Answers.Body: <p>tl;dr: technical difficulties, or sex</p>
  
  <p>For the gorilla, that genome is from a female gorilla (<a href="https://www.nature.com/news/gorilla-joins-the-genome-club-1.10185" rel="noreferrer">Kamilah the gorilla</a>) so she doesn't have a Y chromosome.</p>
  
  <p>For the chimp link, there is a visualization of the chromosomes that you can click on that takes you to the genome browser for the Y chromosome (see image). Notably, there is a <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001515.5" rel="noreferrer">more recent genome build</a> that does have a Y chromosome sequence assembly that is directly linked, they just haven't updated the main reference sequence yet.</p>
  
  <p><a href="https://i.sstatic.net/kw5so.png" rel="noreferrer"><img src="https://i.sstatic.net/kw5so.png" alt="chimp entry"></a></p>
  
  <p>To directly address the question, the Y chromosome is <a href="https://www.cell.com/trends/genetics/pdf/S0168-9525(17)30019-7.pdf" rel="noreferrer">very hard to assemble</a>. The easy part of it to assemble is already on the X chromosome anyways (the pseudoautosomal region), and the hard part of it is often a mess of repeats, especially in mammals. Many groups will decide to just assemble the X as well as they can and call it good, due to the difficulties associated with assembling the Y. If they are working with a male individual the Y sequence is still there, it just may not be anchored to a chromosome sequence, so it's only in the unscaffolded/unanchored assembly ("master WGS" I believe, usually). It is also probably highly fragmented (it isn't a whole chromosome of sequence stitched together, but rather a lot of little pieces of sequence).</p>
  
  <p>In some cases they will focus all sequencing efforts on female individuals specifically to make their assembly job easier, because in females the X is at the same copy number as the autosomes and doesn't have interference from homologous regions on the Y.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-14T05:06:33.640Z
Answers.LastActivityDate: 2020-02-14T05:06:33.640Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I recently downloaded a genome from NCBI for chimpanzee and was surprised to see no Y chromosome.  I added in one from a separate accession and carried on, but then today went to do the same for gorilla and saw the same thing, no Y.</p>
  
  <ul>
  <li>For Gorilla gorilla (western gorilla): <a href="https://www.ncbi.nlm.nih.gov/genome/2156" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/genome/2156</a></li>
  <li>For Pan troglodytes (chimpanzee): <a href="https://www.ncbi.nlm.nih.gov/genome/202" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/genome/202</a></li>
  </ul>
  
  <p>Why would this be?  I can see a separate entry for a Y chromosome for that same exact chimp used for the representative genome (Clint) here, but I don't see why it's not in the representative genome listing itself:</p>
  
  <p><a href="https://www.ncbi.nlm.nih.gov/nuccore/DP000054.3" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/nuccore/DP000054.3</a></p>
  
Tags: <reference-genome><phylogenetics>
Title: Why do these NCBI representative genomes for ape species have no Y chromosome?
ThreadText: # Why do these NCBI representative genomes for ape species have no Y chromosome?
  
  (Asked by: username_0 on 2020-02-13)
  
  I recently downloaded a genome from NCBI for chimpanzee and was surprised to see no Y chromosome. I added in one from a separate accession and carried on, but then today went to do the same for gorilla and saw the same thing, no Y.
  
  * For Gorilla gorilla (western gorilla): <https://www.ncbi.nlm.nih.gov/genome/2156>
  * For Pan troglodytes (chimpanzee): <https://www.ncbi.nlm.nih.gov/genome/202>
  
  Why would this be? I can see a separate entry for a Y chromosome for that same exact chimp used for the representative genome (Clint) here, but I don't see why it's not in the representative genome listing itself:
  
  <https://www.ncbi.nlm.nih.gov/nuccore/DP000054.3>
  
  **Tags:** reference-genome, phylogenetics
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-02-14. Score: 8 | Accepted answer
  
  tl;dr: technical difficulties, or sex
  
  For the gorilla, that genome is from a female gorilla ([Kamilah the gorilla](https://www.nature.com/news/gorilla-joins-the-genome-club-1.10185)) so she doesn't have a Y chromosome.
  
  For the chimp link, there is a visualization of the chromosomes that you can click on that takes you to the genome browser for the Y chromosome (see image). Notably, there is a [more recent genome build](https://www.ncbi.nlm.nih.gov/assembly/GCA_000001515.5) that does have a Y chromosome sequence assembly that is directly linked, they just haven't updated the main reference sequence yet.
  
  [![chimp entry](https://i.sstatic.net/kw5so.png)](https://i.sstatic.net/kw5so.png)
  
  To directly address the question, the Y chromosome is [very hard to assemble](https://www.cell.com/trends/genetics/pdf/S0168-9525(17)30019-7.pdf). The easy part of it to assemble is already on the X chromosome anyways (the pseudoautosomal region), and the hard part of it is often a mess of repeats, especially in mammals. Many groups will decide to just assemble the X as well as they can and call it good, due to the difficulties associated with assembling the Y. If they are working with a male individual the Y sequence is still there, it just may not be anchored to a chromosome sequence, so it's only in the unscaffolded/unanchored assembly ("master WGS" I believe, usually). It is also probably highly fragmented (it isn't a whole chromosome of sequence stitched together, but rather a lot of little pieces of sequence).
  
  In some cases they will focus all sequencing efforts on female individuals specifically to make their assembly job easier, because in females the X is at the same copy number as the autosomes and doesn't have interference from homologous regions on the Y.
  
  
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