the establishment of the primary dna sequence of a species is a key point in modern research .
it permits to obtain subsequently further insights on the functionality of the genes present in a genome . the first plant genome sequenced was that of the eudicot model plant arabidopsis thaliana , which was released in 2000 .
from this date , and mainly after the appearance of next generation sequencing technology in 2005 , the number of sequenced plant species has exponentially increased . in recent years , several reviews had targeted the state of art of the plant sequencing projects [ 1 - 4 ] . among the sequenced species ,
several algae genomes , a moss , a lycophyte , three conifer and examples from the majority of the monocot and eudicot lineages have been sequenced [ 4 , 5 ] .
interestingly , the vast majority of economical important crops have been sequenced and drafts of their genomes have been produced .
once the genomic sequence has been parsed , assembled and annotated ; the corresponding data has been traditionally compiled in a database available for the scientific community .
the importance of the creation of an open - access database comes from the rationale of the biological exploitation of the novel genomic resources generated by the researches .
basic considerations on dealing with crop plant databases utilization in the genomic era has been recently reviewed . in this mini - review ,
the first step in the valorization of a genomic project is to know the availability of related projects completed or in progress .
these searches can be done by two methods . by searching in the internet motor searches using key words or by exploring the specific databases related to genomic projects .
although the information in these databases is not always up to date , second method is more adequate to obtain the best results .
there are four main genomic projects databases that can be used when information on plant genomes is required , gold ( genomes online database ) , ncbi genomes , cogepedia and plabi ( table 1 ) .  
is a world wide web resource for comprehensive access to information regarding genome and metagenome sequencing projects , and their associated metadata .
gold is now hosted by the jgi doe institute and the current release is the version 5 .
the database currently hosts information for more than 20,000 studies , 60,000 biosamples , 60,000 sequencing projects and 50,000 analysis projects .
one of the specific features of gold is that it includes nuclear and organelle genome projects , but also transcriptomic , methylation , exome and re - sequencing projects .
around one hundred and more than 3,400 finished or ongoing projects involve species from the phyla chlorophyta and streptophyta , respectively .
gold is manually curated , their stored metadata are quality - controlled , and fully supports and follows the genomic standards consortium ( gsc ) minimum information standards . 

ncbi genomes   is a resource of the ncbi ( national center for biotechnology information ) which organizes information on genomes including sequences , maps , chromosomes , assemblies , and annotations .
the ncbi genome database collects genomic sequencing projects for a given species and provides links to corresponding records in bioproject , assembly , nucleotide and protein databases . besides
, a list of the current status of all genomes annotated at ncbi is provided .
currently , more than 2,200 eukaryotic genomes have been deposited , and from that , more than 200 corresponds to plant species .
the database provides a versioned assembly accession number that tracks changes to assemblies as they are updated by submitting groups over time .
the assembly database reports metadata such as assembly names , simple statistical reports of the assembly as well as the assembly update history .
links in the assembly resource allow users to easily download sequence and annotations for current versions of genome assemblies from the ncbi genomes ftp site . 

2.3.cogepedia is the official wiki page of coge , a platform for performing comparative genomics research which provides a network of interconnected tools to manage , analyze , and visualize next generation sequenced data .
their interest to plant genomics is the existence of a link in this page with much updated information on sequenced plant genomes .
individual information on each species with links to the genome publication or the genome project main page is provided . 

2.4.plabi is a plant genomic database with a very updated tool to know which plant species have been sequenced .
links to the research articles where each plant genome has been published are also included .
  is a world wide web resource for comprehensive access to information regarding genome and metagenome sequencing projects , and their associated metadata .
gold is now hosted by the jgi doe institute and the current release is the version 5 .
the database currently hosts information for more than 20,000 studies , 60,000 biosamples , 60,000 sequencing projects and 50,000 analysis projects .
one of the specific features of gold is that it includes nuclear and organelle genome projects , but also transcriptomic , methylation , exome and re - sequencing projects .
around one hundred and more than 3,400 finished or ongoing projects involve species from the phyla chlorophyta and streptophyta , respectively .
gold is manually curated , their stored metadata are quality - controlled , and fully supports and follows the genomic standards consortium ( gsc ) minimum information standards . 

