TY - JOUR
T1 - Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics
AU - Choi, In Su
AU - Cardoso, Domingos
AU - de Queiroz, Luciano P.
AU - de Lima, Haroldo C.
AU - Lee, Chaehee
AU - Ruhlman, Tracey A.
AU - Jansen, Robert K.
AU - Wojciechowski, Martin F.
N1 - Funding Information:
This work was supported by grants from the National Science Foundation (DEB-1853010 and DEB-1853024) to MW, RJ, and TR, the Texas Ecological Laboratory (EcoLab) to RJ, TR, and I-SC, the Sidney F. and Doris Blake Professorship in Systematic Botany to RJ, the CNPq (Research Productivity Fellowship no. 308244/2018-4; Universal no. 422325/2018-0), FAPESB (Universal no. APP0037/2016), and UFBA PROQUAD program to DC.
Publisher Copyright:
Copyright © 2022 Choi, Cardoso, de Queiroz, de Lima, Lee, Ruhlman, Jansen and Wojciechowski.
PY - 2022/2/23
Y1 - 2022/2/23
N2 - Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
AB - Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
KW - Leguminosae
KW - Meso-Papilionoideae
KW - Papilionoideae
KW - deep evolution
KW - plastid genome
UR - http://www.scopus.com/inward/record.url?scp=85126197279&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85126197279&partnerID=8YFLogxK
U2 - 10.3389/fpls.2022.823190
DO - 10.3389/fpls.2022.823190
M3 - Article
AN - SCOPUS:85126197279
SN - 1664-462X
VL - 13
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 823190
ER -