Comments on: Oh my, has it really been that long?

By: Thomas Mailund

Thomas Mailund — Fri, 04 Dec 2009 07:25:08 +0000

Yes, it is indeed the repetitive regions that are problematic, and with the current technology it is probably too expensive to complete the genomes…

By: Roald

Roald — Fri, 04 Dec 2009 07:14:37 +0000

I guess what matters with eukaryotes is that large genomes are mainly a consequence of many repeats, so one could say that there are only two really complex repeat-rich genomes that have been finished to a satisfying degree. That is really quite discouraging, but one could hope that new technologies, especially very long read sequencing and new technological alternatives to BAC cloning, will remedy this. Otherwise we will continue to see a flurry of poorly finished and poorly annotated genomes coming out.
It would be especially nice to see a polyploid genome finished to a satisfying degree.

By: Thomas Mailund

Thomas Mailund — Fri, 04 Dec 2009 07:13:59 +0000

Jonathan: Sorry, I thought it was clear from context that I wasn’t referring to prokaryotes where, you are right, we have quite a few more completed genomes. 979 completed genomes, according to NCBI.

I’m not saying that the prokaryotic genomes are not interesting or anything — they definitely are — but it is not the genomes that show up in the news, usually.

By: Jonathan Badger

Jonathan Badger — Thu, 03 Dec 2009 21:34:23 +0000

Only the human and mouse genome are really considered “complete”, the rest are just drafts and in many cases there are still many issues to work out with over-collapsed assemblies and such and with all the troublesome regions missing.

Er…human, mouse, and over 1000 complete prokaryotic genomes. You know, the genomes that actually contain novel genes. Euks (especially the mammals) are all just basically minor variations of each other.

By: Thomas Mailund

Thomas Mailund — Thu, 03 Dec 2009 20:36:29 +0000

They are ~100Mbp and ~250Mbp in size, as far as I remember off the top of my head, so perhaps semi-large ;-) An order of magnitude smaller than what I had in mind, though, thinking of the human genome.

They are considered completed, though, so you are right.

For a list of genome projects with status, see http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html There’s four animal genomes completed, C elegans, D melanogaster (short-ish animal genomes) in addition to man and mouse. There’s also four plan genomes completed, with rice being the other one in addition to A thaliana.

By: Roald

Roald — Thu, 03 Dec 2009 20:23:02 +0000

I do not know if you count them as large, but I would argue that the C Elgans and Arabidobsis genomes are also finished.