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

In the genus <i>Pterodon</i> (Leguminosae, Papilionoideae) <i>P. emarginatus</i> and <i>P. pubescens</i> (both known as “sucupira”) exhibit unclear boundaries due to their incomplete isolation barriers and phylogenetic proximity. Both species have a conserved karyotype with 2<i>n</i> = 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 <i>P. emarginatus</i> and <i>P. pubescens</i> 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 <i>P. emarginatus</i> and <i>P. pubescens</i>. 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 <i>P. emarginatus</i> and <i>P. pubescens</i>. Six satellite DNAs were found, two of which were exclusive to <i>P. emarginatus</i> and four were shared by both species. <i>In situ</i> 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 <i>P. pubescens</i> chromosomes. Our morphological, cytogenetic and genomic data revealed that <i>Pterodon</i> species boundaries are complex corroborating the evolutionary proximity between these species. We suggest that the cytogenetic and genomic stability found in <i>Pterodon</i> 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.