A high-quality blue whale genome, segmental duplications, and historical demography

Bukhman, Yury V.; Morin, Phillip A.; Meyer, Susanne; Chu, Li‐Fang; Jacobsen, Jeff K.; Antosiewicz‐Bourget, Jessica; Mamott, Daniel; Gonzales, Maylie; Argus, Cara; Bolin, Jennifer M.; Berres, Mark E.; Fédrigo, Olivier; Steill, John; Swanson, Scott; Jiang, Peng; Rhie, Arang; Formenti, Giulio; Phillippy, Adam M.; Harris, Robert S.; Wood, Jonathan; Howe, Kerstin; Kirilenko, Bogdan; Munegowda, Chetan; Hiller, Michael; Jain, Aashish; Johnston, J. Spencer; Ionkov, Alexander; Raja, Kalpana; Toh, Huishi; Lang, Aimée R.; Wolf, Magnus; Jarvis, Erich D.; Thomson, James A.; Chaisson, Mark; Stewart, Ron

doi:10.21203/rs.3.rs-1910240/v1

Cited by 8 publications

(12 citation statements)

References 115 publications

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“…The complete genome was sequenced in all individuals to an average depth of ~32× and aligned against the blue whale genome ( 21 ). In all eight trios, the genome sequences confirmed the relationships inferred from the microsatellite data.…”

Section: Nuclear Mutation Ratementioning

confidence: 99%

Wild pedigrees inform mutation rates and historic abundance in baleen whales

Suárez-Menéndez,

Bérubé,

Furni

et al. 2023

Science

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Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.

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Section: Nuclear Mutation Ratementioning

confidence: 99%

Wild pedigrees inform mutation rates and historic abundance in baleen whales

Suárez-Menéndez,

Bérubé,

Furni

et al. 2023

Science

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“…4a ). Details of several other genes on this list linked to longevity ( MT1X ), body size ( CHRNB1, DPEP2 ), development ( FZD5 , CDK20 ), cancer (C2orf78, FZD5, DDX24, NCAM1, MT1X, XRCC1, CDK20 ), obesity and diabetes ( DPEP2 ), and the immune system ( NCAM1 ) are available in Table 2 and Wiki pages on OSF ( Bukhman et al 2021b ).…”

Section: Resultsmentioning

confidence: 99%

“…These sites are not shown in Table 3 . All statistically significant sites and notes are available in supplementary data, Supplementary Material online file on OSF (IGF1/hits.xlsx in ( Bukhman et al 2021b )).…”

Section: Resultsmentioning

confidence: 99%

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Bukhman,

Morin,

Meyer

et al. 2024

Molecular Biology and Evolution

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The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10X, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world’s smallest cetacean, to investigate blue whale’s unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

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“…Accessed reads were trimmed using the bbduk.sh script from bbmap (Bushnell 2014), with the settings ktrim=r, k=23, mink=8, hdist=1, tbo, qtrim=rl, trimq=15, maq=20, and minlen=40. The blue whale ( Balaenoptera musculus ) reference genome (Bukhman et al 2022) was selected for read mapping given its status as a platinum-standard reference genome (Morin et al 2020). Trimmed reads were mapped using the Burrows-Wheeler Aligner Maximal Exact Matches (BWA-MEM) algorithm v.0.7.17 and default settings (Li and Durbin 2009).…”

Section: Methodsmentioning

confidence: 99%

Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands

Dekker,

Mylopotamitaki,

Verbaas

et al. 2024

Preprint

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Identification of the taxonomic origin of bone tools is an important, but often complicated, component of studying past societies. The species used for bone tool production provide insight into what species were exploited, potentially how, and for what purpose. Additionally, the choice of species may have important implications for the place of the tool within the larger toolkit. However, the taxonomic identification of bone tools is often unsuccessful based on morphology. Here we apply three palaeoproteomic techniques, ZooMS, SPIN and a targeted database search to narrow down the taxonomic identification of an unusually large Bronze Age bone tool from Heiloo, the Netherlands, to the North Atlantic right whale (Eubalaena glacialis). Additionally, the tool was investigated for use-wear, which showed that it was likely used for the processing of plant fibres. The assignment of the tool as whale bone adds support to the exploitation of whales by coastal Bronze Age populations, not just for meat, as previously suggested, but also for bone as a resource for tool production. We know of no other parallel of a bone tool such as this in terms of size, use, hafting, and taxonomic identity.

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A high-quality blue whale genome, segmental duplications, and historical demography

Cited by 8 publications

References 115 publications

Wild pedigrees inform mutation rates and historic abundance in baleen whales

Wild pedigrees inform mutation rates and historic abundance in baleen whales

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands

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