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Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)
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  • Tongqing Zhang,
  • Jiawen Yin,
  • Shengkai Tang,
  • Daming Li,
  • Xiankun Gu,
  • Shengyu Zhang,
  • Weiguo Suo,
  • Lei Wu,
  • Xiaqing Yu,
  • Xiaowei Liu,
  • Yanshan Liu,
  • Qicheng Jiang,
  • Muzi Zhao,
  • Yue Yin,
  • Jianlin Pan
Tongqing Zhang
Freshwater Fisheries Research Institute of Jiangsu Province
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Jiawen Yin
Freshwater Fisheries Research Institute of Jiangsu Province
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Shengkai Tang
Freshwater Fisheries Research Institute of Jiangsu Province
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Daming Li
Freshwater Fisheries Research Institute of Jiangsu Province
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Xiankun Gu
Freshwater Fisheries Research Institute of Jiangsu Province
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Shengyu Zhang
Hongze Lake Fisheries Administration Committee Office of Jiangsu Province
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Weiguo Suo
Fisheries Management Commission of Gehu Lake
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Lei Wu
Biomarker Technologies Corporation
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Xiaqing Yu
Nanjing Agricultural University
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Xiaowei Liu
Freshwater Fisheries Research Institute of Jiangsu Province
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Yanshan Liu
Freshwater Fisheries Research Institute of Jiangsu Province
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Qicheng Jiang
Freshwater Fisheries Research Institute of Jiangsu Province
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Muzi Zhao
Freshwater Fisheries Research Institute of Jiangsu Province
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Yue Yin
Freshwater Fisheries Research Institute of Jiangsu Province
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Jianlin Pan
Freshwater Fisheries Research Institute of Jiangsu Province
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Abstract

The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve that is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is high in protein, amino acids, and microelements. In China, C. fluminea plays an important role in the diversity of freshwater ecosystems. The genome of C. fluminea has not yet been characterized, therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4,728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The expanded genes were significantly enriched in 9 terms associated with metabolite synthesis. The phylogenetic tree showed that C. fluminea diverged from the ancestors of marine bivalves ~492.00 million years ago (Mya). Additionally, we identified two MITF genes in C. fluminea and several core genes involved in vitamin B6 metabolic pathways. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

Peer review status:UNDER REVIEW

22 Sep 2020Submitted to Molecular Ecology Resources
14 Oct 2020Assigned to Editor
14 Oct 2020Submission Checks Completed
22 Oct 2020Reviewer(s) Assigned
04 Dec 2020Review(s) Completed, Editorial Evaluation Pending