The Perennial Horse Gram (Macrotyloma axillare) Genome, Phylogeny, and Selection Across the Fabaceae

Abstract

Identification of adaptive genetic variation in plants is important both for improving our understanding of adaptive evolution, as well as tackling the practical challenge of enhancing and developing crops able to tolerate changes in climate, whilst also meeting the demands of a rapidly growing human population. A potentially lucrative source of adaptive alleles could be found in underutilised crops, but their study is currently limited by a lack of genomic resources and knowledge of phylogenetic relationships. Legumes are of interest to both academic and applied endeavours due to their high economic and ecological importance. In this chapter we present a draft genome for perennial horse gram, Macrotyloma axillare (E. Meyer) Verdc., an underutilised forage legume with well documented tolerance of heat and drought. The genome of accession PI 364785 from South Africa is estimated to be 474 Mbp (1C value) and our assembly covers ca. 88% of this, with an N50 of 20.5 Kbp. After filtering out short contigs our assembly covers 74% of the genome, in ca. 50,000 contigs, with an N50 of 29.2 Kbp. In addition, for future endeavours, we assembled the chloroplast (cp) genome and identified ca. 73,000 microsatellites in the genome sequence. Utilising analyses of orthologous coding sequences and tests for positive selection across nine legume species, candidate genes were identified which could play roles in environmental adaptations and/or species diversification across the Fabaceae. Lineage-specific orthogroups, unique to the Dalbergioids, Phaseolinae, Glycininae and Vicioids were identified. In addition, evidence of positive selection was detected in 103 genes shared by all nine legumes, with serine-type protease activity found to be over-represented. Serine-type proteases have putative functions in light acclimation, lateral root development and secondary metabolite biosynthesis, which pose interesting candidates for follow up work. We also used chloroplast DNA phylogenetics to infer relationships between perennial horse gram and some other Macrotyloma species and demonstrate a sister relationship between M. axillare and M. uniflorum, another edible horse gram, but a more distant relationship between these and the geocarpic Kersting’s groundnut (M. geocarpum). The current work adds to the list of legume genomic resources to further the study of legume genetics. Candidate adaptive genes also warrant further investigation to explore the possibility of using these genes to develop hardier, more productive crops for future food and sustainable agriculture.