[MARMAM] New Publication: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

Marijke Autenrieth marauten at uni-potsdam.de
Fri Apr 20 01:46:37 PDT 2018


Dear Colleagues,


my co-authors and I are pleased to announce that our following paper is now 
available online on BioRxiv :

High quality whole genome sequence of an abundant Holarctic odontocete, the 
harbour porpoise (Phocoena phocoena)
Marijke Autenrieth, Stefanie Hartmann, Ljerka Lah, Anna Roos, Alice Dennis, 
Ralph Tiedemann
doi: https://doi.org/10.1101/246173
  <https://doi.org/10.1101/246173>

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank 
underthe accession PKGA00000000. The version described in this paper is 
versionPKGA01000000. The draft annotation is deposited to Dryad 
(doi:10.5061/dryad.vr021gq).
The paper is available online here: 
https://www.biorxiv.org/content/early/2018/04/19/246173

Abstract:
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found 
in waters across the Northern hemisphere. It occurs in coastal water and 
inhabits water basins that vary broadly in salinity, temperature, and food 
availability. These diverse habitats could drive differentiation among 
populations. Here we report the first harbour porpoise genome, assembled de 
novo from a Swedish Kattegat individual. The genome is one of the most 
complete cetacean genomes currently available, with a total size of 2.7 Gb 
and 50% of the total length found in just 34 scaffolds. Using the largest 
122 scaffolds, we were able to validate a high level of homology to the 
chromosome-level genome assembly of the closest related species for which 
such resource was available, the domestic cattle (Bos taurus). The draft 
annotation comprises 22,154 predicted gene models, which we further 
annotated through matches to the NCBI nucleotide database, GO 
categorization, and motif prediction. To infer the adaptive abilities of 
this species, as well as their population history, we performed a Bayesian 
skyline analysis, and produced results that are concordant with the 
demographic history of this species, including expansion and fragmentation 
events. Overall, this genome assembly, together with the draft annotation, 
represents a crucial addition to the limited genetic markers currently 
available for the study of porpoises and Phocoenidae conservation, 
phylogeny, and evolution.


Kind regards,
Marijke Autenrieth


--
Marijke Autenrieth, M.Sc.
PhD student

phone: 0049-(0)-331-977-5586
mobile: 0049-176-81308823
email: marauten at uni-potsdam.de
web: https://mammalsevolve.wordpress.com/

Universität Potsdam
Evolutionsbiologie
Karl-Liebknecht-Str. 24-25
14476 Golm


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.uvic.ca/pipermail/marmam/attachments/20180420/61fbebd6/attachment.html>


More information about the MARMAM mailing list