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Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses

Orchardgrass (Dactylis glomerata L.) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of D. glomerata are still controversial based on current morphological and molecular evidence. The study of chloropl...

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Autores principales: Jiao, Yongjuan, Feng, Guangyan, Huang, Linkai, Nie, Gang, Li, Zhou, Peng, Yan, Li, Dandan, Xiong, Yanli, Hu, Zhangyi, Zhang, Xinquan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9498378/
https://www.ncbi.nlm.nih.gov/pubmed/36140789
http://dx.doi.org/10.3390/genes13091621
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author Jiao, Yongjuan
Feng, Guangyan
Huang, Linkai
Nie, Gang
Li, Zhou
Peng, Yan
Li, Dandan
Xiong, Yanli
Hu, Zhangyi
Zhang, Xinquan
author_facet Jiao, Yongjuan
Feng, Guangyan
Huang, Linkai
Nie, Gang
Li, Zhou
Peng, Yan
Li, Dandan
Xiong, Yanli
Hu, Zhangyi
Zhang, Xinquan
author_sort Jiao, Yongjuan
collection PubMed
description Orchardgrass (Dactylis glomerata L.) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of D. glomerata are still controversial based on current morphological and molecular evidence. The study of chloroplast (cp) genomes has developed into a powerful tool to develop molecular markers for related species and reveal the relationships between plant evolution and phylogenetics. In this study, we conducted comparative genomic analyses and phylogenetic inferences on 14 cp genomes of D. glomerata originating from the Mediterranean and Eurasia. The genome size ranged from 134,375 bp to 134,993 bp and exhibited synteny of gene organization and order. A total of 129–131 genes were identified, including 85–87 protein coding genes, 38 tRNA genes and 8 rRNA genes. The cp sequences were highly conserved, and key sequence variations were detected at the junctions of inverted repeats (IRs)/small single–copy (SSC) regions. Moreover, nine highly variable regions were identified among the subspecies based on a sequence divergence analysis. A total of 285 RNA editing sites were detected that were relevant to 52 genes, where rpoB exhibited the most abundant RNA editing sites. The phylogenetic analysis revealed that all Dactylis subspecies clustered into a monophyletic group and most branches provided a high support bootstrap. The main divergence time of D. glomerata was dated to the Miocene era, and this could have been due to changes in the climate. These findings will provide useful insights for further studies on phylogeny, the identification of subspecies and the development of hypotheses for the evolutionary history of the genus Dactylis and of the Gramineae family.
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spelling pubmed-94983782022-09-23 Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses Jiao, Yongjuan Feng, Guangyan Huang, Linkai Nie, Gang Li, Zhou Peng, Yan Li, Dandan Xiong, Yanli Hu, Zhangyi Zhang, Xinquan Genes (Basel) Article Orchardgrass (Dactylis glomerata L.) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of D. glomerata are still controversial based on current morphological and molecular evidence. The study of chloroplast (cp) genomes has developed into a powerful tool to develop molecular markers for related species and reveal the relationships between plant evolution and phylogenetics. In this study, we conducted comparative genomic analyses and phylogenetic inferences on 14 cp genomes of D. glomerata originating from the Mediterranean and Eurasia. The genome size ranged from 134,375 bp to 134,993 bp and exhibited synteny of gene organization and order. A total of 129–131 genes were identified, including 85–87 protein coding genes, 38 tRNA genes and 8 rRNA genes. The cp sequences were highly conserved, and key sequence variations were detected at the junctions of inverted repeats (IRs)/small single–copy (SSC) regions. Moreover, nine highly variable regions were identified among the subspecies based on a sequence divergence analysis. A total of 285 RNA editing sites were detected that were relevant to 52 genes, where rpoB exhibited the most abundant RNA editing sites. The phylogenetic analysis revealed that all Dactylis subspecies clustered into a monophyletic group and most branches provided a high support bootstrap. The main divergence time of D. glomerata was dated to the Miocene era, and this could have been due to changes in the climate. These findings will provide useful insights for further studies on phylogeny, the identification of subspecies and the development of hypotheses for the evolutionary history of the genus Dactylis and of the Gramineae family. MDPI 2022-09-09 /pmc/articles/PMC9498378/ /pubmed/36140789 http://dx.doi.org/10.3390/genes13091621 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jiao, Yongjuan
Feng, Guangyan
Huang, Linkai
Nie, Gang
Li, Zhou
Peng, Yan
Li, Dandan
Xiong, Yanli
Hu, Zhangyi
Zhang, Xinquan
Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses
title Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses
title_full Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses
title_fullStr Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses
title_full_unstemmed Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses
title_short Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses
title_sort complete chloroplast genomes of 14 subspecies of d. glomerata: phylogenetic and comparative genomic analyses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9498378/
https://www.ncbi.nlm.nih.gov/pubmed/36140789
http://dx.doi.org/10.3390/genes13091621
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