Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma-Gastrochilus clades (Orchidaceae, Aeridinae).

Evolution, Molecular Likelihood Functions Open Reading Frames / genetics Orchidaceae / anatomy & histology Phylogeny Plant Leaves / genetics Plastids / genetics RNA, Ribosomal / chemistry RNA, Transfer / chemistry
Gene loss IR/SSC boundary Inversion Phylogenetic analysis Pseudogene

Journal

Molecular phylogenetics and evolution
ISSN: 1095-9513
Titre abrégé: Mol Phylogenet Evol
Pays: United States
ID NLM: 9304400

Informations de publication

Date de publication:
04 2020
Historique:
received: 05 07 2019
revised: 31 12 2019
accepted: 31 12 2019
pubmed: 12 1 2020
medline: 1 7 2020
entrez: 12 1 2020
Statut: ppublish

Résumé

The Cleisostoma-Gastrochilus clades are among the most speciose and diverse groups of Asian orchids and are a taxonomically problematic group. Phylogenetic relationships among the genera of these clades have remained unresolved with traditional sequences from one or a few markers. We present large-scale phylogenomic data sets, incorporating complete chloroplast genome sequences from 53 species (including 41 species sequenced in this study), to compare plastome structure and to resolve the phylogenetic relationships of these clades. The plastomes of Cleisostoma-Gastrochilus clades possessed the quadripartite structure and plastome genes of typical angiosperms with sizes ranging from 142 to 149 kb and encoding a set of 118-120 genes. Unusual structural features were detected in the plastome of Uncifera acuminata, including the presence of a large 17-kb inversion (19 genes) in the Large Single-Copy region and the loss of the rpl32 gene in Cleisostoma fuerstenbergianum. The pseudogenization of ndh genes was widespread in these clades. Phylogenomic analyses, including 68 plastid protein-coding genes, showed that these clades can be subdivided into three major groupings and six subgroupings: Vandopsis undulata, the Gastrochilus clade (including the Trichoglottis and Gastrochilus subclades) and the Cleisostoma clade (including the Vandopsis, Diploprora, Cleisostoma and Schoenorchis subclades). Two genera, Vandopsis and Cleisostoma, were not monophyletic. A new genus, Cymbilabia, was proposed to avoid non-monophyly of Vandopsis. Our results demonstrate the power of plastid phylogenomics to improve the phylogenetic relationships of intricate groups and provide new insight into plastome evolution in Orchidaceae.

Identifiants

DOI: 10.1016/j.ympev.2019.106729 PMID: 31926307
pubmed: 31926307
pii: S1055-7903(19)30398-7
doi: 10.1016/j.ympev.2019.106729
pii:
doi:

Substances chimiques

RNA, Ribosomal 0
RNA, Transfer 9014-25-9

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

106729

Informations de copyright

Copyright © 2020 Elsevier Inc. All rights reserved.

Auteurs

Ding-Kun Liu (DK)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Xiong-De Tu (XD)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Zhuang Zhao (Z)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Meng-Yao Zeng (MY)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Sai Zhang (S)

Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Liang Ma (L)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Guo-Qiang Zhang (GQ)

Shenzhen Key Laboratory for Orchid Conservation and Utilization, The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China.

Miao-Miao Wang (MM)

Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing 100093, China.

Zhong-Jian Liu (ZJ)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Si-Ren Lan (SR)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Ming-He Li (MH)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: fjalmh@126.com.

Shi-Pin Chen (SP)

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: fjcsp@126.com.

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Classifications MeSH

questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Probabilité › Fonctions de vraisemblance › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Cadres ouverts de lecture › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Lilianae › Asparagales › Orchidaceae › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Structures de plante › Parties aériennes de plante › Feuilles de plante › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Cellules › Structures cellulaires › Espace intracellulaire › Cytoplasme › Structures cytoplasmiques › Organites › Plastes › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › Plastid phylogenomic data yield new and robust...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN de transfert › Plastid phylogenomic data yield new and robust...