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Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constit...

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Autores principales: Ren, Weichao, Liu, Chi, Yan, Song, Jiang, Zhehui, Wang, Tianhao, Wang, Zhen, Zhang, Meiqi, Liu, Meiqi, Sun, Jiaying, Gao, Jinhui, Ma, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9329572/
https://www.ncbi.nlm.nih.gov/pubmed/35910210
http://dx.doi.org/10.3389/fgene.2022.849182
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author Ren, Weichao
Liu, Chi
Yan, Song
Jiang, Zhehui
Wang, Tianhao
Wang, Zhen
Zhang, Meiqi
Liu, Meiqi
Sun, Jiaying
Gao, Jinhui
Ma, Wei
author_facet Ren, Weichao
Liu, Chi
Yan, Song
Jiang, Zhehui
Wang, Tianhao
Wang, Zhen
Zhang, Meiqi
Liu, Meiqi
Sun, Jiaying
Gao, Jinhui
Ma, Wei
author_sort Ren, Weichao
collection PubMed
description Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.
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spelling pubmed-93295722022-07-29 Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus Ren, Weichao Liu, Chi Yan, Song Jiang, Zhehui Wang, Tianhao Wang, Zhen Zhang, Meiqi Liu, Meiqi Sun, Jiaying Gao, Jinhui Ma, Wei Front Genet Genetics Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity. Frontiers Media S.A. 2022-07-14 /pmc/articles/PMC9329572/ /pubmed/35910210 http://dx.doi.org/10.3389/fgene.2022.849182 Text en Copyright © 2022 Ren, Liu, Yan, Jiang, Wang, Wang, Zhang, Liu, Sun, Gao and Ma. 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 Genetics
Ren, Weichao
Liu, Chi
Yan, Song
Jiang, Zhehui
Wang, Tianhao
Wang, Zhen
Zhang, Meiqi
Liu, Meiqi
Sun, Jiaying
Gao, Jinhui
Ma, Wei
Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
title Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
title_full Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
title_fullStr Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
title_full_unstemmed Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
title_short Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus
title_sort structural characterization of the acer ukurunduense chloroplast genome relative to related species in the acer genus
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9329572/
https://www.ncbi.nlm.nih.gov/pubmed/35910210
http://dx.doi.org/10.3389/fgene.2022.849182
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