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Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships
Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862764/ https://www.ncbi.nlm.nih.gov/pubmed/35211136 http://dx.doi.org/10.3389/fpls.2021.814833 |
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author | Odago, Wyclif Ochieng Waswa, Emmanuel Nyongesa Nanjala, Consolata Mutinda, Elizabeth Syowai Wanga, Vincent Okelo Mkala, Elijah Mbandi Oulo, Millicent Akinyi Wang, Yan Zhang, Cai-Fei Hu, Guang-Wan Wang, Qing-Feng |
author_facet | Odago, Wyclif Ochieng Waswa, Emmanuel Nyongesa Nanjala, Consolata Mutinda, Elizabeth Syowai Wanga, Vincent Okelo Mkala, Elijah Mbandi Oulo, Millicent Akinyi Wang, Yan Zhang, Cai-Fei Hu, Guang-Wan Wang, Qing-Feng |
author_sort | Odago, Wyclif Ochieng |
collection | PubMed |
description | Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships. |
format | Online Article Text |
id | pubmed-8862764 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-88627642022-02-23 Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships Odago, Wyclif Ochieng Waswa, Emmanuel Nyongesa Nanjala, Consolata Mutinda, Elizabeth Syowai Wanga, Vincent Okelo Mkala, Elijah Mbandi Oulo, Millicent Akinyi Wang, Yan Zhang, Cai-Fei Hu, Guang-Wan Wang, Qing-Feng Front Plant Sci Plant Science Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships. Frontiers Media S.A. 2022-02-08 /pmc/articles/PMC8862764/ /pubmed/35211136 http://dx.doi.org/10.3389/fpls.2021.814833 Text en Copyright © 2022 Odago, Waswa, Nanjala, Mutinda, Wanga, Mkala, Oulo, Wang, Zhang, Hu and Wang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Odago, Wyclif Ochieng Waswa, Emmanuel Nyongesa Nanjala, Consolata Mutinda, Elizabeth Syowai Wanga, Vincent Okelo Mkala, Elijah Mbandi Oulo, Millicent Akinyi Wang, Yan Zhang, Cai-Fei Hu, Guang-Wan Wang, Qing-Feng Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships |
title | Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships |
title_full | Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships |
title_fullStr | Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships |
title_full_unstemmed | Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships |
title_short | Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships |
title_sort | analysis of the complete plastomes of 31 species of hoya group: insights into their comparative genomics and phylogenetic relationships |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862764/ https://www.ncbi.nlm.nih.gov/pubmed/35211136 http://dx.doi.org/10.3389/fpls.2021.814833 |
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