Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics
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 majo...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.823190/full |
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| author | In-Su Choi Domingos Cardoso Luciano P. de Queiroz Haroldo C. de Lima Chaehee Lee Tracey A. Ruhlman Robert K. Jansen Robert K. Jansen Martin F. Wojciechowski |
| author_facet | In-Su Choi Domingos Cardoso Luciano P. de Queiroz Haroldo C. de Lima Chaehee Lee Tracey A. Ruhlman Robert K. Jansen Robert K. Jansen Martin F. Wojciechowski |
| author_sort | In-Su Choi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T22:53:33Z |
| format | Article |
| id | doaj.art-ecdefdbda9894869904d430755a55e80 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T22:53:33Z |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-ecdefdbda9894869904d430755a55e802022-12-22T00:47:21ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-02-011310.3389/fpls.2022.823190823190Highly Resolved Papilionoid Legume Phylogeny Based on Plastid PhylogenomicsIn-Su Choi0Domingos Cardoso1Luciano P. de Queiroz2Haroldo C. de Lima3Chaehee Lee4Tracey A. Ruhlman5Robert K. Jansen6Robert K. Jansen7Martin F. Wojciechowski8School of Life Sciences, Arizona State University, Tempe, AZ, United StatesNational Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Salvador, BrazilDepartment of Biological Sciences, Universidade Estadual de Feira de Santana, Feira de Santana, BrazilInstituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, BrazilDepartment of Integrative Biology, University of Texas at Austin, Austin, TX, United StatesDepartment of Integrative Biology, University of Texas at Austin, Austin, TX, United StatesDepartment of Integrative Biology, University of Texas at Austin, Austin, TX, United StatesCenter of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi ArabiaSchool of Life Sciences, Arizona State University, Tempe, AZ, United StatesComprising 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.https://www.frontiersin.org/articles/10.3389/fpls.2022.823190/fulldeep evolutionMeso-Papilionoideaeplastid genomePapilionoideaeLeguminosae |
| spellingShingle | In-Su Choi Domingos Cardoso Luciano P. de Queiroz Haroldo C. de Lima Chaehee Lee Tracey A. Ruhlman Robert K. Jansen Robert K. Jansen Martin F. Wojciechowski Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics Frontiers in Plant Science deep evolution Meso-Papilionoideae plastid genome Papilionoideae Leguminosae |
| title | Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics |
| title_full | Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics |
| title_fullStr | Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics |
| title_full_unstemmed | Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics |
| title_short | Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics |
| title_sort | highly resolved papilionoid legume phylogeny based on plastid phylogenomics |
| topic | deep evolution Meso-Papilionoideae plastid genome Papilionoideae Leguminosae |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.823190/full |
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