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Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae

The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relation...

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Autores principales: Zhang, Jun-Yi, Liao, Min, Cheng, Yue-Hong, Feng, Yu, Ju, Wen-Bing, Deng, Heng-Ning, Li, Xiong, Plenković-Moraj, Andelka, Xu, Bo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9257239/
https://www.ncbi.nlm.nih.gov/pubmed/35812969
http://dx.doi.org/10.3389/fpls.2022.911702
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author Zhang, Jun-Yi
Liao, Min
Cheng, Yue-Hong
Feng, Yu
Ju, Wen-Bing
Deng, Heng-Ning
Li, Xiong
Plenković-Moraj, Andelka
Xu, Bo
author_facet Zhang, Jun-Yi
Liao, Min
Cheng, Yue-Hong
Feng, Yu
Ju, Wen-Bing
Deng, Heng-Ning
Li, Xiong
Plenković-Moraj, Andelka
Xu, Bo
author_sort Zhang, Jun-Yi
collection PubMed
description The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relationships within Cypripedium remain controversial. Here, we employed two newly generated Cypripedium chloroplast genomes with five other published genomes to elucidate their genomic characteristics. The two genomes were 162,773–207,142 bp in length and contained 128–130 genes, including 82–84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, and 7,929 variable loci. The increase of repeat sequences (simple sequence repeats and large repeat sequences) causes a significant amplification in the chloroplast genome size of Cypripedium. The expansion of the IR region led to the pseudogenization or loss of genes in the SSC region. In addition, we identified 12 highly polymorphic loci (Pi > 0.09) suitable for inferring the phylogeny of Cypripedium species. Based on data sets of whole chloroplast genomes (IRa excluded) and protein-coding sequences, a well-supported phylogenetic tree was reconstructed, strongly supporting the five subfamilies of Orchidaceae and the genus Cypripedium as monophyletic taxa. Our findings also supported that C. palangshanense belonged to sect. Palangshanensia rather than sect. Retinervia. This study also enriched the genomic resources of Cypripedium, which may help to promote the conservation efforts of these endangered species.
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spelling pubmed-92572392022-07-07 Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae Zhang, Jun-Yi Liao, Min Cheng, Yue-Hong Feng, Yu Ju, Wen-Bing Deng, Heng-Ning Li, Xiong Plenković-Moraj, Andelka Xu, Bo Front Plant Sci Plant Science The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relationships within Cypripedium remain controversial. Here, we employed two newly generated Cypripedium chloroplast genomes with five other published genomes to elucidate their genomic characteristics. The two genomes were 162,773–207,142 bp in length and contained 128–130 genes, including 82–84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, and 7,929 variable loci. The increase of repeat sequences (simple sequence repeats and large repeat sequences) causes a significant amplification in the chloroplast genome size of Cypripedium. The expansion of the IR region led to the pseudogenization or loss of genes in the SSC region. In addition, we identified 12 highly polymorphic loci (Pi > 0.09) suitable for inferring the phylogeny of Cypripedium species. Based on data sets of whole chloroplast genomes (IRa excluded) and protein-coding sequences, a well-supported phylogenetic tree was reconstructed, strongly supporting the five subfamilies of Orchidaceae and the genus Cypripedium as monophyletic taxa. Our findings also supported that C. palangshanense belonged to sect. Palangshanensia rather than sect. Retinervia. This study also enriched the genomic resources of Cypripedium, which may help to promote the conservation efforts of these endangered species. Frontiers Media S.A. 2022-06-22 /pmc/articles/PMC9257239/ /pubmed/35812969 http://dx.doi.org/10.3389/fpls.2022.911702 Text en Copyright © 2022 Zhang, Liao, Cheng, Feng, Ju, Deng, Li, Plenković-Moraj and Xu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Zhang, Jun-Yi
Liao, Min
Cheng, Yue-Hong
Feng, Yu
Ju, Wen-Bing
Deng, Heng-Ning
Li, Xiong
Plenković-Moraj, Andelka
Xu, Bo
Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae
title Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae
title_full Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae
title_fullStr Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae
title_full_unstemmed Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae
title_short Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae
title_sort comparative chloroplast genomics of seven endangered cypripedium species and phylogenetic relationships of orchidaceae
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9257239/
https://www.ncbi.nlm.nih.gov/pubmed/35812969
http://dx.doi.org/10.3389/fpls.2022.911702
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