Genome assembly of a Mesoamerican derived variety of lima bean: a foundational cultivar in the Mid-Atlantic USA

Abstract

Lima bean, Phaseolus lunatus, is closely related to common bean and is high in fiber and protein, with a low glycemic index. Lima bean is widely grown in the state of Delaware, where late summer and early fall weather are conducive to pod production. The same weather conditions also promote diseases such as pod rot and downy mildew, the latter of which has caused previous epidemics. A better understanding of the genes underlying resistance to this and other pathogens is needed to keep this industry thriving in the region. Our current study sought to sequence, assemble and annotate a commercially available cultivar called Bridgeton, which could then serve as a reference genome, a basis of comparison to other Phaseolus taxa and a resource for identification of potential resistance genes. Combined efforts of sequencing, linkage and comparative analysis resulted in a 623 Mb annotated assembly for lima bean, as well as a better understanding of an evolutionarily dynamic resistance locus in legumes.

Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L.

“…To better date the amplification of the TNL from the I cluster, we took advantage of three recently sequenced Phaseolus genomes, namely P. acutifolius (Frijol Bayo, cultivated), P. acutifolius (W6 15578, wild) and P. lunatus (G27455) (Moghaddam et al 2021;Wisser et al 2021). Like in G. max and M. truncatula, the syntenic region corresponding to the I cluster was clearly identified in both species with many genes conserved in order and orientation (Supplementary data Fig.…”

Selection signatures and population dynamics of transposable elements in lima bean

“…The lima bean genome was generated by sequencing of long reads from the MI accession (G27455) cultivated in northern Colombia. A second assembly, built from short reads, is composed of 19,316 scaffolds and belongs to the MI domesticated Bridgeton cultivar 10 . For the G27455 assembly, RNA-seq data from pod, leaf, and flower tissues were also generated, which complemented the transcriptome data generated as part of an assay evaluating resistance to the fungus Trichoderma viride 11 .…”