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In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation
Plants have evolved a sophisticated network of K(+) transport systems to regulate growth and development. Limited K(+) resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K(+) 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/PMC5440519/ https://www.ncbi.nlm.nih.gov/pubmed/28588592 http://dx.doi.org/10.3389/fpls.2017.00804 |
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author | Rehman, Hafiz M. Nawaz, Muhammad A. Shah, Zahid Hussain Daur, Ihsanullah Khatoon, Sadia Yang, Seung Hwan Chung, Gyuhwa |
author_facet | Rehman, Hafiz M. Nawaz, Muhammad A. Shah, Zahid Hussain Daur, Ihsanullah Khatoon, Sadia Yang, Seung Hwan Chung, Gyuhwa |
author_sort | Rehman, Hafiz M. |
collection | PubMed |
description | Plants have evolved a sophisticated network of K(+) transport systems to regulate growth and development. Limited K(+) resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K(+) transporters in plants. Here, we have identified 70 putative K(+) transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K(+) channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes. To clarify the molecular evolution of each family in soybean, we analyzed their phylogeny, mode of duplication, exon structures and splice sites, and paralogs. Additionally, ortholog clustering and syntenic analysis across five other dicots further explored the evolution of these gene families and indicated that the soybean data is suitable as a model for all other legumes. Available microarray data sets from Genevestigator about nodulation was evaluated and further confirmed with the RNA sequencing data available by a web server. For each family, expression models were designed based on Transcripts Per Kilobase Million (TPM) values; the outcomes indicated differential expression linked to nodulation and confirmed the genes' putative roles. In-depth studies such as ours provides the basis for understanding K(+) inventories in all other plants. |
format | Online Article Text |
id | pubmed-5440519 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-54405192017-06-06 In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation Rehman, Hafiz M. Nawaz, Muhammad A. Shah, Zahid Hussain Daur, Ihsanullah Khatoon, Sadia Yang, Seung Hwan Chung, Gyuhwa Front Plant Sci Plant Science Plants have evolved a sophisticated network of K(+) transport systems to regulate growth and development. Limited K(+) resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K(+) transporters in plants. Here, we have identified 70 putative K(+) transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K(+) channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes. To clarify the molecular evolution of each family in soybean, we analyzed their phylogeny, mode of duplication, exon structures and splice sites, and paralogs. Additionally, ortholog clustering and syntenic analysis across five other dicots further explored the evolution of these gene families and indicated that the soybean data is suitable as a model for all other legumes. Available microarray data sets from Genevestigator about nodulation was evaluated and further confirmed with the RNA sequencing data available by a web server. For each family, expression models were designed based on Transcripts Per Kilobase Million (TPM) values; the outcomes indicated differential expression linked to nodulation and confirmed the genes' putative roles. In-depth studies such as ours provides the basis for understanding K(+) inventories in all other plants. Frontiers Media S.A. 2017-05-23 /pmc/articles/PMC5440519/ /pubmed/28588592 http://dx.doi.org/10.3389/fpls.2017.00804 Text en Copyright © 2017 Rehman, Nawaz, Shah, Daur, Khatoon, Yang and Chung. 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 Rehman, Hafiz M. Nawaz, Muhammad A. Shah, Zahid Hussain Daur, Ihsanullah Khatoon, Sadia Yang, Seung Hwan Chung, Gyuhwa In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation |
title | In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation |
title_full | In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation |
title_fullStr | In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation |
title_full_unstemmed | In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation |
title_short | In-Depth Genomic and Transcriptomic Analysis of Five K(+) Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation |
title_sort | in-depth genomic and transcriptomic analysis of five k(+) transporter gene families in soybean confirm their differential expression for nodulation |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440519/ https://www.ncbi.nlm.nih.gov/pubmed/28588592 http://dx.doi.org/10.3389/fpls.2017.00804 |
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