Abstract
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.
Highlights
Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants
Single nucleotide polymorphisms (SNPs) capture some meaningful genomic variations that contribute to phenotypic differences, SVs account for more heritable nucleotide variations than SNPs do [6, 7]
A total of 42,066 protein-coding genes were annotated based on a combination of de novo, homology-based and transcriptome-based predictions, and 97.5% of the total genes were found on chromosomes (Table 1, Table S2)
Summary
Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. They are still a largely unexplored feature in most plant genomes. 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. DNA structural variants (SVs) > 50 bp in length are a major resource of genomic variation and often have profound consequences on phenotypic variation. SVs in most plant species, including the model legume plant Medicago truncatula, remain unexplored
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