Cytogenomic and phylogenomic evidence for new infrageneric relationships in Macroptilium (Benth.) beans

Macroptilium (Benth.) Urb. is native to regions from North to South America. Phylogenetic analyses place it close to Phaseolus L. beans; however, its infrageneric division into two sections is not well supported. Despite its stability in chromosomal number (2n = 22), interspecific ribosomal DNA loci variation enabled species differentiation, suggesting that a cytogenomic approach might be valuable for inferring species relationships and genome evolution.

Here, we: (1) characterized nine Macroptilium species through oligonucleotide-based chromosome painting and barcoding (Oligo-FISH); (2) generated genome skimming data for six species and used them to investigate their repeatome dynamics; and (3) performed phylogenomic reconstruction using complete plastomes.

Oligo-FISH data unveiled de novo translocations between chromosomes 2 and 6, and 3 and 11 in species from proposed groups II and III, respectively, in disagreement with the currently proposed phylogenetic hypothesis. Our phylogenomic (plastid) and repeatome (nuclear) analyses supported groups II and III as clades, with clade-specific satellite DNA families. Group I was paraphyletic and resembled the ancestral Phaseolinae karyotype.

We demonstrated the efficiency of different cytogenomic approaches to characterize Macroptilium species, providing insights into its genomic evolution and indicating the need for a systematic re-evaluation of the genus. These findings also support the power of these approaches to solve phylogenetic relationships even in groups with chromosome number stability and recent diversification.