ncbi genomes   is a resource of the ncbi ( national center for biotechnology information ) which organizes information on genomes including sequences , maps , chromosomes , assemblies , and annotations .
the ncbi genome database collects genomic sequencing projects for a given species and provides links to corresponding records in bioproject , assembly , nucleotide and protein databases . besides
, a list of the current status of all genomes annotated at ncbi is provided .
currently , more than 2,200 eukaryotic genomes have been deposited , and from that , more than 200 corresponds to plant species .
the database provides a versioned assembly accession number that tracks changes to assemblies as they are updated by submitting groups over time .
the assembly database reports metadata such as assembly names , simple statistical reports of the assembly as well as the assembly update history .
links in the assembly resource allow users to easily download sequence and annotations for current versions of genome assemblies from the ncbi genomes ftp site . 

2.3.cogepedia is the official wiki page of coge , a platform for performing comparative genomics research which provides a network of interconnected tools to manage , analyze , and visualize next generation sequenced data .
their interest to plant genomics is the existence of a link in this page with much updated information on sequenced plant genomes .
individual information on each species with links to the genome publication or the genome project main page is provided . 

2.4.plabi is a plant genomic database with a very updated tool to know which plant species have been sequenced .
links to the research articles where each plant genome has been published are also included .
formerly , species specific databases were developed . the arabidopsis initiative resource , tair ( http://www.arabidopsis.org/ ) was the first database created to harbor the genomic sequence of a plant and to surround it with different tools to explore this sequence .
these tools have been increasing with the subsequent releases of the genomic sequence and cover different aspects related not only with the arabidopsis genome , but with some other features such as germplasm , teaching , laboratory protocols or gene expression experiments . with the increasing of genome projects regarding various related species , databases from specific clades
this database comprises the reference genomes of tomato , potato , pepper and solanum pennelli ; the draft genomes of solanum pimpinellifolium , nicotiana benthamiana and nicotiana tabaccum ; and the genomes of two inbred lines of solanum lycopersicum . as for individual databases , a set of tools have been implemented to analyze the genomic sequences .
the individual / clade databases hosting the approximately 140 plant species sequenced to date can be easily found by writing the word genome and the species / clade in any internet search engine . at the same time , secondary databases have arisen to deal with features regarding comparative plant genomics research .
these databases harbor different plant genomes and differ in both , the plant species they host , and the tools and resources they have .
the aim of these projects is to explore how genomics is evolving from largely descriptive to highly predictive driven by quantitative measurements , with algorithms and computation as the domain - adapted language .
several tools are common to all databases . for example , sequence similarity searches are the most reliable strategy to identify homologous proteins or genes by detecting statistically significant similarity .
all databases include in their repertoire of bioinformatics tools a search engine to explore the annotated genome sequences , typically using the blast algorithm
. likewise , genome browsers , such are the commonly used gbrowse or jbrowse , are key tools offered by all databases to provide a graphical interface for users to browse , search , retrieve and analyze genomic sequence and annotation data . because of their importance in modern research , several of the comparative genomic databases
ensembl plants   is an integrative resource presenting genome - scale information for 39 sequenced plant species , including 12 eudicots , 21 monocots , one moss , one pseudofern , two green algae , one red algae and the genome of amborella trichopoda , which belongs to a sister clade of the other angiosperm species .
data provided includes genome sequence , gene models , functional annotation , and polymorphic loci .
gene families , based in an all - versus - all blastp alignment , are provided .
gene trees showing the evolutionary history of each gene family are available under the  plant compara  section .
access to the data is provided through a genome browser with tracks displaying genome sequence and assembly information , additional gene model and variation datasets , and precomputed sequence alignments including ests , rnaseq experiments , repeat features , oligo - probe , and marker sets .
ensembl plants is updated 45 times a year and is developed in collaboration with the gramene database and the transplant project ( http://www.transplantdb.eu ) that aims to facilitate the exchange and integration of plant genome data from distributed resources as well as the development of common standards and protocols . 

