Gorilla genome version

Question

[int11ap1]

Everybody is using the genoem version gorGor3 of Gorilla. Why? There exists an updated version, the gorGor4.

[GenoMax]

Western lowland gorilla genome assembly was recently "upgraded" by using PacBio long reads.

[int11ap1]

Indeed, but it is not assembled into chromosomes. It is just made of long contigs.

Answer 1

[Emily]

gorGor4 has been available on INSDC for a little over a year, which means that technically we can annotate it in Ensembl, according to our browser agreement. However, annotation takes time and resources, which are limited, and the gorilla genome is not high priority. It's been out over a year and you're the first person who's asked about it, so there is not the demand in the community.

[Michael]

My mistake that I didn't find that probably. I was searching Genome: txid9593[orgn], but it wasn't listed there under Assemblies linked from genome. However, when searching Assemblies: txid9593[orgn] then it shows up.

Answer 2

[Michael]

Where did you find that, please provide evidence. People can only use what is available, unless the genome is available in Ensembl or NCBI many would say that genome build does not exist. https://www.ncbi.nlm.nih.gov/assembly?LinkName=genome_assembly&from_uid=2156

Otherwise, genome builds are like software, often it is ok to jump on the latest version, but not always. New versions might not be compatible with your data or previous research, new builds might lack genome annotation or lack the genes you were working with for years. Migration of data, aka. LiftOver cost time.

[int11ap1]

http://hgdownload-test.soe.ucsc.edu/goldenPath/gorGor4/