Genome-wide characterization and expression analysis of GRAS gene family in pepper (Capsicum annuum L.)
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Abstract
Plant-specific GRAS transcription factors diversely participate in the regulation of multiple biological processes including growth and development, signal cross-talking and biotic/abiotic responses. However, this gene family was not characterized detailed in pepper ( Capsicum annuum L.), an economically important vegetable crop. Here, a total of 50 Ca GRAS members were identified in the pepper genome and renamed by their respective chromosomal distribution. Genomic organization revealed that most CaGRAS genes (84%) have no intron. A phylogenetic analysis was carried out using Arabidopsis thaliana to classify pepper GARS genes into at least ten subfamilies. Multiple sequence alignment showed GRAS-typical domains present in those proteins, with the members from the same phylogenetic subfamily exhibiting the similar motif composition. The presence of highly divergent N-terminus may be associated with functional specificity of each CaGRAS protein. Expression of 12 CaGRAS genes was not detected in all tissues tested, suggesting that their functions may be lost during evolution. By contrast, the rest 38 CaGRAS genes were expressed largely in several organs, showing their important roles in pepper life activities. Moreover, 21 CaGRAS genes were differentially expressed under cold, drought, salt and GA treatments, indicating that they play vital roles in response to abiotic stress in pepper. The first comprehensive analysis of GRAS gene family in the pepper genome in this study provide insights into understanding the CRAS-mediated regulation network, benefiting the genetic improvements in pepper and some other relative plants.
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2018. Genome-wide characterization and expression analysis of GRAS gene family in pepper (Capsicum annuum L.) PeerJ Preprints 6:e3522v1 https://doi.org/10.7287/peerj.preprints.3522v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
The RPKM value of each gene in different tissues and development stages
Sequences of primers used for studies of CaGRAS expression
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Liu Baoling conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Sun Yan performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.
Xue Jinai performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.
Li Runzhi conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Funding
This work was supported by National Natural Science Foundation of China (Grant No. 30971806, 31201266, and 31401430), the State Ministry of Agriculture “948” Project (2014-Z39), Shanxi Province Key Projects of Coal-based Science and Technology (FT-2014-01), Research Project Supported by Shanxi Scholarship Council of China (2015-064), and the Key Project of the Key Research and Development Program of Shanxi Province, China (Grant No. 201603D312005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
