A settled sub-family for the orphan tree: The phylogenetic position of the endemic Colombian genus Orphanodendron in the Leguminosae

Castellanos, Clara Inés Vargas; Steeves, Royce; Lewis, Gwilym P.; Bruneau, Anne

doi:10.1007/s12228-016-9451-3

Cited by 6 publications

(3 citation statements)

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“…In addition to providing a model for plastome structural rearrangements, Papilionoideae, the largest legume subfamily with an estimated 501 genera and 14,000 species ( LPWG, 2021 ), also exhibits an impressive morphological diversity ( Lewis et al, 2005 ; LPWG et al, 2017 ). For example, the early diversification of the Papilionoideae is marked by multiple evolutionary shifts in floral architecture ( Ireland et al, 2000 ; Pennington et al, 2001 ; Cardoso et al, 2012a , 2013a , 2013b ; Klitgård et al, 2013 ; Ramos et al, 2016 ; Castellanos et al, 2017 ). Genera that were traditionally classified in the “primitive” tribes Sophoreae and Swartzieae (e.g., Cowan, 1981 ; Polhill, 1981a ) are now phylogenetically scattered among the early-branching lineages of Papilionoideae.…”

Section: Introductionmentioning

confidence: 99%

“…Previous phylogenetic studies using the coding sequences of the plastid rbcL (e.g., Doyle et al, 1997 ; Kajita et al, 2001 ) and matK genes (e.g., Wojciechowski et al, 2004 ; Cardoso et al, 2012a , 2013a , 2015 ; Ramos et al, 2016 ; Castellanos et al, 2017 ; LPWG et al, 2017 ; Queiroz et al, 2017 ), as well as a supermatrix approach ( McMahon and Sanderson, 2006 ), sampled densely across the Papilionoideae, revealed many new clades, unexpected generic re-alignments, and placed several taxonomically orphan genera. However, these studies left the Papilionoideae backbone phylogeny and the placement of several evolutionary key genera largely unresolved.…”

Section: Introductionmentioning

confidence: 99%

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Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

et al. 2022

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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.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

et al. 2022

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“…matK protein proposed to be the only maturase encoded by group II intron of chloroplast genome, and the intron splicing of some chloroplast genes can only be performed by chloroplast maturases, which makes matK an important gene for chloroplast to play its normal function [18]. matK is a fast evolving gene at levels of nucleotides and amino acids, this unique feature makes it widely used in the phylogenetic analysis of land plants [19][20]. However, rapid evolution of chloroplast matK gene will lead to production of pseudogenes as a result of gene inactivation, and the matK gene is often considered a pseudogene due to occasional occurrence of frameshift indels, high frequency of transition/transversion or substitution ratios in some orchid taxa [21][22].…”

Section: Discussionmentioning

confidence: 99%

The MatK Gene of Spiranthes Sinensis Encodes a Maturase Involved in Multiple Biological Processes

Fan¹

2019

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The maturase K gene (matK) encodes the only hypothetical group II intron maturase in the chloroplast genome. To investigate the molecular characteristics and functions of matK gene in Spiranthes sinensis (SsmatK), the Ssmatk protein was systematically analyzed by bioinformatics. The results showed that SsmatK gene encodes an unstable hydrophilic protein located in chloroplast. Sequence alignment showed that SsmatK protein contained a domain X region, which was a specific region of group II intron encoding maturase. Phylogenetic tree analysis showed that SsmatK protein is most closely related to the matK proteins of Schiedeella garayana and Schiedeella romeroana. Post-translational modification analysis revealed that SsmatK protein had 55 phosphorylation sites and 3 glycosylation sites. The result of tertiary structure showed that two potential phosphorylation sites Ser446 and Thr450 in the essential SCARTLARKHK sequence may be two important synergistic sites for SsmatK protein function. Molecular functional analysis of the gene ontology showed that SsmatK protein was defined as binding activity, including specific binding to other proteins, organic cyclic compounds, nucleic acids, heterocyclic compounds and RNA molecules. Biological processes analysis of gene ontology further revealed that SsmatK was mainly involved in metabolic processes, gene expression and RNA processing. The above results suggest that the SsmatK gene located within the chloroplast group II intron encodes a highly conserved maturase and participates in a variety of biological processes. Therefore, strengthening the identification of potential coding genes in chloroplast genome will help to enrich our understanding of the complexity of transcriptional genes.

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