[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
Mon Aug 13 03:38:17 PDT 2018


Dear Colleagues,

my co-authors and I are pleased to announce that our paper, previously 
online at BioRxiv, is now available online on Molecular Ecology Resources:

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/10.1111/1755-0998.12932

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank 
under the accession PKGA00000000. The version described in this paper is 
version PKGA01000000. The draft annotation is deposited to Dryad 
(doi:10.5061/dryad.vr021gq).

Abstract:

The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found 
across the Northern hemisphere. It occurs in coastal waters and inhabits 
basins that vary broadly in salinity, temperature and food availability. 
These diverse habitats could drive subtle differentiation among populations, 
but examination of this would be best conducted with a robust reference 
genome. Here, we report the first harbour porpoise genome, assembled de novo 
from an individual originating in the Kattegat Sea (Sweden). The genome is 
one of the most complete cetacean genomes currently available, with a total 
size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. 
Using 122 of the longest scaffolds, we were able to show high levels of 
synteny with the genome of the domestic cattle (Bos taurus). Our draft 
annotation comprises 22,154 predicted genes, which we further annotated 
through matches to the NCBI nucleotide database, GO categorization and motif 
prediction. Within the predicted genes, we have confirmed the presence of 
>20 genes or gene families that have been associated with adaptive evolution 
in other cetaceans. Overall, this genome assembly and draft annotation 
represent a crucial addition to the genomic resources currently available 
for the study of porpoises and Phocoenidae evolution, phylogeny and 
conservation.


The paper is available online here: 
https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12932


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
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