High-quality genome assembly of Metaphire vulgaris

Feng Jin; Zhaoli Zhou; Qi Guo; Zhenwen Liang; Ruoyu Yang; Jibao Jiang; Yanlin He; Qi Zhao; Qiang Zhao

doi:10.7717/peerj.10313

High-quality genome assembly of Metaphire vulgaris

PeerJ. 2020 Nov 12:8:e10313. doi: 10.7717/peerj.10313. eCollection 2020.

Authors

Feng Jin¹, Zhaoli Zhou², Qi Guo¹, Zhenwen Liang¹, Ruoyu Yang¹, Jibao Jiang³, Yanlin He¹, Qi Zhao³, Qiang Zhao²

Affiliations

¹ College of Rehabilitation Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, China.
² Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China.
³ Department of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.

Abstract

Earthworms enrich the soil and protect the health of their ecological environment. Previous studies on these invertebrates determined their protein content, hormone secretions, medicinal value, and ecological habits, but their whole genomic sequence remains incomplete. We performed whole genome sequencing of Metaphire vulgaris (Chen, 1930), which belongs to the genus Metaphire of the family Megascolecidae. The genome assembly was 729 Mb, with a N50 contig size of 4.2 Mb. In total, 559 contigs were anchored to 41 chromosomes according to the results of Hi-C (High-throughput Chromosome Conformation Capture) technology, which was confirmed by karyological analysis. A comparison of the genomic sequences and genes indicated that there was a whole-genome duplication in M. vulgaris followed by several chromosome fusion events. Hox genes and lumbrokinase genes were identified as partial clusters surrounding the genome. Our high-quality genome assembly of M. vulgaris will provide valuable information for gene function and evolutionary studies in earthworms.

Keywords: Genome assembly; Genome duplication; Hi-C; Hox; Lumbrokinase; Metaphire vulgaris; Whole genome sequencing.

Grants and funding

This study was supported by the National Natural Science Foundation of China (Grant No. 81503640, 41771279 and 81830052); Construction project of Shanghai Key Laboratory of Molecular Imaging (18DZ2260400); Shanghai Municipal Education Commission (Class II Plateau Disciplinary Construction Program of Medical Technology of SUMHS, 2018-2020). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.