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Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae)
Lindera, a core genus of the Lauraceae family, has important economic uses in eastern Asia and North America. However, its historical diversification has not been clarified. In this study, we report nine newly sequenced Lindera plastomes. The plastomes of these nine Lindera species range from 152,21...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995902/ https://www.ncbi.nlm.nih.gov/pubmed/29891996 http://dx.doi.org/10.1038/s41598-018-27090-0 |
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author | Zhao, Mei-Li Song, Yu Ni, Jun Yao, Xin Tan, Yun-Hong Xu, Zeng-Fu |
author_facet | Zhao, Mei-Li Song, Yu Ni, Jun Yao, Xin Tan, Yun-Hong Xu, Zeng-Fu |
author_sort | Zhao, Mei-Li |
collection | PubMed |
description | Lindera, a core genus of the Lauraceae family, has important economic uses in eastern Asia and North America. However, its historical diversification has not been clarified. In this study, we report nine newly sequenced Lindera plastomes. The plastomes of these nine Lindera species range from 152,211 (L. nacusua) to 152,968 bp (L. metcalfiana) in length, similar to that of another Lauraceae species, Litsea glutinosa (152,618 bp). The length variation of these plastomes derived from the length variation in the loci ycf1, ycf2, ψycf1, and ndhF-ψycf1. Comparing our sequences with other available plastomes in the Lauraceae indicated that eight hypervariable loci, ihbA-trnG, ndhA, ndhF-rpl32, petA-psbJ, psbK-psbI, rps16, trnS-trnG, and ycf1, could serve as DNA barcodes for species delineation, and that the inverted repeats (IRs) showed contraction/expansion. Further phylogenetic analyses were performed using 32 complete plastomes of Lauraceae and seven barcodes from 14 additional species of Lindera and related species in the core Lauraceae. The results showed that these Lindera species grouped into two or four sub-clades, and that two Litsea species and Laurus nobilis were located in the same sub-clade as five Lindera species. These data support a close relationship between the genera Laurus, Lindera, and Litsea, and suggest that Lindera is polyphyletic. |
format | Online Article Text |
id | pubmed-5995902 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-59959022018-06-21 Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) Zhao, Mei-Li Song, Yu Ni, Jun Yao, Xin Tan, Yun-Hong Xu, Zeng-Fu Sci Rep Article Lindera, a core genus of the Lauraceae family, has important economic uses in eastern Asia and North America. However, its historical diversification has not been clarified. In this study, we report nine newly sequenced Lindera plastomes. The plastomes of these nine Lindera species range from 152,211 (L. nacusua) to 152,968 bp (L. metcalfiana) in length, similar to that of another Lauraceae species, Litsea glutinosa (152,618 bp). The length variation of these plastomes derived from the length variation in the loci ycf1, ycf2, ψycf1, and ndhF-ψycf1. Comparing our sequences with other available plastomes in the Lauraceae indicated that eight hypervariable loci, ihbA-trnG, ndhA, ndhF-rpl32, petA-psbJ, psbK-psbI, rps16, trnS-trnG, and ycf1, could serve as DNA barcodes for species delineation, and that the inverted repeats (IRs) showed contraction/expansion. Further phylogenetic analyses were performed using 32 complete plastomes of Lauraceae and seven barcodes from 14 additional species of Lindera and related species in the core Lauraceae. The results showed that these Lindera species grouped into two or four sub-clades, and that two Litsea species and Laurus nobilis were located in the same sub-clade as five Lindera species. These data support a close relationship between the genera Laurus, Lindera, and Litsea, and suggest that Lindera is polyphyletic. Nature Publishing Group UK 2018-06-11 /pmc/articles/PMC5995902/ /pubmed/29891996 http://dx.doi.org/10.1038/s41598-018-27090-0 Text en © The Author(s) 2018 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Zhao, Mei-Li Song, Yu Ni, Jun Yao, Xin Tan, Yun-Hong Xu, Zeng-Fu Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) |
title | Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) |
title_full | Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) |
title_fullStr | Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) |
title_full_unstemmed | Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) |
title_short | Comparative chloroplast genomics and phylogenetics of nine Lindera species (Lauraceae) |
title_sort | comparative chloroplast genomics and phylogenetics of nine lindera species (lauraceae) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995902/ https://www.ncbi.nlm.nih.gov/pubmed/29891996 http://dx.doi.org/10.1038/s41598-018-27090-0 |
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