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A new myco-heterotrophic genus, Yunorchis, and the molecular phylogenetic relationships of the tribe Calypsoeae (Epidendroideae, Orchidaceae) inferred from plastid and nuclear DNA sequences.

ABSTRACT: We identified a new holomycotrophic orchid that is related to the myco-heterotrophic Calypsoeae. Because chloroplast genes are primarily lacking or are highly divergent, key morphological characters are either reduced or lost from many myco-heterotrophs, and the phylogenetic relationships of weakly supported paraphyletic Calypsoeae within Epidendroideae have been poorly understood in previous molecular systematic studies. Using chloroplast rbcL, psaB, and matK and nuclear Xdh and ITS sequences, we determined the circumscription and systematic positions of the new orchid and the tribe. The results indicate that the epidendroid taxa include most of the clades that are successively sister to the grade of clades representing previously recognized tribes. Calypsoeae comprising four well-supported clades with 12 genera (except for the previous temporarily placed Wullschlaegelia) is supported as a monophyletic and sister clade to Epidendreae (excluding Coeliinae). The new orchid is nested in Calypsoeae and is a sister to Dactylostalix and/or Calypso. This new holomycotrophic orchid presents a subumbel inflorescence that grows underground, and flower with a long pedicel reputing the ground to open and two fragments at the base of the hook, which are obviously morphologically different from those of Calypsoeae. To accommodate this species in the current generic circumscription, a new genus Yunorchis was created.

SUBMITTER: Zhang GQ

PROVIDER: S-EPMC4406536 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Project description:Background and aimsPhylogenetic relationships of subtribes Cranichidinae and Prescottiinae, two diverse groups of neotropical terrestrial orchids, are not satisfactorily understood. A previous molecular phylogenetic study supported monophyly for Cranichidinae, but Prescottiinae consisted of two clades not sister to one another. However, that analysis included only 11 species and eight genera of these subtribes. Here, plastid and nuclear DNA sequences are analysed for an enlarged sample of genera and species of Cranichidinae and Prescottiinae with the aim of clarifying their relationships, evaluating the phylogenetic position of the monospecific genera Exalaria, Ocampoa and Pseudocranichis and examining the value of various structural traits as taxonomic markers.MethodsApprox. 6000 bp of nucleotide sequences from nuclear ribosomal (ITS) and plastid DNA (rbcL, matK-trnK and trnL-trnF) were analysed with cladistic parsimony and Bayesian inference for 45 species/14 genera of Cranichidinae and Prescottiinae (plus suitable outgroups). The utility of flower orientation, thickenings of velamen cell walls, hamular viscidium and pseudolabellum to mark clades recovered by the molecular analysis was assessed by tracing these characters on the molecular trees.Key resultsSpiranthinae, Cranichidinae, paraphyletic Prescottia (with Pseudocranichis embedded), and a group of mainly Andean 'prescottioid' genera (the 'Stenoptera clade') were strongly supported. Relationships among these clades were unresolved by parsimony but the Bayesian tree provided moderately strong support for the resolution (Spiranthinae-(Stenoptera clade-(Prescottia/Pseudocranichis-Cranichidinae))). Three of the four structural characters mark clades on the molecular trees, but the possession of a pseudolabellum is variable in the polyphyletic Ponthieva.ConclusionsNo evidence was found for monophyly of Prescottiinae and the reinstatement of Cranichidinae s.l. (including the genera of 'Prescottiinae') is favoured. Cranichidinae s.l. are diagnosed by non-resupinate flowers. Lack of support from parsimony for relationships among the major clades of core spiranthids is suggestive of a rapid morphological radiation or a slow rate of molecular evolution.

Project description:Background and aimsThe largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification.MethodsSequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed.Key resultsLikelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement.ConclusionsAll tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel.

Project description:BackgroundThe orchid genus Pholidota Lindl. ex Hook. is economically important as some species has long been used in traditional medicine. However, the systematic status of the genus and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling and lack of informative sites. So far, only limited genomic information has been available. The taxonomy of Pholidota remains unresolved and somewhat controversial. In this study, the complete chloroplast (cp.) genomes of thirteen Pholidota species were sequenced and analyzed to gain insight into the phylogeny of Pholidota and mutation patterns in their cp. genomes.ResultsAll examined thirteen Pholidota cp. genomes exhibited typical quadripartite circular structures, with the size ranging from 158,786 to 159,781 bp. The annotation contained a total of 135 genes in each cp. genome, i.e., 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The codon usage analysis indicated the preference of A/U-ending codons. Repeat sequence analysis identified 444 tandem repeats, 322 palindromic repeats and 189 dispersed repeats. A total of 525 SSRs, 13,834 SNPs and 8,630 InDels were detected. Six mutational hotspots were identified as potential molecular markers. These molecular markers and highly variable regions are expected to facilitate future genetic and genomic studies. Our phylogenetic analyses confirmed the polyphyletic status of the genus Pholidota, with species grouped into four main clades: Pholidota s.s. was resolved as the sister to a clade containing species of Coelogyne; the other two clades clustered together with species of Bulleyia and Panisea, respectively; species P. ventricosa was placed at the basal position, deviated from all other species.ConclusionThis is the first study to comprehensively examine the genetic variations and systematically analyze the phylogeny and evolution of Pholidota based on plastid genomic data. These findings contribute to a better understanding of plastid genome evolution of Pholidota and provide new insights into the phylogeny of Pholidota and its closely related genera within the subtribe Coelogyninae. Our research has laid the foundation for future studies on the evolutionary mechanisms and classification of this economically and medicinally important genus.

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A new myco-heterotrophic genus, Yunorchis, and the molecular phylogenetic relationships of the tribe Calypsoeae (Epidendroideae, Orchidaceae) inferred from plastid and nuclear DNA sequences.

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