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High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (Collembola)
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  • Yun-Xia Luan,
  • Yingying Cui,
  • Wan-Jun Chen,
  • Jianfeng Jin,
  • Ai-Min Liu,
  • Cheng-Wang Huang,
  • Mikhail Potapov,
  • Yun Bu,
  • Shuai Zhan,
  • Feng Zhang,
  • Sheng Li
Yun-Xia Luan
South China Normal University

Corresponding Author:[email protected]

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Yingying Cui
South China Normal University
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Wan-Jun Chen
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Jianfeng Jin
Nanjing Agricultural University
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Ai-Min Liu
South China Agricultural University
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Cheng-Wang Huang
Chinese Academy of Sciences
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Mikhail Potapov
Moscow State Pedagogical University
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Yun Bu
Shanghai Natural History Museum
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Shuai Zhan
Chinese Academy of Sciences
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Feng Zhang
Nanjing Agricultural University
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Sheng Li
South China Normal University
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The collembolan Folsomia candida Willem, 1902, is an important representative soil arthropod that is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal “standard” because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we present two high-quality chromosome-level genomes of F. candida, for the parthenogenetic Danish strain (FCDK, 219.08 Mb, N50 of 38.47 Mb, 25,139 protein-coding genes) and the sexual Shanghai strain (FCSH, 153.09 Mb, N50 of 25.75 Mb, 21,609 protein-coding genes). The seven chromosomes of FCDK are each 25–54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to its broader environmental adaptation. In addition, the overall sequence identity of the two mitogenomes is only 78.2%, and FCDK has fewer strain-specific microRNAs than FCSH. In conclusion, FCDK and FCSH have accumulated independent genetic changes and evolved into distinct species since diverging 10 Mya. Our work shows that F. candida represents a good model of rapidly cryptic speciation. Moreover, it provides important genomic resources for studying the mechanisms of species differentiation, soil arthropod adaptation to soil ecosystems, and Wolbachia-induced parthenogenesis as well as the evolution of Collembola, a pivotal phylogenetic clade between Crustacea and Insecta.
30 Nov 2021Submitted to Molecular Ecology Resources
17 Dec 2021Submission Checks Completed
17 Dec 2021Assigned to Editor
22 Dec 2021Reviewer(s) Assigned
10 Mar 2022Review(s) Completed, Editorial Evaluation Pending
31 Mar 2022Editorial Decision: Revise Minor
29 Apr 2022Review(s) Completed, Editorial Evaluation Pending
29 Apr 20221st Revision Received
04 May 2022Reviewer(s) Assigned
14 Jul 2022Editorial Decision: Revise Minor
08 Aug 2022Review(s) Completed, Editorial Evaluation Pending
08 Aug 20222nd Revision Received
09 Aug 2022Editorial Decision: Accept
05 Sep 2022Published in Molecular Ecology Resources. 10.1111/1755-0998.13699