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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.

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

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tl;dr: technical difficulties, or sex

For the gorilla, that genome is from a female gorilla (Kamilah the gorilla) 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 that does have a Y chromosome sequence assembly that is directly linked, they just haven't updated the main reference sequence yet.

chimp entry

To directly address the question, the Y chromosome is very hard to assemble. 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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