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Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio
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  • Lin Chen,
  • Bijun Li,
  • Baohua Chen,
  • Chengyu Li,
  • Zhixiong Zhou,
  • Weidi Yang,
  • Tao Zhou,
  • Peng Xu
Lin Chen
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Bijun Li
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Baohua Chen
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Chengyu Li
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Zhixiong Zhou
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Weidi Yang
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Tao Zhou
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Peng Xu
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms
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Abstract

The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploidy evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technology. The assembled genome size was 1021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic dataset created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.

Peer review status:Published

01 Sep 2020Submitted to Molecular Ecology Resources
05 Nov 2020Submission Checks Completed
05 Nov 2020Assigned to Editor
08 Nov 2020Reviewer(s) Assigned
23 Dec 2020Review(s) Completed, Editorial Evaluation Pending
13 Jan 2021Editorial Decision: Revise Minor
27 Jan 2021Review(s) Completed, Editorial Evaluation Pending
27 Jan 20211st Revision Received
16 Feb 2021Editorial Decision: Accept
04 Mar 2021Published in Molecular Ecology Resources. 10.1111/1755-0998.13365