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Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa

Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF...

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Autores principales: Paul, Parameswari, Dhandapani, Vignesh, Rameneni, Jana Jeevan, Li, Xiaonan, Sivanandhan, Ganesan, Choi, Su Ryun, Pang, Wenxing, Im, Subin, Lim, Yong Pyo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822780/
https://www.ncbi.nlm.nih.gov/pubmed/27049520
http://dx.doi.org/10.1371/journal.pone.0151522
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author Paul, Parameswari
Dhandapani, Vignesh
Rameneni, Jana Jeevan
Li, Xiaonan
Sivanandhan, Ganesan
Choi, Su Ryun
Pang, Wenxing
Im, Subin
Lim, Yong Pyo
author_facet Paul, Parameswari
Dhandapani, Vignesh
Rameneni, Jana Jeevan
Li, Xiaonan
Sivanandhan, Ganesan
Choi, Su Ryun
Pang, Wenxing
Im, Subin
Lim, Yong Pyo
author_sort Paul, Parameswari
collection PubMed
description Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in Brassica rapa (B. rapa). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in B. rapa using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the B. rapa Aux/IAA (BrIAA) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of BrIAA with Arabidopsis thaliana, Oryza sativa and Zea mays identified 51 sister pairs including 15 same species (BrIAA—BrIAA) and 36 cross species (BrIAA—AtIAA) IAA genes. Among the 55 BrIAA genes, expression of 43 and 45 genes were verified using Genebank B. rapa ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of BrIAA genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the BrIAA genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between IAA genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in B. rapa. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of Brassica crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in B. rapa.
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spelling pubmed-48227802016-04-22 Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa Paul, Parameswari Dhandapani, Vignesh Rameneni, Jana Jeevan Li, Xiaonan Sivanandhan, Ganesan Choi, Su Ryun Pang, Wenxing Im, Subin Lim, Yong Pyo PLoS One Research Article Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in Brassica rapa (B. rapa). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in B. rapa using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the B. rapa Aux/IAA (BrIAA) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of BrIAA with Arabidopsis thaliana, Oryza sativa and Zea mays identified 51 sister pairs including 15 same species (BrIAA—BrIAA) and 36 cross species (BrIAA—AtIAA) IAA genes. Among the 55 BrIAA genes, expression of 43 and 45 genes were verified using Genebank B. rapa ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of BrIAA genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the BrIAA genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between IAA genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in B. rapa. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of Brassica crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in B. rapa. Public Library of Science 2016-04-06 /pmc/articles/PMC4822780/ /pubmed/27049520 http://dx.doi.org/10.1371/journal.pone.0151522 Text en © 2016 Paul et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Paul, Parameswari
Dhandapani, Vignesh
Rameneni, Jana Jeevan
Li, Xiaonan
Sivanandhan, Ganesan
Choi, Su Ryun
Pang, Wenxing
Im, Subin
Lim, Yong Pyo
Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
title Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
title_full Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
title_fullStr Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
title_full_unstemmed Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
title_short Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
title_sort genome-wide analysis and characterization of aux/iaa family genes in brassica rapa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822780/
https://www.ncbi.nlm.nih.gov/pubmed/27049520
http://dx.doi.org/10.1371/journal.pone.0151522
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