Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

Abstract The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through lon...

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Autores principales:	Jiawei Zhou, Shuo Zhang, Jie Wang, Hongmei Shen, Bin Ai, Wei Gao, Cuijun Zhang, Qili Fei, Daojun Yuan, Zhiqiang Wu, Luke R. Tembrock, Sen Li, Cuihua Gu, Xuezhu Liao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5d369b04f5bb4984b4cc640eab859ab2
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spelling	oai:doaj.org-article:5d369b04f5bb4984b4cc640eab859ab22021-12-02T15:37:57ZChloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution10.1038/s41598-021-88160-42045-2322https://doaj.org/article/5d369b04f5bb4984b4cc640eab859ab22021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88160-4https://doaj.org/toc/2045-2322Abstract The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.Jiawei ZhouShuo ZhangJie WangHongmei ShenBin AiWei GaoCuijun ZhangQili FeiDaojun YuanZhiqiang WuLuke R. TembrockSen LiCuihua GuXuezhu LiaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jiawei Zhou Shuo Zhang Jie Wang Hongmei Shen Bin Ai Wei Gao Cuijun Zhang Qili Fei Daojun Yuan Zhiqiang Wu Luke R. Tembrock Sen Li Cuihua Gu Xuezhu Liao Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
description	Abstract The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
format	article
author	Jiawei Zhou Shuo Zhang Jie Wang Hongmei Shen Bin Ai Wei Gao Cuijun Zhang Qili Fei Daojun Yuan Zhiqiang Wu Luke R. Tembrock Sen Li Cuihua Gu Xuezhu Liao
author_facet	Jiawei Zhou Shuo Zhang Jie Wang Hongmei Shen Bin Ai Wei Gao Cuijun Zhang Qili Fei Daojun Yuan Zhiqiang Wu Luke R. Tembrock Sen Li Cuihua Gu Xuezhu Liao
author_sort	Jiawei Zhou
title	Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
title_short	Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
title_full	Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
title_fullStr	Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
title_full_unstemmed	Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
title_sort	chloroplast genomes in populus (salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5d369b04f5bb4984b4cc640eab859ab2
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Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

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