Genome Sequences of Right Whales: Resource for Studies of Population History and Health

The world's three species of right whales (Eubalaena spp.) were hunted nearly to extinction.  Southern right whales (E. australis) are recovering well, with a population of roughly 12,000 individuals, but North Atlantic (E. glacialis) and North Pacific (E. japonica) right whales are still endangered, with populations of 500 or fewer.  We have sequenced four southern, three North Atlantic and one North Pacific right whales to a depth of ~40x using the Illumina TruSeq Nano DNA sample prep. For one of the southern whales, we generated 3-, 5- and 7-kb mate-pair libraries and sequenced them to a depth of ~60x. This individual was also sequenced using the Illumina Moleculo protocol, producing ~5kb (sd=2.5kb) virtual reads to a depth of ~3x. We assembled the Illumina reads with the ALLPATHS assembler and used PBjelly to fill gaps in the assembly using the Moleculo reads. The resulting assembly has a 379kb scaffold N50. CEGMA analysis of the assembly reported that 237 (95%) of the 248 ultra-conserved core eukaryotic genes are full length, with an additional 10 (4%) present but less than 70% complete, indicating the assembly includes ~99% of the genome’s protein coding genes, with ~95% complete.  We have annotated the assembly with the MAKER genome annotation pipeline, aligned the read data from all individuals to this reference assembly, and called variants. These data have been analyzed to estimate the nuclear mutation rate for right whales and to address questions about the historic sizes and migration histories of the three populations.