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Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae
Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect....
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786250/ https://www.ncbi.nlm.nih.gov/pubmed/31608166 http://dx.doi.org/10.7717/peerj.7662 |
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author | Tian, Xiangyu Ye, Junwei Song, Yu |
author_facet | Tian, Xiangyu Ye, Junwei Song, Yu |
author_sort | Tian, Xiangyu |
collection | PubMed |
description | Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate. |
format | Online Article Text |
id | pubmed-6786250 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-67862502019-10-11 Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae Tian, Xiangyu Ye, Junwei Song, Yu PeerJ Bioinformatics Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate. PeerJ Inc. 2019-10-07 /pmc/articles/PMC6786250/ /pubmed/31608166 http://dx.doi.org/10.7717/peerj.7662 Text en © 2019 Tian et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Tian, Xiangyu Ye, Junwei Song, Yu Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae |
title | Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae |
title_full | Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae |
title_fullStr | Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae |
title_full_unstemmed | Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae |
title_short | Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae |
title_sort | plastome sequences help to improve the systematic position of trinerved lindera species in the family lauraceae |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786250/ https://www.ncbi.nlm.nih.gov/pubmed/31608166 http://dx.doi.org/10.7717/peerj.7662 |
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