Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108

BMC Plant Biology

Kunjing Qu¹  Nawal Shrestha¹  Guangpeng Ren¹  Ai Liu¹  Shuang Wu¹  Jinli Yang¹  Ao Li¹  Hongyin Hu¹  Jianquan Liu² 

[1] State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China;State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China;Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China;

关键词: Chromatin organization;    Genome assembly;    Medicago truncatula;    Jemalong A17;    R108;    Structural variants;   

DOI  :  10.1186/s12870-022-03469-0

来源: Springer

【 摘 要 】

BackgroundStructural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However, they are still a largely unexplored feature in most plant genomes. Here, we present the whole-genome landscape of SVs between two model legume Medicago truncatula ecotypes–Jemalong A17 and R108– that have been extensively used in various legume biology studies.ResultsTo catalogue SVs, we first resolved the previously published R108 genome assembly (R108 v1.0) to chromosome-scale using 124 × Hi-C data, resulting in a high-quality genome assembly. The inter-chromosomal reciprocal translocations between chromosomes 4 and 8 were confirmed by performing syntenic analysis between the two genomes. Combined with the Hi-C data, it appears that these translocation events had a significant effect on chromatin organization. Using both whole-genome and short-read alignments, we identified the genomic landscape of SVs between the two genomes, some of which may account for several phenotypic differences, including their differential responses to aluminum toxicity and iron deficiency, and the development of different anthocyanin leaf markings. We also found extensive SVs within the nodule-specific cysteine-rich gene family which encodes antimicrobial peptides essential for terminal bacteroid differentiation during nitrogen-fixing symbiosis.ConclusionsOur results provide a near-complete R108 genome assembly and the first genomic landscape of SVs obtained by comparing two M. truncatula ecotypes. This may provide valuable genomic resources for the functional and molecular research of legume biology in the future.

【 授权许可】

CC BY