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Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets
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  • Lei Han,
  • Tianming Lan,
  • Desheng Li,
  • Haimeng Li,
  • Linhua Deng,
  • Zhiwei Peng,
  • Shaowen He,
  • Yanqiang Zhou,
  • Ruobing Han,
  • Lingling Li,
  • Yaxian Lu,
  • Haorong Lu,
  • Qing Wang,
  • Shangchen Yang,
  • Yixin Zhu,
  • Yunting Huang,
  • Xiaofang Cheng,
  • Jieyao Yu,
  • Yulong Wang,
  • Heting Sun,
  • Hongliang Chai,
  • Huanming Yang,
  • Xun Xu,
  • Michael Lisby,
  • Quan Liu,
  • Karsten Kristiansen,
  • Huan Liu,
  • Zhijun Hou
Lei Han
Northeast Forestry University

Corresponding Author:c-hanlei1@genomics.cn

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Tianming Lan
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
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Desheng Li
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Haimeng Li
BGI-Shenzhen
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Linhua Deng
Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park (CCRCGP)
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Zhiwei Peng
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Shaowen He
Foping National Nature Reserve
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Yanqiang Zhou
Northeast Forestry University
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Ruobing Han
Northeast Forestry University
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Lingling Li
Northeast Forestry University
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Yaxian Lu
Northeast Forestry University
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Haorong Lu
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
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Qing Wang
University of Chinese Academy of Sciences
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Shangchen Yang
Zhejiang University
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Yixin Zhu
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
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Yunting Huang
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
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Xiaofang Cheng
MGI, BGI-Shenzhen
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Jieyao Yu
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
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Yulong Wang
Northeast Forestry University
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Heting Sun
Northeast Forestry University
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Hongliang Chai
Northeast Forestry University
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Huanming Yang
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
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Michael Lisby
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen
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Quan Liu
Northeast Forestry University
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Karsten Kristiansen
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Huan Liu
University of Copenhagen
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Zhijun Hou
Northeast Forestry University
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Abstract

Helminth diseases have long been a threat to the health of humans and animals. Roundworms are important organisms for studying parasitic mechanisms, disease transmission and prevention. The study of parasites in the giant panda is of importance for understanding how roundworms adapt to the host. Here, we report a high-quality chromosome-scale genome of Baylisascaris schroederi with a genome size of 253.60 Mb and 19,262 predicted protein-coding genes. We found that gene families related to epidermal chitin synthesis and environmental information processes in the roundworm genome have expanded significantly. Furthermore, we demonstrated unique genes involved in essential amino acid metabolism in the B. schroederi genome, inferred to be essential for the adaptation to the giant panda-specific diet. In addition, under different deworming pressures, we found that four resistance-related genes (glc-1, nrf-6, bre-4 and ced-7) were under strong positive selection in a captive population. Finally, 23 known drug targets and 47 potential drug target proteins (essential homologues linked to lethal phenotypes) were identified. The genome provides a unique reference for inferring the early evolution of roundworms and their adaptation to the host. Population genetic analysis and drug sensitivity prediction provide insights revealing the impact of deworming history on population genetic structure of importance for disease prevention.
30 Jun 2021Submitted to Molecular Ecology Resources
01 Jul 2021Reviewer(s) Assigned
15 Jul 2021Review(s) Completed, Editorial Evaluation Pending
19 Jul 2021Editorial Decision: Revise Minor
29 Jul 2021Review(s) Completed, Editorial Evaluation Pending
29 Jul 20211st Revision Received
30 Jul 2021Editorial Decision: Revise Minor
03 Aug 2021Review(s) Completed, Editorial Evaluation Pending
03 Aug 20212nd Revision Received
31 Aug 2021Editorial Decision: Accept
Feb 2022Published in Molecular Ecology Resources volume 22 issue 2 on pages 768-785. 10.1111/1755-0998.13504