[MARMAM] Genome sequencing of marine mammals -- sharing of plans

Per Palsböll Per.Palsboll at gmt.su.se
Thu May 5 09:13:17 PDT 2011


Dear fellow MarMammers,

As many of you are aware of then sequencing genomes and "transcriptomes" (basically the mRNA from the target cells) is the latest and hottest in genetics.

There are several high-level initiatives, the most significant probably the Comparative Genomics project funded and led by NIH in the US as well as the Genome 10k initiative, which, with the major sequencing facilities, is trying to coordinate overall efforts to ensure a broad phylogenetic coverage (across vertebrates) and to avoid duplication of efforts.

The main sequencing facility in the US, funded mostly by NIH, is the Broad Institute at MIT. They will sequence several 100s (mainly) mammal and vertebrate genomes during the coming year.

This is a tremendous opportunity to get some marine mammals on the "list" and have the genome sequences essentially done for free. The species priority was discussed under the last Genome 10k meeting in Santa Cruz in March. Three "marine mammal" folks were at this workshop, Terri Williams, Neil Gemmel and myself. Scott Baker was at the first Genome 10k meeting and made sure that marine mammals got the deserved attention then, and he has since stayed involved as well.

In addition to Broad's efforts then there are also other genome sequencing projects "privately" funded or in the planning by individual labs and/or consortia.

Although it is much, much less costly to get a genome sequence today, then it still ends up being a significant monetary and research effort to get to the final assembled stage. A final "genome" sequence today is probably not what most people envision, but mainly a bunch (10,000s) of very long (couple of million base pairs in average) DNA sequences (contigs), which we usually do not know how they go together on chromosomes. To get to something like chromosomal placement (mapping contigs) is another 60 - 100,000 USD.

I attach the Genome 10k list as it looks right now. You will see some marine mammals on the list. One key issue is the appropriate amount and quality samples to sequence a genome. Even if the list states that Broad has samples then (upon talking with the people in charge) it turns out that is not the case. So ANY help in getting samples from the targeted species (or a close relative) will be of tremendous value. Basically  500 micrograms of exceedingly HQ DNA is needed. The tissue basically needs to be flash frozen in liquid nitrogen at the sampling, stored in liquid nitrogen or -80 degrees Celsius for a short time and shipped on dry ice to the sequencing facility. Oh... and the sample has to be from the one and same individual AND it has to be a female. We are, with Jooke Robbins and the UC Santa Cruz genome sequencing facility, finding out how much DNA is obtained from a whole standard skin biopsy collected in this manner as in many cases there are permit limitations upon the number and size of skin biopsies that may be collected. We will post the result.

As far as I know (in addition to the attached list) then the following genome sequencing projects are done, funded or planned for marine mammals.

Done (sort of):

Bottlenose dolphin (in Genbank):
x2 (how many times each part of the genome has been sequenced) Sanger (the "older" HQ sequencing methods, but too expensive by today's standard) sequencing genome done by the Baylor Sequencing facility several years back. Data consists of some 45,000 contigs and likely a rather incomplete coverage of the dolphin genome.


Californian Sea  lion (http://sealiongenome.org/):
454 based genome generated by students at San Diego State University. Probably also a rather incomplete coverage of the genome but new classes will continue sequencing thereby increasing coverage.

Ongoing (funded "privately" and in addition to MIT/Broad):

Narwhal
Illumina sequencing of narwhal genome by UC Santa Cruz in collaboration with Terri Williams.

North Atlantic humpback whale
Illumina-based sequencing of a North Atlantic humpback whale at UC Santa Cruz with Jooke Robbins (Center for Coastal Studies), Carlo Maley (UC San Francisco) and Martine Berube/Per Palsboll (soon at CEES, Groningen University in Holland).

Other initiatives I am aware of but unsure of their status;


Australian humpback whale. Was contacted by Will Ditcham, from Murdoch University Marine Mammal Health Project, who seems to aim for sequencing a humpback whale genome.



Korean minke whale. Was contacted by Dr. Hyung-Soon Yim, Marine Biotechnology Research Center, Korea Ocean Research & Development Institute, and it appears they might sequence a minke whale

North Atlantic harbor porpoise: Maley and Martine Berube and I will also sequence the harbor porpoise if we have sufficient funds after completing the North Atlantic humpback whale

PROPOSAL to fellow MarMammers:

It is obvious that we are already entering a phase of potential duplication of efforts. I think we stand a unique chance to get a really good coverage of the marine mammals, which makes sense as they are unique mammals. However, to maximize our community efforts I suggest we make some sort of web-site/group page where we can post plans and follow-ups on these to (a) avoid duplication, (b) maximize coverage (c) relay experiences, and (d) foster collaborations. Since most genome sequences will/should go on-line more or less right when completed, then it should be obvious that coordination is best for all involved and to spend our overall resources as optimally as possible.

I will be happy to make and curate such a site/page IF people think this is the way to move forward and will post on the site?

I would be most grateful for feedback on the above.

Best regards,


Per J. Palsboll

During 2010/2011:
Hrdy Fellow
Department of Organismic and Evolutionary Biology
Harvard University
BioLabs 4092
16 Divinity Ave
Cambridge, MA 02138
U.S.A.

Office location: 16 Divinity Ave., BioLabs 4092
Office phone: +1 (617) 495-1568
Cell phone: +1 (857) 544 5844

Otherwise;

Untill September 1st, 2011:
Stockholm University
Department of Genetics, Microbiology and Toxicology
106 91 Stockholm
Sweden

Visiting address: Svante Arrheniusväg 20, room 545

Office  phone: +46 (0)8 16 1998
Mobile phone: +46 (0)73 518 2364

Thereafter;

Marine Evolution and Conservation
Center for Ecological and Evolutionary Studies
Univesity of Groningen
Centre for Life Sciences
Postbox 11103
9700 CC Groningen
The Netherlands

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