily based on Sanger BAC-by-BAC strategy. The genome size of Maize, 2.3 Gb and 10 chromosomes, is significantly larger than that of rice and Arabidopsis. To assemble the genome of maize a set of 16,848 minimally overlapping BAC clones derived
from combinations of physical and genetic map were selected and sequenced. The assembly on maize was performed in addition with external information data. The data was obtained from cDNA and sequences from libraries with methyl-filtered DNA (libraries that uses the knowledge that the bases in genic sequences tends to be less heavily methylated than those in non-genic regions) and high C0 t techniques.
Nuclear DNA
Human Genome Project (1990-2003)" heights="80">
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Ehud Shapiro
In 2005, Prof. Shapiro presented a vision of the next grand challenge in Human biology: To uncover the Human cell lineage tree. Inside all of us is a cell lineage tree the history of how our body grows from a single cell (the fertilized egg) to 100 trillion cells. The biological and biomedical impact of such a success could be of a magnitude similar, if not larger than that of the Human Genome Project. In his TEDxTel-Aviv talk "Uncovering The Human Cell Lineage Tree The next grand scientific challenge" Prof. Shapiro described the system and results obtained with it so far, and a proposal for a FET Flagship project "Human Cell Lineage Flagship initiative" for uncovering the Human cell lineage tree in health and disease.
Movie Genome
The Movie Genome concept is borrowed from the Human Genome Project, a scientific project to identify and map all human genes. Similarly, a Movie Genome, as used by semantic movie discovery engine Jinni, identifies and indexes multiple “genes” (elements and aspects) of a movie.
Genome Project-Write
The Genome Project - Write (also known as GP-Write) includes sub-projects like Human Genome Project-Write (HGP-Write), formally announced on 2 Jun 2016, is an extension of Genome Projects (aimed at reading genomes since 1984), now to include development of technologies for synthesis and testing of many genomes of microbes, plants and animals. This leverages two decades of work on Synthetic Biology and Artificial gene synthesis.
Human Genome Project
The $3-billion project was formally founded in 1990 by the US Department of Energy and the National Institutes of Health, and was expected to take 15 years. In addition to the United States, the international consortium comprised geneticists in the United Kingdom, France, Australia, China and myriad other spontaneous relationships. Considering the inflation, the project roughly costed $5 billion.
ENCODE
The MODel organism ENCyclopedia Of DNA Elements (modENCODE) project is a continuation of the original ENCODE project targeting the identification of functional elements in selected model organism genomes, specifically "Drosophila melanogaster" and "Caenorhabditis elegans". The extension to model organisms permits biological validation of the computational and experimental findings of the ENCODE project, something that is difficult or impossible to do in humans. Funding for the modENCODE project was announced by the National Institutes of Health (NIH) in 2007 and included several different research institutions in the US. The project completed its work in 2012.
Craig Venter
In 2000, Venter and Francis Collins of the National Institutes of Health and U.S. Public Genome Project jointly made the announcement of the mapping of the human genome, a full three years ahead of the expected end of the Public Genome Program. The announcement was made along with U.S. President Bill Clinton, and UK Prime Minister Tony Blair. Venter and Collins thus shared an award for "Biography of the Year" from A&E Network.
On 15 February 2001, the Human Genome Project consortium published the first Human Genome in the journal Nature, and was followed, one day later, by a Celera publication in Science. Despite some claims that shotgun sequencing was in some ways less accurate than the clone-by-clone method chosen by the Human Genome Project, the technique became widely accepted by the scientific community.
GEN2PHEN
By providing a complete Homo sapiens ‘parts list’ (the gene sequences) and a powerful ‘toolkit’ (technologies), the Human Genome Project has revolutionised mankind’s ability to explore how genes cause disease and other phenotypes. Studies in this domain are proceeding at a rapid and ever-increasing pace, generating unprecedented amounts of raw and processed data. It is now imperative that the scientific community finds ways to effectively manage and exploit this flood of information for knowledge creation and practical benefit to society. This fundamental goal lies at the heart of the “Genotype-To-Phenotype Databases: A Holistic Solution (GEN2PHEN)” project.
