Cargando…
Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles
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...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8361139/ https://www.ncbi.nlm.nih.gov/pubmed/34385515 http://dx.doi.org/10.1038/s41598-021-95776-z |
_version_ | 1783737897834250240 |
---|---|
author | Shao, Wenhao Huang, Shiqing Zhang, Yongzhi Jiang, Jingmin Li, Hui |
author_facet | Shao, Wenhao Huang, Shiqing Zhang, Yongzhi Jiang, Jingmin Li, Hui |
author_sort | Shao, Wenhao |
collection | PubMed |
description | 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 | Online Article Text |
id | pubmed-8361139 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83611392021-08-17 Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles Shao, Wenhao Huang, Shiqing Zhang, Yongzhi Jiang, Jingmin Li, Hui Sci Rep Article 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. Nature Publishing Group UK 2021-08-12 /pmc/articles/PMC8361139/ /pubmed/34385515 http://dx.doi.org/10.1038/s41598-021-95776-z Text en © The Author(s) 2021 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 Shao, Wenhao Huang, Shiqing Zhang, Yongzhi Jiang, Jingmin Li, Hui Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles |
title | 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_short | 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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8361139/ https://www.ncbi.nlm.nih.gov/pubmed/34385515 http://dx.doi.org/10.1038/s41598-021-95776-z |
work_keys_str_mv | AT shaowenhao comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT huangshiqing comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT zhangyongzhi comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT jiangjingmin comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles AT lihui comparativetranscriptomicsprovidesastrategyforphylogeneticanalysisandssrmarkerdevelopmentinchaenomeles |