Phylogenomics of the Glycininae subtribe, with a focus on the systematics of Calopogonium (Leguminosae, Papilionoideae, Phaseoleae)

• Grant number: 25/07644-8
• Support Opportunities: Regular Research Grants
• Start date: June 01, 2025
• End date: May 31, 2028
• Field of knowledge: Biological Sciences - Botany - Plant Taxonomy
• Principal Investigator: Ana Paula Fortuna Perez
• Grantee: Ana Paula Fortuna Perez
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Associated researchers: Annelise Frazão Nunes ; Gildean Macedo do Nascimento ; Gwilym Peter Lewis ; Juliana Santos Silva ; Mohammad Vatanparast ; Rafaela Jorge Trad ; Tânia Maria de Moura ; Vidal de Freitas Mansano

Abstract

Leguminosae Juss. is the third most diverse family among angiosperms, comprising around 800 genera and 22,000 species with a cosmopolitan distribution. It is currently divided into six subfamilies: Caesalpinoideae (including the former Mimosoideae clade), Cercidoideae, Detarioideae, Dialioideae, Duparquetioideae, and Papilionoideae. The latter is the most diverse, with over 500 genera and approximately 14,000 species, notable for its broad morphological variation-particularly in floral architecture-and its significant economic value. Key representatives include soybean (Glycine max), common beans (Phaseolus spp., Vigna spp.), and peas (Pisum sativum), all within the Phaseoleae tribe. The subtribe Glycininae, though part of a broader non-monophyletic tribe (Phaseoleae), was recovered as monophyletic in molecular studies of Lee & Hymowitz in 2001. It includes genera such as Calopogonium and Pachyrhizus, previously grouped within Diocleinae, now recognized as the tribe Diocleae. However, morphological overlap among Glycininae genera complicates taxonomic delimitation both within the subtribe and with closely related groups like Diocleae. Morphologically, Glycininae is generally characterized by trifoliolate, eglandular, glabrous leaves, non-nodose or slightly nodose inflorescences, and smooth or granular seeds with a short hilum. Nonetheless, more recent studies have revealed significant variation in both floral and vegetative traits. The subtribe comprises around 20 genera with pantropical distribution, especially across the Old World. Genetic studies also suggest genomic instability in some species, such as those in Pueraria, showing genome duplications and/or triplications, possibly from recent events. The genus Calopogonium consists of climbing or prostrate subshrubs, currently comprising eight recognized species with pantropical distribution. In Brazil, four species are recorded: C. caeruleum, C. galactioides, C. mucunoides, and C. velutinum. Across South America, one additional species is recognized (C. racemosum, from Venezuela). Among them, C. mucunoides is the most widespread, occurring throughout Brazil and in many South American countries, except Chile, Uruguay, and Paraguay. The last taxonomic revision of Calopogonium was conducted in 1982 by Carvalho-Okano, focusing on Brazilian species. Four species were recognized, with several synonymized taxa. However, many of these synonyms display distinctive morphological traits that may justify their revalidation. Due to this complexity and the lack of comprehensive phylogenetic studies, an updated revision and phylogenomic analysis are urgently needed. Calopogonium was previously considered part of Diocleinae due to shared traits like leaf symmetry and nodose floral peduncles. However, morphological and molecular evidence indicated stronger affinities with Glycininae, particularly with Pachyrhizus, supporting the reclassification proposed by Lee & Hymowitz in 2001, which made the subtribe monophyletic. A recent study by Kates et al. (2024) examining nitrogen-fixing taxa in angiosperms, including extensive Leguminosae sampling, revealed that Calopogonium is polyphyletic. For instance, C. galactioides and the North American C. lanceolatum were more closely related to Glycine and Teramnus, while C. caeruleum formed a distinct clade with Pachyrhizus and Pueraria s.l., suggesting that phylogenetic relationships within the subtribe remain unclear. Given that the last revision of Calopogonium occurred over four decades ago and that few phylogenetic studies have focused on the subtribe, this study aims to conduct a taxonomic revision of Calopogonium and a phylogenomic analysis of Glycininae. The goal is to clarify species boundaries, resolve relationships among taxa, and contribute to a more accurate understanding of the diversity and systematics of this important legume group. (AU)