gramene   is a curated online resource for comparative functional genomics in crops and model plant species , currently hosting 45 sequenced reference genomes in its build number 48 . since 2009 gramene has partnered with the plants division of ensembl genomes ( http://www.plants.ensemb.orgl/ ) to jointly produce the genome browser described above , which takes advantage of the ensembl infrastructure and provides an interface for exploration of genome features , functional ontologies , variation data and comparative phylogenomics .
gramene includes a wide array of potentially useful tools such as genetic and physical maps with genes , ests and qtls locations , genetic diversity data sets , structure - function analysis of proteins , plant pathways databases ( biocyc and plant reactome platforms ) , and descriptions of phenotypic traits and mutations . 

plant gdb   is a web resource devoted to develop robust genome annotation methods , tools , and standard training sets for plant genomes . from 2012
plant gdb also provides annotated transcript assemblies for more than 250 plant species , with transcripts mapped to their cognate genomic context where available , integrated with a variety of sequence analysis tools and web services .
plant gdb hosts a plant genomics research outreach portal that facilitates access to a large number of resources for research and training . from july 2015
the plant gdb 's funding has ended and the website is no longer being updated . 
 3.4 .
plants db   is a database that has been developed by the plant genomics group of the pgsb ( plant genome and systems biology , formerly mips ) .
plants db aims to provide a data and information resource for individual plant species , especially complex triticeae genomes , and currently hosts 13 monocot and dicot species .
the database framework integrates genome data from both model and crop plants and facilitates knowledge transfer between them using state - of - the - art comparative genomics tools such as crowsnest , created to visualize and investigate syntenic relationships between monocot genomes , and the genome zipper concept for an ordered gene annotation in cereals .
phytozome   is the plant comparative genomics portal of the department of energy 's joint genome institute ( doe jgi ) . in the current release v10.3
, phytozome provides access to sixty - one sequenced and annotated green plant genomes , forty - seven of which have been clustered into gene families at 12 evolutionarily significant nodes .
it harbors the individual species genomic sequences compiled in the doe jgi , and links to the individual pages of the other genomes it hosts .
families of related genes representing the modern descendants of ancestral genes are available . they have been constructed from an all - versus - all blastp alignment used to compute the evolutionary distance between each two proteins , the identification of orthologs via reciprocal best hit or synteny analysis , and the accretion of paralogs using outgroup scores .
these families allow easy access to clade - specific orthology / paralogy relationships as well as insights into clade - specific novelties and expansions
. each gene has been annotated with available pfam , kog , kegg , panther and go assignments , and its evolutionary history at the level of sequence , gene structure , gene family and genome organization is provided . besides , phytozome provides access to the plant genomes it hosts using the jbrowse genome browsers available for all genomes . 

plaza   is a platform designed to make comparative genomics in plants and developed in the university of ghent .
the current version plaza 3.0 hosts 37 plant species covering a broad taxonomic range and includes 25 eudicot , 8 monocot , one moss and two algae species , as well as the genome of amborella trichopoda .
plaza provides detailed structural and functional annotation of the genes , which has been expanded in the new version and now comprises data from gene ontology , mapman , uniprotkb / swiss - prot , plntfdb and planttfdb . from the more than one million genes annotated in the genomes it harbors , gene families and subfamilies have been delineated .
first , by computing the protein sequence similarity through an all - against - all blast , and then by applying graph - based clustering methods implemented in tribemcl and orthomcl . other relevant data available in this database consist of phylogenetic trees to identify biologically relevant duplication and speciation events , and detailed information about genome organization to unveil small and large genome duplication events .
furthermore , this database provides tools to transfer functional annotation from well - characterized plant genomes to other plant species . 

greenphyldb   is a comparative genomics database jointly developed by biodiversity international and the international cooperation center for agricultural research for development ( cirad ) .
the current version greenphyldb 4.0 hosts 37 species of the plantae kingdom including one red alga , two green algae , one moss , one lycophyte , one conifer , the ancestral angiosperm amborella , ten monocots and 20 eudicot species .
this software uses different pairwise similarity matrices obtained by running protein - protein blast using increasing stringent thresholds .
then , these matrices are used by a markov cluster algorithm to group proteins in families at different levels of clustering ( 1 to 4 ) .
results of the automatic clustering are manually annotated using cross reference databases and analyzed by a phylogenetic - based approach to predict homologous relationships .
currently , greenphyldb contains 8,347 clusters with more than 5 sequences at level 1 , from which 2,939 are annotated and 4,788 have available phylogenetic trees . for each gene cluster , this database offers an easy access to the gene composition by species , and provides protein domains , orthologous gene predictions and relevant external links . 

