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Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

BACKGROUND: Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most sp...

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Autores principales: Dong, Wenpan, Liu, Yanlei, Xu, Chao, Gao, Yongwei, Yuan, Qingjun, Suo, Zhili, Zhang, Zhixiang, Sun, Jiahui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060999/
https://www.ncbi.nlm.nih.gov/pubmed/33888057
http://dx.doi.org/10.1186/s12864-021-07590-6
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author Dong, Wenpan
Liu, Yanlei
Xu, Chao
Gao, Yongwei
Yuan, Qingjun
Suo, Zhili
Zhang, Zhixiang
Sun, Jiahui
author_facet Dong, Wenpan
Liu, Yanlei
Xu, Chao
Gao, Yongwei
Yuan, Qingjun
Suo, Zhili
Zhang, Zhixiang
Sun, Jiahui
author_sort Dong, Wenpan
collection PubMed
description BACKGROUND: Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. RESULTS: The Distylium chloroplast genome size was 159,041–159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. CONCLUSIONS: The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07590-6.
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spelling pubmed-80609992021-04-22 Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae) Dong, Wenpan Liu, Yanlei Xu, Chao Gao, Yongwei Yuan, Qingjun Suo, Zhili Zhang, Zhixiang Sun, Jiahui BMC Genomics Research Article BACKGROUND: Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. RESULTS: The Distylium chloroplast genome size was 159,041–159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. CONCLUSIONS: The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07590-6. BioMed Central 2021-04-22 /pmc/articles/PMC8060999/ /pubmed/33888057 http://dx.doi.org/10.1186/s12864-021-07590-6 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 Article
Dong, Wenpan
Liu, Yanlei
Xu, Chao
Gao, Yongwei
Yuan, Qingjun
Suo, Zhili
Zhang, Zhixiang
Sun, Jiahui
Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)
title Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)
title_full Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)
title_fullStr Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)
title_full_unstemmed Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)
title_short Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)
title_sort chloroplast phylogenomic insights into the evolution of distylium (hamamelidaceae)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060999/
https://www.ncbi.nlm.nih.gov/pubmed/33888057
http://dx.doi.org/10.1186/s12864-021-07590-6
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