The Genome of the Beluga Whale (Delphinapterus leucas)

Abstract

The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

“…With a GC‐content of 41.4% and a total length of 2.7 GB, this assembly is comparable to other high‐quality cetacean genomes (Table ; Groenen et al., ; Zimin et al., ). In support of this, the scaffold N50 and sequence coverage are similar to the recently published high‐quality genomes of the beluga whale (Jones et al., ), sperm whale (Warren et al., ) and bottlenose dolphin (Neely et al., ) (Table ). Scans for core genes from the BUSCO and CEGMA databases identified a near completeness of these genes in the assembly and support that we have largely reconstructed the entire genome.…”

“…Genetic resources available for cetaceans do not yet adequately cover the diversity of this group (Foote et al., ; Keane et al., ; Nery et al., ; Sun et al., ; Yim et al., ; Zhou et al., ). Thus far, sequenced genomes include at least three baleen whales (DeWoody et al., ; Kishida et al., ; Yim et al., ) and six species of the toothed whales (Foote et al., ; Jones et al., ; Lindblad‐Toh et al., ; Neely et al., ; Warren et al., ; Yuan et al., ; Zhou et al., , ). While the number of available genomes is growing rapidly, they do not fully represent extant taxa, and the completeness of their assemblies varies (Table ).…”

An epigenetic clock to estimate the age of living beluga whales

“…The sequencing of the beluga whale genome (Jones et al, 2017) Research that compares epigenetic aging of Cook Inlet beluga whales with other populations will inform the applicability of this epigenetic clock to circumpolar populations of beluga whales. Data from other populations of beluga whales could also improve the accuracy of the beluga epigenetic clock by increasing sample size (the most accurate human clocks were trained on thousands of samples, e.g.…”

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

“…First, inactivating mutations shared between the four cetaceans used in the genomic screen imply that other species that descended from their common ancestor should share these mutations. We tested this by manually inspecting the genomes of two additional odontocetes (Yangtze river dolphin (23) and beluga whale (42)) and an additional mysticete (bowhead whale (43)), which confirmed the presence of shared inactivating mutations. It should be noted that the presence of the same inactivating mutations in independent genome assemblies of multiple related species excludes the possibility that these mutations are sequencing or assembly errors, which is corroborated by DNA sequencing reads ( Figure S1).…”

“…For all genes listed in Table S1, we investigated whether shared inactivating mutations are present in the genomes of three additional cetaceans that were not part of the wholegenome alignment (130), the Yangtze river dolphin, beluga whale and bowhead whale (23,42,43). To this end, we aligned these genomes to the hg38 assembly as described above and manually confirmed the presence of shared inactivation mutations.…”