plantordb   is a genome - wide database created to classify genes in families and to find orthologous genes clusters . the recently launched first version of plantordb hosts 41 species including six green algae , one moss , one lycophyte , six monocots and 27 eudicot species .
gene families are available , which have been generated from an all - against - all blast search approach .
the web interfaces provided by plantordb display information on the evolutionary features of an individual gene and its homolog gene family , which can be deduced from multiple sequence alignments and phylogenetics trees . tools to provide an accurate classification of a query sequence within a phylogenetic tree and a multiple sequence alignment are also available . 

salad   is a comparative genomics database constructed from plant - genome - based proteome data sets .
the version 3.0 , appeared in 2009 , hosts 10 species including a yeast species .
the most important singularity of this database is the construction of dendrograms for protein families using the information derived from conserved motifs discovered using the meme software .
protein clusters are determined from blastp searches and , then , meme motifs are used to select the proteins displayed in the dendrograms . a viewer to see microarray data sets of paralogous genes in the dendrograms is also provided .
planttribes   is a gene family resource for comparative genomics in plants that launched its current 2.0 version in 2007 .
it harbors the proteome of ten plant species , from green algae to angiosperms , from which putative gene families were created by a blastp approach and the use of the mcl algorithm for clustering .
the database is currently active and permits identify groups of related genes and their expression patterns , using the microarray information existing at the date the current version was released . 

plantgenie.org   is a collection of web resources for searching , visualizing and analyzing genomics and transcriptomics data recently developed for different plant species .
currently , it includes dedicated web portals for enabling in - depth exploration of poplar , norway spruce , and arabidopsis genomes .
standard features , including genome browsers , gene list annotation , blast tools and gene information pages are provided .
the aim of this database is to continue and develop the resource by inclusion of additional species , maintaining a focus on woody species . 

pogs2   is a relational database designed to facilitate cross - species inferences about gene functions and gene models in plants . in its current 2.0 version , the database integrates data from rice , maize , arabidopsis thaliana , and poplar by placing the complete predicted proteomes into  putative orthologous groups 
each pog entry includes putative orthologs annotated with gene descriptions imported from species - specific databases , graphical representations of conserved protein domains and phylogenetic trees showing closely - related proteins . 

extant genomes of 16 eudicot and 10 monocot plants can be analyzed , as well as 23 ancestral reconstructed genomes . in the current 16.03 version ,
all the data on extant species come from the annotations of selected genomes available in ensembl plants and phytozome .
a distinctive feature of this database is that the displayed genomic context of a gene is showed in parallel to the genomic context of all its orthologous and paralogous copies evolutionarily ordered in a phylogenetic tree . 

piece   is a comparative genomics database focused in the comparison of exon - intron plant gene structures and their evolutionary and functional relationships . in the first and current version , annotated genes were extracted from 25 species , from green algae to angiosperms , and classified based on pfam motifs .
phylogenetics trees are available for each gene family , which integrate exon - intron and protein motif information .
both the sequences and gene structure information for each identified gene are also available . 

plantseed   is a database created to support subsystems - based annotation and metabolic model reconstruction for plant genomes .
annotations of protein families from ensembl plants for five eudicot and five monocot species have been used to construct subsystems , which are the integration of metabolic pathways or other biological processes with genome annotations .
the manual curation of the subsystems permits a rapid reconstruction and modelling of primary metabolism for all plant genomes in the database . 

pgdbj   is the plant genome database japan , a portal website that aims to integrate plant genome - related information from databases .
the main tool developed in this web is the ortholog db , which comprises clusters of homologous sequences .
clusters were obtained from reciprocal blast searches using the proteome of 20 plant species from the main clades of the viridiplantae kingdom .
pgdbj also provides dna marker and qtl information of important agronomic traits for many plant species .
the new high - throughput genomic methods implies the generation of massive data . computation capability is a major challenge for the handling of these data .
the accessibility to computational tools easy to manage for a scientist without programming or informatics expertise is a solution to address this problem . in recent years , several web - based platforms
have been created to store next - generation sequencing data and to host different applications to work with these data to extract biological relevant information .
galaxy is an open web - based platform for genomic research with many tools to work with computation - reliant results .
recently , an open - source project specific for plants , the iplant , has been launched . 

