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Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species
BACKGROUND: The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveil...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9125854/ https://www.ncbi.nlm.nih.gov/pubmed/35606691 http://dx.doi.org/10.1186/s12870-022-03643-4 |
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author | Huang, Yuying Li, Jing Yang, Zerui An, Wenli Xie, Chunzhu Liu, Shanshan Zheng, Xiasheng |
author_facet | Huang, Yuying Li, Jing Yang, Zerui An, Wenli Xie, Chunzhu Liu, Shanshan Zheng, Xiasheng |
author_sort | Huang, Yuying |
collection | PubMed |
description | BACKGROUND: The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species. RESULTS: The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus. CONCLUSION: The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03643-4. |
format | Online Article Text |
id | pubmed-9125854 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-91258542022-05-24 Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species Huang, Yuying Li, Jing Yang, Zerui An, Wenli Xie, Chunzhu Liu, Shanshan Zheng, Xiasheng BMC Plant Biol Research BACKGROUND: The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species. RESULTS: The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus. CONCLUSION: The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03643-4. BioMed Central 2022-05-23 /pmc/articles/PMC9125854/ /pubmed/35606691 http://dx.doi.org/10.1186/s12870-022-03643-4 Text en © The Author(s) 2022 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 Huang, Yuying Li, Jing Yang, Zerui An, Wenli Xie, Chunzhu Liu, Shanshan Zheng, Xiasheng Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species |
title | Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species |
title_full | Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species |
title_fullStr | Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species |
title_full_unstemmed | Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species |
title_short | Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species |
title_sort | comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten ficus species |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9125854/ https://www.ncbi.nlm.nih.gov/pubmed/35606691 http://dx.doi.org/10.1186/s12870-022-03643-4 |
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