Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Peart, Claire R.; Williams, Christina L.; Pophaly, Saurabh D.; Neely, Benjamin A.; Gulland, Frances M. D.; Adams, David J.; Ng, Bee Ling; Cheng, William; Goebel, Michael E.; Fédrigo, Olivier; Haase, Bettina; Mountcastle, Jacquelyn; Fungtammasan, Arkarachai; Formenti, Giulio; Collins, Joanna; Wood, Jonathan; Sims, Ying; Torrance, James; Tracey, Alan S.; Howe, Kerstin; Rhie, Arang; Hoffman, Joseph I.; Johnson, Jeremy; Jarvis, Erich D.; Breen, Matthew; Wolf, Jochen B. W.

doi:10.1111/1755-0998.13443

Cited by 10 publications

(15 citation statements)

References 116 publications

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“…While the X chromosome assembled well, the Y chromosome, due to long blocks of repetitive sequence, was problematic. Nevertheless, we were able to assemble portions of the Y chromosome ( Table 3 ) corresponding to the gene-rich region seen in other species, which showed good agreement with that of Zalophus californianus [ 35 ] with a total of 20 loci identified in both.…”

Section: Discussionsupporting

confidence: 64%

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

Mohr

Gaughran

Paschall

et al. 2022

Genes

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The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.

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Section: Discussionsupporting

confidence: 64%

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

Mohr

Gaughran

Paschall

et al. 2022

Genes

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“…Sequence homology searches between the mitochondrial ( Nagel et al 2019 ) and nuclear genome ( Peart et al 2021 ) of the Antarctic fur seal reveal a total of 25 putative numts varying in length between 294 and 14,199 bp and consisting of between one and four separate fragments (see Materials and Methods, fig. 1 and table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…This may have introduced novel mitochondrial variation that, if integrated into the nuclear genome, would appear divergent from homologous A. gazella mitochondrial sequences. Second, both a high quality, chromosome-level, nuclear reference genome ( Humble et al 2018 , 2016 ; Peart et al 2021 ) and a mitochondrial ( Nagel et al 2019 ) genome are available for this species.…”

Section: Introductionmentioning

confidence: 99%

Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals

Vendrami

Gossmann

Chakarov

et al. 2022

Genome Biology and Evolution

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Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared to their mitochondrial homologs to characterize synonymous to non-synonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterise 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to non-canonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.

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“…This explains the relatively low contig N50 (159.6 kb) and incomplete telomeres and centromeres observed in the Visayan warty pig genome assembly. However, the contig N50 is less likely to affect Hi-C-based genome scaffolding ( Zhang et al 2019 ; Peart et al 2021 ). Thus, the clustering, ordering, and orientation of the final assembly are reliable.…”

Section: Discussionmentioning

confidence: 99%

The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs

Liu

Megens

Crooijmans

et al. 2022

Molecular Biology and Evolution

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It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.

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Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 10 publications

References 116 publications

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals

The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs

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