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Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum

Rhododendron × pulchrum, an important horticultural species, is widely distributed in Europe, Asia, and North America. To analyze the phylogenetic and organelle genome information of R. × pulchrum and its related species, the organelle genome of R. × pulchrum was sequenced and assembled. The complet...

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Autores principales: Shen, Jianshuang, Li, Xueqin, Li, Mingzhi, Cheng, Hefeng, Huang, Xiaoling, Jin, Songheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9532937/
https://www.ncbi.nlm.nih.gov/pubmed/36212362
http://dx.doi.org/10.3389/fpls.2022.969765
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author Shen, Jianshuang
Li, Xueqin
Li, Mingzhi
Cheng, Hefeng
Huang, Xiaoling
Jin, Songheng
author_facet Shen, Jianshuang
Li, Xueqin
Li, Mingzhi
Cheng, Hefeng
Huang, Xiaoling
Jin, Songheng
author_sort Shen, Jianshuang
collection PubMed
description Rhododendron × pulchrum, an important horticultural species, is widely distributed in Europe, Asia, and North America. To analyze the phylogenetic and organelle genome information of R. × pulchrum and its related species, the organelle genome of R. × pulchrum was sequenced and assembled. The complete mitochondrial genome showed lineage DNA molecules, which were 816,410 bp long and contained 64 genes, namely 24 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 37 protein-coding genes. The chloroplast genome of R. × pulchrum was reassembled and re-annotated; the results were different from those of previous studies. There were 42 and 46 simple sequence repeats (SSR) identified from the mitochondrial and chloroplast genomes of R. × pulchrum, respectively. Five genes (nad1, nad2, nad4, nad7, and rps3) were potentially useful molecular markers. The R. × pulchrum mitochondrial genome collinear alignment among five species of the Ericaceae showed that the mitochondrial genomes of these related species have a high degree of homology with R. × pulchrum in this gene region, and the most conservative genes were trnC-GCA, trnD-GUC, trnM-CAU, trnN-GUU, trnY-GUA, atp4, nad4, nad2, nad5, ccmC, and rrn26. The phylogenetic trees of mitochondrial genome showed that R. simsii was a sister to R. × pulchrum. The results verified that there was gene rearrangement between R. × pulchrum and R. simsii mitochondrial genomes. The codon usage bias of 10 Ericaceae mitochondrial genes and 7 Rhododendron chloroplast genes were influenced by mutation, while other genes codon usages had undergone selection. The study identified 13 homologous fragments containing gene sequences between the chloroplast and mitochondrial genomes of R. × pulchrum. Overall, our results illustrate the organelle genome information could explain the phylogenetics of plants and could be used to develop molecular markers and genetic evolution. Our study will facilitate the study of population genetics and evolution in Rhododendron and other genera in Ericaceae.
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spelling pubmed-95329372022-10-06 Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum Shen, Jianshuang Li, Xueqin Li, Mingzhi Cheng, Hefeng Huang, Xiaoling Jin, Songheng Front Plant Sci Plant Science Rhododendron × pulchrum, an important horticultural species, is widely distributed in Europe, Asia, and North America. To analyze the phylogenetic and organelle genome information of R. × pulchrum and its related species, the organelle genome of R. × pulchrum was sequenced and assembled. The complete mitochondrial genome showed lineage DNA molecules, which were 816,410 bp long and contained 64 genes, namely 24 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 37 protein-coding genes. The chloroplast genome of R. × pulchrum was reassembled and re-annotated; the results were different from those of previous studies. There were 42 and 46 simple sequence repeats (SSR) identified from the mitochondrial and chloroplast genomes of R. × pulchrum, respectively. Five genes (nad1, nad2, nad4, nad7, and rps3) were potentially useful molecular markers. The R. × pulchrum mitochondrial genome collinear alignment among five species of the Ericaceae showed that the mitochondrial genomes of these related species have a high degree of homology with R. × pulchrum in this gene region, and the most conservative genes were trnC-GCA, trnD-GUC, trnM-CAU, trnN-GUU, trnY-GUA, atp4, nad4, nad2, nad5, ccmC, and rrn26. The phylogenetic trees of mitochondrial genome showed that R. simsii was a sister to R. × pulchrum. The results verified that there was gene rearrangement between R. × pulchrum and R. simsii mitochondrial genomes. The codon usage bias of 10 Ericaceae mitochondrial genes and 7 Rhododendron chloroplast genes were influenced by mutation, while other genes codon usages had undergone selection. The study identified 13 homologous fragments containing gene sequences between the chloroplast and mitochondrial genomes of R. × pulchrum. Overall, our results illustrate the organelle genome information could explain the phylogenetics of plants and could be used to develop molecular markers and genetic evolution. Our study will facilitate the study of population genetics and evolution in Rhododendron and other genera in Ericaceae. Frontiers Media S.A. 2022-09-21 /pmc/articles/PMC9532937/ /pubmed/36212362 http://dx.doi.org/10.3389/fpls.2022.969765 Text en Copyright © 2022 Shen, Li, Li, Cheng, Huang and Jin. 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
Shen, Jianshuang
Li, Xueqin
Li, Mingzhi
Cheng, Hefeng
Huang, Xiaoling
Jin, Songheng
Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum
title Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum
title_full Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum
title_fullStr Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum
title_full_unstemmed Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum
title_short Characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of Rhododendron × pulchrum
title_sort characterization, comparative phylogenetic, and gene transfer analyses of organelle genomes of rhododendron × pulchrum
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9532937/
https://www.ncbi.nlm.nih.gov/pubmed/36212362
http://dx.doi.org/10.3389/fpls.2022.969765
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