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Chromosome-level analysis of the Mauremys mutica genome reveals adaptation of temperature-dependent sex-associated genes
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  • Xinping Zhu,
  • Xiao Li Liu,
  • Yakun Wang,
  • Ju Yuan,
  • Fang Liu,
  • Xiaoyou Hong,
  • Wei Li,
  • Chen Chen,
  • Lingyun Yu,
  • Wei Ni,
  • Haiyang Liu,
  • Jian Zhao,
  • Chengqing Wei,
  • Haigang Chen,
  • Yihui Liu
Xinping Zhu
Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

Corresponding Author:[email protected]

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Xiao Li Liu
Institute of Hydrobiology Chinese Academy of Sciences
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Yakun Wang
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Xiaoyou Hong
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Lingyun Yu
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Haiyang Liu
Chinese Academy of Fishery Sciences Pearl River Fisheries Research Institute
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Chengqing Wei
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Haigang Chen
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Abstract

Knowledge of the sex determination system and sex-associated genes has important implications in physiology, ecology and evolution, but the mechanisms underlying sexual determination systems in turtles has not been fully elucidated, due to their remarkable variability and a lack of reference genomes in some species. In this report, we describe the first genome assembled at the chromosome scale for Mauremys mutica using Illumina and high-throughput chromatin conformation capture (Hi-C) technology. A total of 280.42 Gb of clean data were generated using the Pacific Biosciences platforms, which represented approximately 119× coverage of the Mauremys mutica genome. The assembly comprised 2.23 Gb with a contig N50 of 8.53 Mb and scaffold N50 of 141.98 Mb. Genome Hi-C scaffolding resulted in 26 pseudochromosomes containing 99.98% of the total assembly. Genome annotation predicted 24,751 protein-coding genes, and 97.23% of them were annotated. Comparative genomics analysis indicated that the lizard-snake-tuatara clade diverged from the bird-crocodilian-turtle clade at approximately 283.1-320.5 Mya. Additionally, positive selection of genes and gene families related to calcium signaling, neuroactive ligand-receptor interaction, and expansion of the hormone signaling pathway were identified, implicating their roles of sex regulation inMauremys mutica. High-quality genome assembly may provide a valuable genomic resource for further research investigating gene-environment interactions in Mauremys mutica.
31 Aug 2021Submitted to Molecular Ecology Resources
20 Sep 2021Submission Checks Completed
20 Sep 2021Assigned to Editor
29 Sep 2021Reviewer(s) Assigned
28 Oct 2021Review(s) Completed, Editorial Evaluation Pending
08 Nov 2021Editorial Decision: Revise Minor
25 Nov 2021Review(s) Completed, Editorial Evaluation Pending
25 Nov 20211st Revision Received