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Cited by 45Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsMarine animal studies overview

The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution

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Fan, Guangyi, Zhang, Yaolei, Liu, Xiaochuan, Wang, Jiahao, Sun, Zeguo, Sun, Shuai, Zhang, He, Chen, Jianwei +38 more·2019·Molecular Ecology Resources
DOI 10.1111/1755-0998.13003
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Abstract

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome‐level marine mammal genome assembly based on the data generated by the BGISEQ‐500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.

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  • Comparing a highly-fragmented with a highly-contiguous assembly of two sperm whale species showed that orthologous genes located on a single scaffold in both species have a much higher sequence identity (mean 98.70%) than paralogous genes (mean 75.18%).

    “Indeed, comparing a highly-fragmented with a highly-contiguous assembly of two sperm whale species (27, 29) showed that orthologous genes located on a single scaffold in both species have a much higher sequence identity (mean 98.70%) than paralogous genes (mean 75.18%) (Fig. 4B).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [29]

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Authors
Fan, G., Zhang, Y., Liu, X., Wang, J., Sun, Z., Sun, S., Zhang, H., Chen, J., Lv, M., Han, K., Tan, X., Hu, J., Guan, R., Fu, Y., Liu, S., Chen, X., Xu, Q., Qin, Y., Liu, L., Bai, J., Wang, O., Tang, J., Lu, H., Shang, Z., Wang, B., Hu, G., Zhao, X., Zou, Y., Chen, A., Gong, M., Zhang, W., Lee, S. M. ‐., Li, S., Liu, J., Li, Z., Lu, Y., Sabir, J. S. M., Sabir, M. J., Khan, M., Hajrah, N. H., Yin, Y., Kristiansen, K., Yang, H., Wang, J., Xu, X., & Liu, X.
Affiliations
  • BGI Group (China) (CN)
  • Guangdong Pearl River Estuary Chinese White Dolphin National Nature Reserve Administration Zhu Hai Guangdong China
  • China National GeneBank (CN)
  • University of Macau (MO)
  • Chinese Academy of Sciences (CN)
  • Health and Family Planning Integrated Supervision Enforcement Bureau of Shinan District Qingdao City China
  • Guangdong Ocean University (CN)
  • King Abdulaziz University (SA)
  • University of Copenhagen (DK)
Corresponding author
Liu, Xin
ORCID
Venue
Molecular Ecology Resources
Publisher
Wiley
Published
2019-05-09
Volume
19
Issue
4
Pages
944-956
ISSN
  • 1755-098X (ISSN-L)
  • 1755-0998
DOI
10.1111/1755-0998.13003
OpenAlex
W2914147444
Cited by
45
References
3
Citations by year
2026: 6 · 2025: 4 · 2024: 7 · 2023: 7 · 2022: 5 · 2021: 4 · 2020: 6 · 2019: 5
FWCI
1.72
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations
  • Molecular Ecology Resources (publishedVersion)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
  • Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
Funders
Government of Jiangxi Province
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Physical Sciences › Environmental Science › Ecology › Marine animal studies overview
Keywords
sperm whale, chromosome-level genome assembly, karyotype evolution, ancestral chromosomes, chromosomal rearrangements, convergent evolution, aquatic adaptation, long interspersed nuclear elements, major histocompatibility complex, positive selection, population decline, Pliocene-Pleistocene transition, comparative genomics
MeSH terms
Adaptation, Biological, Animals, Cattle, Female, Sheep, Genome, Ecosystem, Evolution, Molecular, Sperm Whale, Aquatic Organisms

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