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Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications
BACKGROUND: Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value an...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245475/ https://www.ncbi.nlm.nih.gov/pubmed/37280518 http://dx.doi.org/10.1186/s12870-023-04323-7 |
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author | Zhao, Yu-Juan Liu, Jian Yin, Gen-Shen Gong, Xun |
author_facet | Zhao, Yu-Juan Liu, Jian Yin, Gen-Shen Gong, Xun |
author_sort | Zhao, Yu-Juan |
collection | PubMed |
description | BACKGROUND: Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data. RESULTS: Fourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127–128 genes, including 82–83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset. CONCLUSION: These findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04323-7. |
format | Online Article Text |
id | pubmed-10245475 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-102454752023-06-08 Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications Zhao, Yu-Juan Liu, Jian Yin, Gen-Shen Gong, Xun BMC Plant Biol Research BACKGROUND: Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data. RESULTS: Fourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127–128 genes, including 82–83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset. CONCLUSION: These findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04323-7. BioMed Central 2023-06-07 /pmc/articles/PMC10245475/ /pubmed/37280518 http://dx.doi.org/10.1186/s12870-023-04323-7 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Zhao, Yu-Juan Liu, Jian Yin, Gen-Shen Gong, Xun Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications |
title | Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications |
title_full | Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications |
title_fullStr | Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications |
title_full_unstemmed | Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications |
title_short | Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications |
title_sort | characteristics of plastid genomes in the genus ceratostigma inhabiting arid habitats in china and their phylogenomic implications |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245475/ https://www.ncbi.nlm.nih.gov/pubmed/37280518 http://dx.doi.org/10.1186/s12870-023-04323-7 |
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