the iplant collaborative   ( https://de.iplantcollaborative.org/ ) is a united states national science foundation ( nsf ) funded project created as an innovative , comprehensive , and foundational cyberinfrastructure in support of plant biology research .
iplant includes the use of high - performance computing , use of large shared data storage , and the establishment of collaborations and virtual organizations around shared analysis tools and analyzed data .
iplant hosts bioinformatics tools for most of the modern research challenges , such as data importers , sequence alignments and phylogenetic tree building , phylogenetic and evolutionary analyses , qtl mapping and genome - wide association studies , ultrahigh - throughput sequence processing , functional analyses , clustering and network analyses , variant detection and annotation , rnaseq analyses and chip - seq studies .
in particular , to manage and serve published plant genome data , iplant has developed a workspace named dna subway .
dna subway has been conceived to be a space for gene annotation and genome analysis that currently hosts tools to predict and annotate genes , prospect entire plant genomes for related genes and sequences , determine sequence relationships and analyze rna - seq reads to measure differential expression . to prospect genomes
, it harbors the target program that permits a search for homologous sequences in 18 plant genomes , covering different clades from algae to angiosperms , and builds multiple sequence alignments and phylogenetic trees with the obtained sequences .
bioinformatic programs and algorithms have arisen as key tools for modern research . in plants ,
the number and relevance of these tools have been increased in recent years , mainly those related to genomics aspects .
new science implies the existence of databases where the genomes are hosted and exhaustive analysis can be performed .
although these databases should be continuously updated , the assembly and annotation of many of the draft genomic sequences have not been improved from its first release .
this is an actual challenge , since it is easy now to produce a new draft sequence but more complicated to improve its quality .
for example , the pre - release of the version number 11 for the arabidopsis genome has appeared in araport ( https://www.araport.org/ ) in october 2015 with genomic sequences assembled in its five chromosomes .
on the contrary , the first release of the genome of the lycophyte selaginella moellendorffii appeared in 2007 assembled into 768 scaffolds and has not been subsequently updated . as a next step in plant genomics
, new databases have been developed to deal with the issue of comparing the increasing number of sequenced genomes .
most comparative genomic databases are periodically updated and have become powerful tools to extract shared information coming from evolutionarily related plant species .
however , the extremely high new information obtained in modern laboratories using computational approaches makes necessary the existence of new high - performance computational developments that uses the computational power of the internet and the storage of resources in the cloud . as a new challenge , actual projects in arabidopsis and rice
are directed to the comparison of thousands of genomes obtaining from different genotypes of the same species .
innovative solutions for storage and visualization , such as the rice snp - seek database ( http://oryzasnp.org/iric-portal/ ) , have to be developed to use efficiently the massive new information obtained .
as an example of the continuous evolution of genomic databases , the iplant collaborative resource has evolved into the cyverse cyberinfrastructure , which provides tools not only for plant research ( http://www.cyverse.org/ ) .
 in recent years , the genomic sequence of numerous plant species including the main crop species has been determined . 
 computational tools have been developed to deal with the issue of which plant has been sequenced and where is the sequence hosted . in this mini - review , 
 the databases for genome projects , the databases created to host species / clade projects and the databases developed to perform plant comparative genomics are revised . 
 because of their importance in modern research , an in - depth analysis of the plant comparative genomics databases has been performed . 
 this comparative analysis is focused in the common and specific computational tools developed to achieve the particular objectives of each database . besides , emerging high - performance bioinformatics tools specific for plant research are commented . 
 what kind of computational approaches should be implemented in next years to efficiently analyze plant genomes is discussed . 
OVERVIEW
GENOMIC PROJECTS DATABASES
Gold 
PLANT GENOMIC DATABASES
EMERGING HIGH-PERFORMANCE COMPUTING WEB RESOURCES
CONCLUDING REMARKS
NOTE ADDED IN PROOF
CONFLICT OF INTEREST