High-quality genome assembly of Metaphire vulgaris

被引：10

作者：

Jin, Feng ^{[1
]}

Zhou, Zhaoli ^{[2
]}

Guo, Qi ^{[1
]}

Liang, Zhenwen ^{[1
]}

Yang, Ruoyu ^{[1
]}

Jiang, Jibao ^{[3
]}

He, Yanlin ^{[1
]}

Zhao, Qi ^{[3
]}

Zhao, Qiang ^{[2
]}

机构：

[1] Shanghai Univ Med & Hlth Sci, Coll Rehabil Sci, Shanghai, Peoples R China

[2] Shanghai Univ Med & Hlth Sci, Shanghai Key Lab Mol Imaging, Shanghai, Peoples R China

[3] Shanghai Jiao Tong Univ, Dept Agr & Biol, Shanghai, Peoples R China

来源：

PEERJ | 2020年 / 8卷

基金：

中国国家自然科学基金;

关键词：

Genome assembly; Metaphire vulgaris; Whole genome sequencing; Hi-C; Genome duplication; Hox; Lumbrokinase; FIBRINOLYTIC ENZYME; READ ALIGNMENT; EARTHWORM; TRANSCRIPTOME; ANNOTATION;

D O I：

10.7717/peerj.10313

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：16

共 46 条

[11] OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy [J].

Emms, David M. ;

Kelly, Steven .

GENOME BIOLOGY, 2015, 16

[12] Full-length transcriptome assembly from RNA-Seq data without a reference genome [J].

Grabherr, Manfred G. ;

Haas, Brian J. ;

Yassour, Moran ;

Levin, Joshua Z. ;

Thompson, Dawn A. ;

Amit, Ido ;

Adiconis, Xian ;

Fan, Lin ;

Raychowdhury, Raktima ;

Zeng, Qiandong ;

Chen, Zehua ;

Mauceli, Evan ;

Hacohen, Nir ;

Gnirke, Andreas ;

Rhind, Nicholas ;

di Palma, Federica ;

Birren, Bruce W. ;

Nusbaum, Chad ;

Lindblad-Toh, Kerstin ;

Friedman, Nir ;

Regev, Aviv .

NATURE BIOTECHNOLOGY, 2011, 29 (07) :644-U130

[13] Genome size estimates for some oligochaete annelids [J].

Gregory, TR ;

Hebert, PDN .

CANADIAN JOURNAL OF ZOOLOGY-REVUE CANADIENNE DE ZOOLOGIE, 2002, 80 (08) :1485-1489

[14] Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis [J].

Guan, De-Long ;

Yang, Jie ;

Liu, Ying-Kui ;

Li, Yuan ;

Mi, Da ;

Ma, Li-Bin ;

Wang, Zhe-Zhi ;

Xu, Sheng-Quan ;

Qiu, Qiang .

FRONTIERS IN GENETICS, 2020, 10

[15] Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments [J].

Haas, Brian J. ;

Salzberg, Steven L. ;

Zhu, Wei ;

Pertea, Mihaela ;

Allen, Jonathan E. ;

Orvis, Joshua ;

White, Owen ;

Buell, C. Robin ;

Wortman, Jennifer R. .

GENOME BIOLOGY, 2008, 9 (01)

[16] Fibrinolytic and anticoagulative activities from the earthworm Eisenia foetida [J].

Hrzenjak, T ;

Popovic, M ;

Bozic, T ;

Grdisa, M ;

Kobrehel, D ;

Tiska-Rudman, L .

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY, 1998, 119 (04) :825-832

[17] de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer [J].

Istace, Benjamin ;

Friedrich, Anne ;

d'Agata, Leo ;

Faye, Sebastien ;

Payen, Emilie ;

Beluche, Odette ;

Caradec, Claudia ;

Davidas, Sabrina ;

Cruaud, Corinne ;

Liti, Gianni ;

Lemainque, Arnaud ;

Engelen, Stefan ;

Wincker, Patrick ;

Schacherer, Joseph ;

Aury, Jean-Marc .

GIGASCIENCE, 2017, 6 (02)

[18]

Jiang Jibao, 2018, Biodiversity Science, V26, P1074, DOI 10.17520/biods.2018105

[19] Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype [J].

Kim, Daehwan ;

Paggi, Joseph M. ;

Park, Chanhee ;

Bennett, Christopher ;

Salzberg, Steven L. .

NATURE BIOTECHNOLOGY, 2019, 37 (08) :907-+

[20] Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation [J].

Koren, Sergey ;

Walenz, Brian P. ;

Berlin, Konstantin ;

Miller, Jason R. ;

Bergman, Nicholas H. ;

Phillippy, Adam M. .

GENOME RESEARCH, 2017, 27 (05) :722-736

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