ArticleBMC plant biology2022
Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108.
Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- QTL detection and genomic prediction for resistance to anthracnose in alfalfa (Medicago sativa).The plant genome · 2025Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza.BMC plant biology · 2024Article
- Article
- CRISPR/Cas9-Mediated Generation of Mutant Lines inBiology · 2024Article
- Ion Changes and Signaling under Salt Stress in Wheat and Other Important Crops.Plants (Basel, Switzerland) · 2023Review
- A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera.Communications biology · 2023Article
- Review
- Genomic Variations Explorer (GenVarX): a toolset for annotating promoter and CNV regions using genotypic and phenotypic differences.Frontiers in genetics · 2023Article
- Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions.Scientific reports · 2022Article
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9 authors.
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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.
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