Answers.Body: <p>The reason is simple, insect genomes are often heavily fragmented and historically relied on wet-lab experimentation - polytene chromosome hybridisation to correcty assemble the chromosomes. Thus you probe the various contigs, prep the contigs often from salivary glands, stick them under a microscope and map the location of the probes. Hence, the reluctance to assign a 'genome' based on contigs because the chromosomes cannot be assembled. This is particularly true for a very close relative to the premier model of the Insecta <em>D. melanogaster</em>. A lot of work will have gone into the correct chromosome annotation of this genome. Thus, you can't simply 'promote' a genome without further genomics analysis and it will be a community decision based on the analysis (i.e. reviewers).</p>
  <p>Bioinformatic assemblies often get it right. What I would do is use a reference genome assembly based on the nearest ancestor, which you'll know more than me, I'm pretty sure its not <em>D. melanogaster</em>. This is within the context of a comparative genomic analysis between the species/subspecies associated with <em>D. subobscura</em> and then say to NCBI 'thats a genome'. You then have to publish the analysis and submit your assembled genome to NCBI. Its not trivial, but if you 'live next door' to one of the genetic models of eukaryotes (well metazoa) the standards of annotation and assembly will be high.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-04T22:03:55.460Z
Answers.LastActivityDate: 2022-10-04T23:09:23.960Z
Answers.LastEditDate: 2022-10-04T23:09:23.960Z
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Body: <p>Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.</p>
  <p>I'm working with <em>Drosophila subobscura</em>. (spring fruit fly)</p>
  <p>I see here <a href="https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=7241" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=7241</a> that there are at least 2 assemblies of better quality than the only available genome (I checked checked N50 and number of scaffolds).</p>
  <ul>
  <li><a href="https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_903684685.1/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_903684685.1/</a></li>
  <li><a href="https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_018903505.1/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_018903505.1/</a></li>
  </ul>
  <p>However, these assemblies weren't promoted to genomes.</p>
  <p><strong>Questions</strong></p>
  <ol>
  <li><p>What is required to consider them genomes?</p>
  </li>
  <li><p>Is it the scaffold to chromosome notation that is missing? Or also the annotations?</p>
  </li>
  <li><p>How would I promote the better assemblies into genomes?</p>
  </li>
  <li><p>And also, if I wanted to annotate one of the better assemblies, how would I proceed?</p>
  </li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-04T17:44:58.613Z
Comments.Text: I'd suggest splitting the fourth question off into its own question. Genome annotation is a very different subject than the NCBI controlled vocabulary and content management procedures. Annotation is also much easier to answer, as it's merely a technical question! E.g. NCBI has their own [annotation pipeline](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/), or you could use [MAKER](http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018).
Comments.UserDisplayName: Maximilian Press
Tags: <genome><assembly><phylogenetics>
Title: How to promote assemblies into genomes in NCBI?
ThreadText: # How to promote assemblies into genomes in NCBI?
  
  (Asked by: username_0 on 2022-10-04)
  
  Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.
  
  I'm working with *Drosophila subobscura*. (spring fruit fly)
  
  I see here <https://www.ncbi.nlm.nih.gov/data-hub/genome/?taxon=7241> that there are at least 2 assemblies of better quality than the only available genome (I checked checked N50 and number of scaffolds).
  
  * <https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_903684685.1/>
  * <https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_018903505.1/>
  
  However, these assemblies weren't promoted to genomes.
  
  **Questions**
  
  1. What is required to consider them genomes?
  2. Is it the scaffold to chromosome notation that is missing? Or also the annotations?
  3. How would I promote the better assemblies into genomes?
  4. And also, if I wanted to annotate one of the better assemblies, how would I proceed?
  
  **Tags:** genome, assembly, phylogenetics
  
  > **Comments:**
  > **username_1**: I'd suggest splitting the fourth question off into its own question. Genome annotation is a very different subject than the NCBI controlled vocabulary and content management procedures. Annotation is also much easier to answer, as it's merely a technical question! E.g. NCBI has their own [annotation pipeline](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/), or you could use [MAKER](http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-10-04. Score: 1
  
  The reason is simple, insect genomes are often heavily fragmented and historically relied on wet-lab experimentation - polytene chromosome hybridisation to correcty assemble the chromosomes. Thus you probe the various contigs, prep the contigs often from salivary glands, stick them under a microscope and map the location of the probes. Hence, the reluctance to assign a 'genome' based on contigs because the chromosomes cannot be assembled. This is particularly true for a very close relative to the premier model of the Insecta *D. melanogaster*. A lot of work will have gone into the correct chromosome annotation of this genome. Thus, you can't simply 'promote' a genome without further genomics analysis and it will be a community decision based on the analysis (i.e. reviewers).
  
  Bioinformatic assemblies often get it right. What I would do is use a reference genome assembly based on the nearest ancestor, which you'll know more than me, I'm pretty sure its not *D. melanogaster*. This is within the context of a comparative genomic analysis between the species/subspecies associated with *D. subobscura* and then say to NCBI 'thats a genome'. You then have to publish the analysis and submit your assembled genome to NCBI. Its not trivial, but if you 'live next door' to one of the genetic models of eukaryotes (well metazoa) the standards of annotation and assembly will be high.
  
  
  ---
  
  