Genome sequences of right whales: resource for studies of population history and health

CAMPBELL, MICHAEL S; DALLEY, BRIAN K; EROH, GUY; CHIRIFE, ANDREA; DI MARTINO, MATIAS; MARON, CARINA; SIRONI, MARIANO; VALENZUELA, LUCIANO O; LEACHMAN, SANCY A; WHITE, BRADLEY N; UHART, MARCELA; ROWNTREE, VICTORIA; YANDELL, MARK; SEGER, JON

San Juan

Encuentro; Society for Molecular Biology and Evolution Annual Meeting; 2014

Society for Molecular Biology and Evolution

The worlds three species of right whales (Eubalaena spp.) werehunted nearly to extinction. Southern right whales (E. australis)are recovering well, with a population of roughly 12,000 individuals, but NorthAtlantic (E. glacialis) and North Pacific (E. japonica) rightwhales are still endangered, with populations of 500 or fewer. We havesequenced three southern right whale individuals to a depth ofapproximately 40x using the Illumina TruSeq Nano DNA sample prep with meaninsert sizes of 200bp and 600bp. Using only these short-read libraries,we generated a 2.2gb test assembly with a scaffold N50 of 46kb. CEGMAanalysis of this assembly returned 187 (75%) of the 248 ultra-conserved coreeukaryotic genes at full length, with an additional 46 (19%) present but lessthan 70% complete, indicating that the assembly contains ~94% of the genome?sprotein coding genes. We have also aligned the short reads back to thereference and called variants to estimate levels and patterns of polymorphism. Recentlywe sequenced a fourth individual using the Illumina Moleculo protocol,producing ~5kb (sd=2.5kb) virtual reads to a depth of ~3x. We arecurrently generating a new assembly using these reads, which should have a muchlonger scaffold N50. This will allow us to carry out synteny analyses andannotate the genome. Results of these analyses will be presented anddiscussed. Next we plan to sequence additional individuals from theclosely related North Atlantic and North Pacific right whales, to facilitatecomparative genetic studies of their reduced variation which has been proposedas a factor that may contribute to their slower rates of recovery fromexploitation.