A chromosome-scale genome assembly of mungbean (Vigna radiata)

被引：0
作者：
Khanbo, Supaporn [1 ]
Phadphon, Poompat [1 ]
Naktang, Chaiwat [1 ]
Sangsrakru, Duangjai [1 ]
Waiyamitra, Pitchaporn [1 ]
Narong, Nattapol [1 ]
Yundaeng, Chutintorn [1 ]
Tangphatsornruang, Sithichoke [1 ]
Laosatit, Kularb [2 ]
Somta, Prakit [2 ]
Pootakham, Wirulda [1 ]
机构：
[1] Natl Sci & Technol Dev Agcy NSTDA, Natl Ctr Genet Engn & Biotechnol BIOTEC, Natl Om Ctr, Pathum Thani, Thailand
[2] Kasetsart Univ, Fac Agr Kamphaeng Saen, Dept Agron, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
来源：
PEERJ | 2024年 / 12卷
关键词：
Mungbean; Vigna radiata; Chromosome-scale; Genome assembly; Hi-C; Annotation; DE-NOVO IDENTIFICATION; SEQUENCE; ALIGNMENT; DATABASE; UPDATE; FAMILIES; ACCURATE; PROVIDES; PROGRAM;
D O I：
10.7717/peerj.18771
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：
Background. Mungbean (Vigna radiata) is one of the most socio-economically important leguminous food crops of Asia and a rich source of dietary protein and micronutrients. Understanding its genetic makeup is crucial for genetic improvement and cultivar development. Methods. In this study, we combined single-tube long-fragment reads (stLFR) sequencing technology with high-throughput chromosome conformation capture (Hi-C) technique to obtain a chromosome-level assembly of V. radiata cultivar 'KUML4'. Results. The final assembly of the V. radiata genome was 468.08 Mb in size, with a scaffold N50 of 40.75 Mb. This assembly comprised 11 pseudomolecules, covering 96.94% of the estimated genome size. The genome contained 253.85 Mb (54.76%) of repetitive sequences and 27,667 protein-coding genes. Our gene prediction recovered 98.3% of the highly conserved orthologs based on Benchmarking Universal SingleCopy Orthologs (BUSCO) analysis. Comparative analyses using sequence data from single-copy orthologous genes indicated that V. radiata diverged from V. mungo approximately 4.17 million years ago. Moreover, gene family analysis revealed that major gene families associated with defense responses were significantly expanded in V. radiata. Conclusion. Our chromosome-scale genome assembly of V. radiata cultivar KUML4 will provide a valuable genomic resource, supporting genetic improvement and molecular breeding. This data will also be valuable for future comparative genomics studies among legume species.
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页数：21
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