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Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance
Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE t...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383727/ https://www.ncbi.nlm.nih.gov/pubmed/28439276 http://dx.doi.org/10.3389/fpls.2017.00425 |
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author | Yang, Qianying Shohag, M. J. I. Feng, Ying He, Zhenli Yang, Xiaoe |
author_facet | Yang, Qianying Shohag, M. J. I. Feng, Ying He, Zhenli Yang, Xiaoe |
author_sort | Yang, Qianying |
collection | PubMed |
description | Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca(2+)) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance. |
format | Online Article Text |
id | pubmed-5383727 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-53837272017-04-24 Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance Yang, Qianying Shohag, M. J. I. Feng, Ying He, Zhenli Yang, Xiaoe Front Plant Sci Plant Science Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca(2+)) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance. Frontiers Media S.A. 2017-04-07 /pmc/articles/PMC5383727/ /pubmed/28439276 http://dx.doi.org/10.3389/fpls.2017.00425 Text en Copyright © 2017 Yang, Shohag, Feng, He and Yang. http://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) or licensor 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 | Plant Science Yang, Qianying Shohag, M. J. I. Feng, Ying He, Zhenli Yang, Xiaoe Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance |
title | Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance |
title_full | Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance |
title_fullStr | Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance |
title_full_unstemmed | Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance |
title_short | Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance |
title_sort | transcriptome comparison reveals the adaptive evolution of two contrasting ecotypes of zn/cd hyperaccumulator sedum alfredii hance |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383727/ https://www.ncbi.nlm.nih.gov/pubmed/28439276 http://dx.doi.org/10.3389/fpls.2017.00425 |
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