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Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers
Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogeneti...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7938781/ https://www.ncbi.nlm.nih.gov/pubmed/33717697 http://dx.doi.org/10.7717/peerj.10964 |
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author | Su, Danmei Xie, Fumin Liu, Haiying Xie, Dengfeng Li, Juan He, Xingjin Guo, Xianlin Zhou, Songdong |
author_facet | Su, Danmei Xie, Fumin Liu, Haiying Xie, Dengfeng Li, Juan He, Xingjin Guo, Xianlin Zhou, Songdong |
author_sort | Su, Danmei |
collection | PubMed |
description | Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium. |
format | Online Article Text |
id | pubmed-7938781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-79387812021-03-12 Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers Su, Danmei Xie, Fumin Liu, Haiying Xie, Dengfeng Li, Juan He, Xingjin Guo, Xianlin Zhou, Songdong PeerJ Genomics Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium. PeerJ Inc. 2021-03-05 /pmc/articles/PMC7938781/ /pubmed/33717697 http://dx.doi.org/10.7717/peerj.10964 Text en ©2021 Su 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 | Genomics Su, Danmei Xie, Fumin Liu, Haiying Xie, Dengfeng Li, Juan He, Xingjin Guo, Xianlin Zhou, Songdong Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers |
title | Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers |
title_full | Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers |
title_fullStr | Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers |
title_full_unstemmed | Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers |
title_short | Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers |
title_sort | comparative analysis of complete plastid genomes from lilium lankongense franchet and its closely related species and screening of lilium-specific primers |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7938781/ https://www.ncbi.nlm.nih.gov/pubmed/33717697 http://dx.doi.org/10.7717/peerj.10964 |
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