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Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae)
Iris is one of the largest genera in the family Iridaceae, comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588056/ https://www.ncbi.nlm.nih.gov/pubmed/33104732 http://dx.doi.org/10.1371/journal.pone.0241178 |
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author | Kang, Yang Jae Kim, Soonok Lee, Jungho Won, Hyosig Nam, Gi-Heum Kwak, Myounghai |
author_facet | Kang, Yang Jae Kim, Soonok Lee, Jungho Won, Hyosig Nam, Gi-Heum Kwak, Myounghai |
author_sort | Kang, Yang Jae |
collection | PubMed |
description | Iris is one of the largest genera in the family Iridaceae, comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris, is needed for correct species delineation. To this end, identification of diverse genetic markers from Iris genomes would facilitate molecular identification and resolve ambiguous classifications from molecular analyses; however, only two Iris plastid genomes, from Iris gatesii and Iris sanguinea, have been sequenced. Here, we used high-throughput next-generation sequencing, combined with Sanger sequencing, to construct the plastid genomes of 14 Korean-native Iris species with one outgroup and predict their gene content. Using these data, combined with previously published plastid genomes from Iris and one outgroup (Sisyrinchium angustifolium), we constructed a Bayesian phylogenetic tree showing clear speciation among the samples. We further identified sub-genomic regions that have undergone neutral evolution and accurately recapitulate Bayesian-inferred speciation. These contain key markers that could be used to identify and classify Iris samples into taxonomic clades. Our results confirm previously reported speciation patterns and resolve questionable relationships within the Iris genus. These data also provide a valuable resource for studying genetic diversity and refining phylogenetic relationships between Iris species. |
format | Online Article Text |
id | pubmed-7588056 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-75880562020-10-30 Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) Kang, Yang Jae Kim, Soonok Lee, Jungho Won, Hyosig Nam, Gi-Heum Kwak, Myounghai PLoS One Research Article Iris is one of the largest genera in the family Iridaceae, comprising hundreds of species, including numerous economically important horticultural plants used in landscape gardening and herbal medicine. Improved taxonomic classification of Iris species, particularly the endangered Korean-native Iris, is needed for correct species delineation. To this end, identification of diverse genetic markers from Iris genomes would facilitate molecular identification and resolve ambiguous classifications from molecular analyses; however, only two Iris plastid genomes, from Iris gatesii and Iris sanguinea, have been sequenced. Here, we used high-throughput next-generation sequencing, combined with Sanger sequencing, to construct the plastid genomes of 14 Korean-native Iris species with one outgroup and predict their gene content. Using these data, combined with previously published plastid genomes from Iris and one outgroup (Sisyrinchium angustifolium), we constructed a Bayesian phylogenetic tree showing clear speciation among the samples. We further identified sub-genomic regions that have undergone neutral evolution and accurately recapitulate Bayesian-inferred speciation. These contain key markers that could be used to identify and classify Iris samples into taxonomic clades. Our results confirm previously reported speciation patterns and resolve questionable relationships within the Iris genus. These data also provide a valuable resource for studying genetic diversity and refining phylogenetic relationships between Iris species. Public Library of Science 2020-10-26 /pmc/articles/PMC7588056/ /pubmed/33104732 http://dx.doi.org/10.1371/journal.pone.0241178 Text en © 2020 Kang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Kang, Yang Jae Kim, Soonok Lee, Jungho Won, Hyosig Nam, Gi-Heum Kwak, Myounghai Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) |
title | Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) |
title_full | Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) |
title_fullStr | Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) |
title_full_unstemmed | Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) |
title_short | Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae) |
title_sort | identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 korean-native iris species (iridaceae) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588056/ https://www.ncbi.nlm.nih.gov/pubmed/33104732 http://dx.doi.org/10.1371/journal.pone.0241178 |
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