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Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses

BACKGROUND: Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in mod...

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Autores principales: Shaban, Muhammad, Ahmed, Muhammad Mahmood, Sun, Heng, Ullah, Abid, Zhu, Longfu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085620/
https://www.ncbi.nlm.nih.gov/pubmed/30092779
http://dx.doi.org/10.1186/s12864-018-4985-2
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author Shaban, Muhammad
Ahmed, Muhammad Mahmood
Sun, Heng
Ullah, Abid
Zhu, Longfu
author_facet Shaban, Muhammad
Ahmed, Muhammad Mahmood
Sun, Heng
Ullah, Abid
Zhu, Longfu
author_sort Shaban, Muhammad
collection PubMed
description BACKGROUND: Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited. RESULTS: A total of 64 putative LOX genes were identified in four cotton species (Gossypium (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii)). In the phylogenetic tree, these genes were clustered into three categories (9-LOX, 13-LOX type I, and 13-LOX type II). Segmental duplication of putative LOX genes was observed between homologues from A2 to A(t) and D5 to D(t) hinting at allopolyploidy in cultivated tetraploid species (G. hirsutum and G. barbadense). The structure and motif composition of GhLOX genes appears to be relatively conserved among the subfamilies. Moreover, many cis-acting elements related to growth, stresses, and phytohormone signaling were found in the promoter regions of GhLOX genes. Gene expression analysis revealed that all GhLOX genes were induced in at least two tissues and the majority of GhLOX genes were up-regulated in response to heat and salinity stress. Specific expressions of some genes in response to exogenous phytohormones suggest their potential roles in regulating growth and stress responses. In addition, functional characterization of two candidate genes (GhLOX12 and GhLOX13) using virus induced gene silencing (VIGS) approach revealed their increased sensitivity to salinity stress in target gene-silenced cotton. Compared with controls, target gene-silenced plants showed significantly higher chlorophyll degradation, higher H(2)O(2), malondialdehyde (MDA) and proline accumulation but significantly reduced superoxide dismutase (SOD) activity, suggesting their reduced ability to effectively degrade accumulated reactive oxygen species (ROS). CONCLUSION: This genome-wide study provides a systematic analysis of the cotton LOX gene family using bioinformatics tools. Differential expression patterns of cotton LOX genes in different tissues and under various abiotic stress conditions provide insights towards understanding the potential functions of candidate genes. Beyond the findings reported here, our study provides a basis for further uncovering the biological roles of LOX genes in cotton development and adaptation to stress conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4985-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-60856202018-08-16 Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses Shaban, Muhammad Ahmed, Muhammad Mahmood Sun, Heng Ullah, Abid Zhu, Longfu BMC Genomics Research Article BACKGROUND: Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited. RESULTS: A total of 64 putative LOX genes were identified in four cotton species (Gossypium (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii)). In the phylogenetic tree, these genes were clustered into three categories (9-LOX, 13-LOX type I, and 13-LOX type II). Segmental duplication of putative LOX genes was observed between homologues from A2 to A(t) and D5 to D(t) hinting at allopolyploidy in cultivated tetraploid species (G. hirsutum and G. barbadense). The structure and motif composition of GhLOX genes appears to be relatively conserved among the subfamilies. Moreover, many cis-acting elements related to growth, stresses, and phytohormone signaling were found in the promoter regions of GhLOX genes. Gene expression analysis revealed that all GhLOX genes were induced in at least two tissues and the majority of GhLOX genes were up-regulated in response to heat and salinity stress. Specific expressions of some genes in response to exogenous phytohormones suggest their potential roles in regulating growth and stress responses. In addition, functional characterization of two candidate genes (GhLOX12 and GhLOX13) using virus induced gene silencing (VIGS) approach revealed their increased sensitivity to salinity stress in target gene-silenced cotton. Compared with controls, target gene-silenced plants showed significantly higher chlorophyll degradation, higher H(2)O(2), malondialdehyde (MDA) and proline accumulation but significantly reduced superoxide dismutase (SOD) activity, suggesting their reduced ability to effectively degrade accumulated reactive oxygen species (ROS). CONCLUSION: This genome-wide study provides a systematic analysis of the cotton LOX gene family using bioinformatics tools. Differential expression patterns of cotton LOX genes in different tissues and under various abiotic stress conditions provide insights towards understanding the potential functions of candidate genes. Beyond the findings reported here, our study provides a basis for further uncovering the biological roles of LOX genes in cotton development and adaptation to stress conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4985-2) contains supplementary material, which is available to authorized users. BioMed Central 2018-08-09 /pmc/articles/PMC6085620/ /pubmed/30092779 http://dx.doi.org/10.1186/s12864-018-4985-2 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Shaban, Muhammad
Ahmed, Muhammad Mahmood
Sun, Heng
Ullah, Abid
Zhu, Longfu
Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
title Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
title_full Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
title_fullStr Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
title_full_unstemmed Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
title_short Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
title_sort genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085620/
https://www.ncbi.nlm.nih.gov/pubmed/30092779
http://dx.doi.org/10.1186/s12864-018-4985-2
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