Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes.

Phylogeny DNA Barcoding, Taxonomic Orchidaceae / genetics Genome, Plastid Nucleotides Genome, Chloroplast
Aeridinae Chloroplast genome DNA barcoding Phylogenetic analysis Small inversions

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
06 Dec 2023
Historique:
received: 06 01 2023
accepted: 27 11 2023
medline: 11 12 2023
pubmed: 7 12 2023
entrez: 6 12 2023
Statut: epublish

Résumé

Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation. We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnN This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.

Sections du résumé

BACKGROUND BACKGROUND
Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation.
RESULTS RESULTS
We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnN
CONCLUSION CONCLUSIONS
This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.

Identifiants

DOI: 10.1186/s12864-023-09847-8 PMID: 38057701 PMC: PMC10702055
pubmed: 38057701
doi: 10.1186/s12864-023-09847-8
pii: 10.1186/s12864-023-09847-8
pmc: PMC10702055
doi:

Substances chimiques

Nucleotides 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

749

Subventions

Organisme : Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University
ID : 72202200205
Organisme : National Key Research and Development Program of China
ID : 2019YFD1000400

Informations de copyright

© 2023. The Author(s).

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Auteurs

Ding-Kun Liu (DK)

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

Cheng-Yuan Zhou (CY)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Xiong-De Tu (XD)

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

Zhuang Zhao (Z)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Jin-Liao Chen (JL)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Xu-Yong Gao (XY)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Shao-Wei Xu (SW)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Meng-Yao Zeng (MY)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Liang Ma (L)

Fujian Health College, Fuzhou, 350101, Fujian, China.

Sagheer Ahmad (S)

Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Ming-He Li (MH)

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

Siren Lan (S)

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

Zhong-Jian Liu (ZJ)

College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjliu@fafu.edu.cn.
Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjliu@fafu.edu.cn.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Phylogenèse › Comparative and phylogenetic analysis of...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Codage à barres de l'ADN pour la taxonomie › Comparative and phylogenetic analysis of...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Lilianae › Asparagales › Orchidaceae › Comparative and phylogenetic analysis of...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome plastidique › Comparative and phylogenetic analysis of...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Nucléotides › Comparative and phylogenetic analysis of...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome plastidique › Génome de chloroplaste › Comparative and phylogenetic analysis of...