Integrative systematics of the Brazilian tree “sucupira”: morphological, cytogenetic and genomic boundaries of Pterodon emarginatus Vogel and P. pubescens (Benth.) Benth. (Leguminosae, Papilionoideae)

In the genus Pterodon (Leguminosae, Papilionoideae) P. emarginatus and P. pubescens (both known as “sucupira”) exhibit unclear boundaries due to their incomplete isolation barriers and phylogenetic proximity. Both species have a conserved karyotype with 2n = 16, featuring small and morphologically similar chromosomes, and they form hybrids in sympatric areas of distribution in the Neotropical Savanna. Here, we aimed to revisit the systematics of P. emarginatus and P. pubescens based on morphometry of vegetative and reproductive characters, cytogenetics and genome skimming (low coverage Illumina sequencing). The morphometric analysis based on continuous data resulted in unclear distinctiveness between P. emarginatus and P. pubescens. However, the discrete characters of pubescence on leaves and flowers allow us to distinguish these species and individuals with intermediate morphology. The species presented similar genome sizes (1 C = ca. 0.64 pg) and stable karyotypes with two pairs of CMA+/DAPI− bands/35S rDNA and one pair of 5S rDNA sites. Similarities were also observed in the repetitive genomic fraction (∼25%) with few differences in the retrotransposons (RTs) abundances. The most representative RTs in both species were Ty1/copia-SIRE, Ty3/gypsy-Athila and Ty3/gypsy-Tekay. Remarkably, we found a difference in the 5S rDNA cluster, with the nontranscribed spacer (NTS) regions varying in length and similarity between P. emarginatus and P. pubescens. Six satellite DNAs were found, two of which were exclusive to P. emarginatus and four were shared by both species. In situ hybridization revealed that the most abundant repeats were enriched in proximal CMA+ heterochromatin in both species, except for the Ty1/copia-Ale retroelement, which was widely dispersed across all P. pubescens chromosomes. Our morphological, cytogenetic and genomic data revealed that Pterodon species boundaries are complex corroborating the evolutionary proximity between these species. We suggest that the cytogenetic and genomic stability found in Pterodon may facilitate the natural interspecific gene flow reported in sympatric populations, complicating the interpretation of morphological traits and the understanding of their systematics and evolution.