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Genomewide analysis of sperm whale E2 ubiquitin conjugating enzyme genes

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Abstract

Marine mammals are exposed to the oxidative stress induced by hypoxia/reoxygenation cycles yet resist cellular damage. The availability of high-quality genomes promises to provide insights on how this is achieved. In this study, we considered the ubiquitin-conjugating enzymes (E2) gene family, UBE2 genes, which encodes enzymes with critical roles in cellular physiology, including the oxidative stress response. The sperm whale was the first marine mammal with a chromosome-level genome, allowing the study of gene family repertories, phylogenetic relationships, chromosome gene organization, and other evolutionary patterns on a genomewide basis. Here, 39 UBE2 genes (similar to human, including 32 intact genes, one partial gene, six pseudogenes) were identified in sperm whale genome. These genes were found on 17 chromosomes and were assigned into 23 subfamilies, 16 subgroups, and four classes based on structural characteristics and functions, phylogeny and conserved domains, respectively. Although the gene structure and motif distribution of sperm whale UBE2 genes are conserved in each subfamily, motif variation and intron gain/loss may contribute to functional divergence. Segmental duplications were detected in six gene pairs, which could drive UBE2 gene innovation in the sperm whale. Contrasting seven cetaceans and five terrestrial taxa, we found that cetaceans have experienced shifts in selective constraint on UBE2 genes, which may contribute to oxidative stress tolerance during the adaptation to aquatic life. Our results provide the first comprehensive survey of cetacean UBE2 genes.

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Acknowledgements

This work was financially supported by the Key Project of the National Natural Science Foundation of China (NSFC) (no. 31630071, 32030011), the National Natural Science Foundation of China (NSFC) (no. 31900310; 31950410545), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

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  1. Ran Tian and Chen Yang contributed equally to this work.

Authors and Affiliations

  1. Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, Jiangsu, People’s Republic of China

    Ran Tian & Guang Yang

  2. Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, Jiangsu, People’s Republic of China

    Ran Tian, Chen Yang, Yuepan Geng & Inge Seim

  3. School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia

    Inge Seim

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  1. Ran Tian
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Correspondence to Inge Seim or Guang Yang.

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Corresponding editor: Punyasloke Bhadury

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Tian, R., Yang, C., Geng, Y. et al. Genomewide analysis of sperm whale E2 ubiquitin conjugating enzyme genes. J Genet 100, 78 (2021). https://doi.org/10.1007/s12041-021-01333-y

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