Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles

Abstract The genus Chaenomeles has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of Chaenomeles mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10 Chaenomeles ge...

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Autores principales:	Wenhao Shao, Shiqing Huang, Yongzhi Zhang, Jingmin Jiang, Hui Li
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8d9b909c4b7e4133a16f2c6b222dbbc7
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spelling	oai:doaj.org-article:8d9b909c4b7e4133a16f2c6b222dbbc72021-12-02T18:50:55ZComparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles10.1038/s41598-021-95776-z2045-2322https://doaj.org/article/8d9b909c4b7e4133a16f2c6b222dbbc72021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95776-zhttps://doaj.org/toc/2045-2322Abstract The genus Chaenomeles has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of Chaenomeles mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10 Chaenomeles germplasms supplemented with one outgroup species, Docynia delavayi (D. delavayi), on the Illumina HiSeq2500 platform. After de novo assemblies, we generated from 40,084 to 49,571 unigenes for each germplasm. After pairwise comparison of the orthologous sequences, 9,659 orthologues within the 11 germplasms were obtained, with 6,154 orthologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationships for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare their functional similarities and differences. Selective pressure analysis based on 6,154 common single-copy genes revealed that 45 genes were under positive selection. Most of these genes are involved in building the plant disease defence system. A total of 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their functions in secondary metabolism pathways. Finally, 10 primers were chosen as SSR marker candidates for Chaenomeles germplasms by comprehensive standards. Our research provides a new methodology and reference for future related research in Chaenomeles and is also useful for improvement, breeding and selection projects in other related species.Wenhao ShaoShiqing HuangYongzhi ZhangJingmin JiangHui LiNature 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 Wenhao Shao Shiqing Huang Yongzhi Zhang Jingmin Jiang Hui Li Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
description	Abstract The genus Chaenomeles has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of Chaenomeles mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10 Chaenomeles germplasms supplemented with one outgroup species, Docynia delavayi (D. delavayi), on the Illumina HiSeq2500 platform. After de novo assemblies, we generated from 40,084 to 49,571 unigenes for each germplasm. After pairwise comparison of the orthologous sequences, 9,659 orthologues within the 11 germplasms were obtained, with 6,154 orthologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationships for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare their functional similarities and differences. Selective pressure analysis based on 6,154 common single-copy genes revealed that 45 genes were under positive selection. Most of these genes are involved in building the plant disease defence system. A total of 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their functions in secondary metabolism pathways. Finally, 10 primers were chosen as SSR marker candidates for Chaenomeles germplasms by comprehensive standards. Our research provides a new methodology and reference for future related research in Chaenomeles and is also useful for improvement, breeding and selection projects in other related species.
format	article
author	Wenhao Shao Shiqing Huang Yongzhi Zhang Jingmin Jiang Hui Li
author_facet	Wenhao Shao Shiqing Huang Yongzhi Zhang Jingmin Jiang Hui Li
author_sort	Wenhao Shao
title	Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
title_short	Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
title_full	Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
title_fullStr	Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
title_full_unstemmed	Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
title_sort	comparative transcriptomics provides a strategy for phylogenetic analysis and ssr marker development in chaenomeles
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8d9b909c4b7e4133a16f2c6b222dbbc7
work_keys_str_mv	AT wenhaoshao comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT shiqinghuang comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT yongzhizhang comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT jingminjiang comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT huili comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles
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Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles

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