Q:
In Pseudogene.org, the pseudogene datasets of zebrafish (Danio rerio)
was based on old annotations (Ensembl 55?). There were about ~1800
processed pseudogenes. However, based on a recent research
(http://www.nature.com/nature/journal/v496/n7446/full/nature12111.html),
there were rare pseudogenes in zebrafish. (Only 21 processed
pseudogenes, according to Supplementary Table 14 in the published
manuscript).

Is this great conflict due to the old annotations?

A:
You are right about the zebrafish pseudogenes in the pseudogene.org. The results were based on an old genome assembly, ENSEMBL release 55, which was done in year 2009. We do notice that the pseudogene number is way too high, which we believe partially due to the quality of the genome assembly, and partially due to the reason that the pipeline parameters were optimized with primates. Given that, for up-to-date pseudogene information in Zebrafish, people should refer to the Nature publication: http://www.nature.com/nature/journal/v496/n7446/full/nature12111.html.

Thanks for pointing this out to us.