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Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly...

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Autores principales: Wang, Ying, Chen, Shengjia, Chen, Jiajun, Chen, Chaojie, Lin, Xiaojian, Peng, He, Zhao, Qian, Wang, Xingya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9840629/
https://www.ncbi.nlm.nih.gov/pubmed/36641495
http://dx.doi.org/10.1038/s41598-022-24327-x
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author Wang, Ying
Chen, Shengjia
Chen, Jiajun
Chen, Chaojie
Lin, Xiaojian
Peng, He
Zhao, Qian
Wang, Xingya
author_facet Wang, Ying
Chen, Shengjia
Chen, Jiajun
Chen, Chaojie
Lin, Xiaojian
Peng, He
Zhao, Qian
Wang, Xingya
author_sort Wang, Ying
collection PubMed
description Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly and annotation of Photinia serratifolia, which is 473,579 bp in length, contains 38 protein-coding genes, 23 tRNAs, and 6 rRNAs, with 61 genes have no introns. The rps2 and rps11 genes are missing in the P. serratifolia mitogenome. Although there are more editing sites (488) in the P. serratifolia mitogenome than in most angiosperms, fewer editing types were found in the P. serratifolia mitogenome, showing a clear bias in RNA-editing. Phylogenetic analysis based on the mitogenomes of P. serratifolia and 8 other taxa of the Rosaceae family reflected the exact evolutionary and taxonomic status of P. serratifolia. However, Ka/Ks analysis revealed that 72.69% of the protein-coding genes in the P. serratifolia mitogenome had undergone negative selections, reflecting the importance of those genes in the P. serratifolia mitogenome. Collectively, these results will provide valuable information for the evolution of P. serratifolia and provide insight into the evolutionary relationships within Photinia and the Rosaceae family.
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spelling pubmed-98406292023-01-16 Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia Wang, Ying Chen, Shengjia Chen, Jiajun Chen, Chaojie Lin, Xiaojian Peng, He Zhao, Qian Wang, Xingya Sci Rep Article Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly and annotation of Photinia serratifolia, which is 473,579 bp in length, contains 38 protein-coding genes, 23 tRNAs, and 6 rRNAs, with 61 genes have no introns. The rps2 and rps11 genes are missing in the P. serratifolia mitogenome. Although there are more editing sites (488) in the P. serratifolia mitogenome than in most angiosperms, fewer editing types were found in the P. serratifolia mitogenome, showing a clear bias in RNA-editing. Phylogenetic analysis based on the mitogenomes of P. serratifolia and 8 other taxa of the Rosaceae family reflected the exact evolutionary and taxonomic status of P. serratifolia. However, Ka/Ks analysis revealed that 72.69% of the protein-coding genes in the P. serratifolia mitogenome had undergone negative selections, reflecting the importance of those genes in the P. serratifolia mitogenome. Collectively, these results will provide valuable information for the evolution of P. serratifolia and provide insight into the evolutionary relationships within Photinia and the Rosaceae family. Nature Publishing Group UK 2023-01-14 /pmc/articles/PMC9840629/ /pubmed/36641495 http://dx.doi.org/10.1038/s41598-022-24327-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This 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/) .
spellingShingle Article
Wang, Ying
Chen, Shengjia
Chen, Jiajun
Chen, Chaojie
Lin, Xiaojian
Peng, He
Zhao, Qian
Wang, Xingya
Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia
title Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia
title_full Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia
title_fullStr Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia
title_full_unstemmed Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia
title_short Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia
title_sort characterization and phylogenetic analysis of the complete mitochondrial genome sequence of photinia serratifolia
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9840629/
https://www.ncbi.nlm.nih.gov/pubmed/36641495
http://dx.doi.org/10.1038/s41598-022-24327-x
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