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Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

BACKGROUND: Dicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown....

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Autores principales: Wang, Lei, Li, Fuxing, Wang, Ning, Gao, Yongwei, Liu, Kangjia, Zhang, Gangmin, Sun, Jiahui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9717546/
https://www.ncbi.nlm.nih.gov/pubmed/36460956
http://dx.doi.org/10.1186/s12864-022-09049-8
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author Wang, Lei
Li, Fuxing
Wang, Ning
Gao, Yongwei
Liu, Kangjia
Zhang, Gangmin
Sun, Jiahui
author_facet Wang, Lei
Li, Fuxing
Wang, Ning
Gao, Yongwei
Liu, Kangjia
Zhang, Gangmin
Sun, Jiahui
author_sort Wang, Lei
collection PubMed
description BACKGROUND: Dicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome of D. leptopodum to discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae. RESULTS: The chloroplast genome size of D. leptopodum was 162,942 bp, and D. leptopodum exhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). The D. leptopodum chloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed that D. leptopodum formed a clade with the tribe Chelidonieae. CONCLUSIONS: Our study provides detailed information on the D. leptopodum chloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09049-8.
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spelling pubmed-97175462022-12-03 Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae Wang, Lei Li, Fuxing Wang, Ning Gao, Yongwei Liu, Kangjia Zhang, Gangmin Sun, Jiahui BMC Genomics Research BACKGROUND: Dicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome of D. leptopodum to discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae. RESULTS: The chloroplast genome size of D. leptopodum was 162,942 bp, and D. leptopodum exhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). The D. leptopodum chloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed that D. leptopodum formed a clade with the tribe Chelidonieae. CONCLUSIONS: Our study provides detailed information on the D. leptopodum chloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09049-8. BioMed Central 2022-12-02 /pmc/articles/PMC9717546/ /pubmed/36460956 http://dx.doi.org/10.1186/s12864-022-09049-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Wang, Lei
Li, Fuxing
Wang, Ning
Gao, Yongwei
Liu, Kangjia
Zhang, Gangmin
Sun, Jiahui
Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
title Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
title_full Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
title_fullStr Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
title_full_unstemmed Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
title_short Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
title_sort characterization of the dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily papaveroideae
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9717546/
https://www.ncbi.nlm.nih.gov/pubmed/36460956
http://dx.doi.org/10.1186/s12864-022-09049-8
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