Personal Genome Project
Scientists at the Wyss Institute for Biologically Inspired Engineering and the Harvard Medical School Personal Genome Project (PGP) planned to recruit 10,000 members from the PGP, to perform a set of cognitive tests from Lumos Labs’ NeuroCognitive Performance Test, a brief, repeatable, online assessment to evaluate participants’ memory functions, including object recall, object pattern memorization, and response times. The researchers would then correlate extremely high performance scores with naturally occurring variations in the participants’ genomes. To validate their findings, the team would sequence, edit, and visualize DNA, model neuronal development in 3-D brain organoids ex vivo, and finally test emerging hypotheses in experimental models of neurodegeneration.
World Community Grid
The Genome Comparison project is sponsored by the Brazilian research institution Fiocruz. The project was launched on November 21, 2006, and completed on July 21, 2007. The project seeks to compare gene sequences of different organisms against each other in order to find similarities between them. Scientists hope to discover what purpose a particular gene sequence serves in a particular function of one organism, via comparing it to a similar gene sequence of known function in another organism.
KEGG
The KEGG database project was initiated in 1995 by Minoru Kanehisa, Professor at the Institute for Chemical Research, Kyoto University, under the then ongoing Japanese Human Genome Program. Foreseeing the need for a computerized resource that can be used for biological interpretation of genome sequence data, he started developing the KEGG PATHWAY database. It is a collection of manually drawn KEGG pathway maps representing experimental knowledge on metabolism and various other functions of the cell and the organism. Each pathway map contains a network of molecular interactions and reactions and is designed to link genes in the genome to gene products (mostly proteins) in the pathway. This has enabled the analysis called KEGG pathway mapping, whereby the gene content in the genome is compared with the KEGG PATHWAY database to examine which pathways and associated functions are likely to be encoded in the genome.
Human Genome Project
The Human Genome Project was a 15-year-long, publicly funded project initiated in 1990 with the objective of determining the DNA sequence of the entire euchromatic human genome within 15 years. In May 1985, Robert Sinsheimer organized a workshop to discuss sequencing the human genome, but for a number of reasons the NIH was uninterested in pursuing the proposal. The following March, the Santa Fe Workshop was organized by Charles DeLisi and David Smith of the Department of Energy's Office of Health and Environmental Research (OHER). At the same time Renato Dulbecco proposed whole genome sequencing in an essay in Science. James Watson followed two months later with a workshop held at the Cold Spring Harbor Laboratory.
Genome project
Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.
George Weinstock
As a postdoctoral fellow with Dr. I. R. Lehman at Stanford University School of Medicine, Dr. Weinstock and Kevin McEntee discovered that the RecA protein of "E. coli" catalyzed strand transfer in genetic recombination. Later, as a faculty member at the University of Texas at Houston, he led one of the first bacterial genome projects, collaborating with The Institute for Genomic Research to sequence the entire genome of a bacterium, "Treponema pallidum", the organism that causes syphilis. In 1999 he joined Richard Gibbs at the HGSC as one of the five main centers to work on the Human Genome Project. The HGSC produced sequences of human chromosomes 3, 12 and X. Dr. Weinstock was a principal investigator in projects producing genome sequences for rat, mouse, macaque, bovine, sea urchin, honey bee, fruit fly and many microbial genomes, as well as one of the first personal genome projects, sequencing Dr. James Watson’s genome using next-generation sequencing technology.
Chimpanzee genome project
Analysis of the genome was published in "Nature" on September 1, 2005, in an article produced by the Chimpanzee Sequencing and Analysis Consortium, a group of scientists which is supported in part by the National Human Genome Research Institute, one of the National Institutes of Health. The article marked the completion of the draft genome sequence. A database now exists containing the genetic differences between human and chimpanzee genes, with about thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. Gene duplications account for most of the sequence differences between humans and chimps. Single-base-pair substitutions account for about half as much genetic change as does gene duplication.
Medicago truncatula
The assembly of the genome sequence in "M. truncatula" was based on bacterial artificial chromosomes (BACs). This is the same approach used to sequence the genomes of humans, the fruitfly, "Drosophila melanogaster", and the model plant, "Arabidopsis thaliana". In July 2013, version 4.0 of the genome was released. This version combined sequences gained from shotgun sequencing with the BAC-based sequence assemblies, which has helped to fill in the gaps in the previously mapped sequences.
