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A near-complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods

文献类型： 外文期刊

作者： Yang, Yi 1 ; Wu, Zhikun 3 ; Wu, Zengxiang 1 ; Li, Tinyao 1 ; Shen, Zhuo 1 ; Zhou, Xuan 1 ; Wu, Xinyi 4 ; Li, Guojing 4 ; Zhang, Yan 1 ;

作者机构： 1.Guangdong Acad Agr Sci, Vegetable Res Inst, Guangzhou, Peoples R China

2.Guangdong Key Lab New Technol Res Vegetables, Guangzhou, Peoples R China

3.Sun Yat Sen Univ, Zhongshan Ophthalm Ctr, State Key Lab Ophthalmol, Guangzhou, Peoples R China

4.Zhejiang Acad Agr Sci, Inst Vegetable, Hangzhou, Peoples R China

关键词： asparagus bean; reference genome; segmental and tandem duplication; anthocyanin biosynthesis

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：13.8； 五年影响因子：13.2 ）

ISSN： 1467-7644

年卷期： 2023 年

页码：

收录情况： SCI

摘要： Asparagus bean (Vigna unguiculata ssp. sesquipedialis), a subspecies of V. unguiculata, is a vital legume crop widely cultivated in Asia for its tender pods consumed as vegetables. However, the existing asparagus bean assemblies still contain numerous gaps and unanchored sequences, which presents challenges to functional genomics research. Here, we present an improved reference genome sequence of an elite asparagus bean variety, Fengchan 6, achieved through the integration of nanopore ultra-long reads, PacBio high-fidelity reads, and Hi-C technology. The improved assembly is 521.3 Mb in length and demonstrates several enhancements, including a higher N50 length (46.4 Mb), an anchor ratio of 99.8%, and the presence of only one gap. Furthermore, we successfully assembled 14 telomeres and all 11 centromeres, including four telomere-to-telomere chromosomes. Remarkably, the centromeric regions cover a total length of 38.1 Mb, providing valuable insights into the complex architecture of centromeres. Among the 30 594 predicted protein-coding genes, we identified 2356 genes that are tandemly duplicated in segmental duplication regions. These findings have implications for defence responses and may contribute to evolutionary processes. By utilizing the reference genome, we were able to effectively identify the presence of the gene VuMYB114, which regulates the accumulation of anthocyanins, thereby controlling the purple coloration of the pods. This discovery holds significant implications for understanding the underlying mechanisms of color determination and the breeding process. Overall, the highly improved reference genome serves as crucial resource and lays a solid foundation for asparagus bean genomic studies and genetic improvement efforts.

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