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Chromosome-level genome assembly of the Chinese Longsnout catfish Leiocassis longirostris
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  • Wenping He,
  • Jian Zhou,
  • Zhe Li,
  • Tingseng Jing,
  • Chunhua Li,
  • Yuejing Yang,
  • Mengbin Xiang,
  • Chaowei Zhou,
  • Guangjun Lv,
  • Hongyan Xu,
  • Hui Luo,
  • Hua Ye
Wenping He
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)
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Jian Zhou
Fisheries Institute of Sichuan Academy of Agricultural Science
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Zhe Li
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Tingseng Jing
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Chunhua Li
BGI-Qingdao, BGI-Shenzhen
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Yuejing Yang
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Mengbin Xiang
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Chaowei Zhou
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Guangjun Lv
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Hongyan Xu
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University
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Hui Luo
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)
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Hua Ye
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)
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Abstract

The Chinese Longsnout catfish Leiocassis longirostris (L. longirostris) is one of the most economically important freshwater catfish in China. It is a valuable model for studies on sexual dimorphism, comparative and conservation biology since its wild resources have declined sharply. However, there is lack of high-quality chromosome-level genome information for comparative genomic analysis and genome evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris using a combined strategy of BGI-SEQ500, Nanopore, and Hi-C technologies. The assembled genome of L. longirostris contained a total length of 703.19 Mb with 389 contigs, and an N50 size of 4.29 Mb. Using the Hi-C data, we finally successfully generated 82 chromosome-level scaffolds anchored onto 26 chromosomes with a total length of 685.53 Mb (97.44% of the total genome sequences), ranging in size from 17.36 Mb to 43.97 Mb. A total of 23,708 protein-coding genes were identified in the L. longirostris genome, and up to 97.73% of L. longirostris genes were functionally annotated. In addition, the genome contained 239.11 Mb (33.99% in the total genome) repetitive sequences and 6,303 non-coding RNAs. The phylogenetic analysis indicated that the divergence time between L. longirostris and their closest relative species Pelteobagrus fulvidraco was approximately 26.6 million years. Collinearity analyses showed 26 chromosomes of L. longirostris displayed high homology with the corresponding scaffold (≥3M) of P. fulvidraco and the corresponding chromosomes of the Ictalurus punctatus. The high-quality reference genome of L. longirostris was assembled for the first time and will pave a way for genome-scale selective breeding, genome comparisons and evolution investigations.

Peer review status:POSTED

15 Oct 2020Submitted to Molecular Ecology Resources
03 Nov 2020Assigned to Editor
03 Nov 2020Submission Checks Completed