Human germline engineering
Human germline engineering is the process by which the genome of an individual is edited in such a way that the change is heritable. This is achieved through genetic alterations within the germinal cells, or the reproductive cells, such as the oocyte and spermatogonium. Human germline engineering should not be confused with gene therapy. Gene therapy consists of altering somatic cells, which are all cells in the body that are not involved in reproduction. While gene therapy does change the genome of the targeted cells, these cells are not within the germline, so the alterations are not heritable and cannot be passed on to the next generation.
Human
One human genome was sequenced in full in 2003, and currently efforts are being made to achieve a sample of the genetic diversity of the species (see International HapMap Project). By present estimates, humans have approximately 22,000 genes. The variation in human DNA is very small compared to other species, possibly suggesting a population bottleneck during the Late Pleistocene (around 100,000 years ago), in which the human population was reduced to a small number of breeding pairs. Nucleotide diversity is based on single mutations called single nucleotide polymorphisms (SNPs). The nucleotide diversity between humans is about 0.1%, i.e. 1 difference per 1,000 base pairs. A difference of 1 in 1,000 nucleotides between two humans chosen at random amounts to about 3 million nucleotide differences, since the human genome has about 3 billion nucleotides. Most of these single nucleotide polymorphisms (SNPs) are neutral but some (about 3 to 5%) are functional and influence phenotypic differences between humans through alleles.
Genome
The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant "Arabidopsis thaliana", the puffer fish, and the bacteria E. coli. In December 2013, scientists first sequenced the entire "genome" of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave.
1000 Plant Genomes Project
The goals of the two projects are significantly different. While the 1000 Genomes Project focuses on genetic variation in a single species, the 1000 Plant Genomes Project looks at the evolutionary relationships and genes of 1000 different plant species.
Human Genome Project
The sequence of the DNA is stored in databases available to anyone on the Internet. The U.S. National Center for Biotechnology Information (and sister organizations in Europe and Japan) house the gene sequence in a database known as GenBank, along with sequences of known and hypothetical genes and proteins. Other organizations, such as the UCSC Genome Browser at the University of California, Santa Cruz, and Ensembl present additional data and annotation and powerful tools for visualizing and searching it. Computer programs have been developed to analyze the data, because the data itself is difficult to interpret without such programs. Generally speaking, advances in genome sequencing technology have followed Moore's Law, a concept from computer science which states that integrated circuits can increase in complexity at an exponential rate. This means that the speeds at which whole genomes can be sequenced can increase at a similar rate, as was seen during the development of the above-mentioned Human Genome Project.
Human genome
The Human Genome Project produced the first complete sequences of individual human genomes, with the first draft sequence and initial analysis being published on February 12, 2001 simultaneously with Celera Corporation. The human genome was the first of all vertebrates to be completely sequenced. As of 2012, thousands of human genomes have been completely sequenced, and many more have been mapped at lower levels of resolution. The resulting data are used worldwide in biomedical science, anthropology, forensics and other branches of science. There is a widely held expectation that genomic studies will lead to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution.
Ewan Birney
Birney is one of the founders of the Ensembl genome browser and other databases, and has played a key role in many large-scale genomics projects, notably the sequencing of the Human Genome in 2000 and the analysis of genome function in the ENCODE project. He has played a role in annotating the genome sequences of the human, mouse, chicken and several other organisms. His research group focuses on genomic algorithms and inter-individual differences in human and other animal species.
Plant breeding
Sometimes many different genes can influence a desirable trait in plant breeding. The use of tools such as molecular markers or DNA fingerprinting can map thousands of genes. This allows plant breeders to screen large populations of plants for those that possess the trait of interest. The screening is based on the presence or absence of a certain gene as determined by laboratory procedures, rather than on the visual identification of the expressed trait in the plant. The purpose of marker assisted selection, or plant genomes analysis, is to identify the location and function (phenotype) of various genes within the genome. If all of the genes are identified it leads to Genome sequence. All plants have varying sizes and lengths of genomes with genes that code for different proteins, but many are also the same. If a gene's location and function is identified in one plant species, a very similar gene likely can also be found in a similar location in another species genome.
Plant genome assembly
A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA (deoxyribonucleic acid) fragments that are obtained from different types of sequencing technology.