Genome-Wide Identification and Expression Analysis of Respiratory Burst Oxidase Homolog (RBOH) Gene Family in Eggplant (Solanum melongena L.) under Abiotic and Biotic Stress

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Abstract

Respiratory burst oxidase homologs (RBOHs) are important proteins that catalyze the production of reactive oxygen species (ROS), which play important roles in growth and stress response. For a comprehensive analysis of SmRBOH genes, we conducted genome-wide identification of the SmRBOH gene family in eggplant (Solanum melongena L.) and analyzed the expression of SmRBOHs under abiotic (salt, high-temperature, and low-temperature) and biotic stress (Verticillium dahliae inoculation) by quantitative real-time PCR (qRT-PCR). The result showed that a total of eight SmRBOH members were identified from the genome database of eggplant, and they were relatively evenly distributed across seven chromosomes. The analysis of Motif and the conserved domain showed that SmRBOHs have high similarity in protein sequences and functions. Based on phylogenetics, SmRBOHs were classified into three distinct clades. Furthermore, the promoter regions of SmRBOHs were found to contain different cis-elements. Additionally, the results of the qRT-PCR demonstrated differential expression patterns of SmRBOHs in different tissues (the roots, stems, and leaves) and stress conditions. SmRBOHB, SmRBOHD, SmRBOHH1, and SmRBOHH2 showed significant upregulation (>20-fold) under at least one stress condition. Subcellular localization analysis of the above four members further confirmed that they localized on the plasma membrane. This study provides a theoretical foundation for understanding the functions of SmRBOHs in eggplant.

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TBtools - an integrative toolkit developed for interactive analyses of big biological data

Chengjie Chen, Hao Chen, Yi Zhang … (2020)

The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.

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CDD/SPARCLE: the conserved domain database in 2020

Shennan Lu, Jiyao Wang, Farideh Chitsaz … (2020)

As NLM’s Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

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NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis.

June M. Kwak, Izumi C. Mori, Zhen-Ming Pei … (2003)

Reactive oxygen species (ROS) have been proposed to function as second messengers in abscisic acid (ABA) signaling in guard cells. However, the question whether ROS production is indeed required for ABA signal transduction in vivo has not yet been addressed, and the molecular mechanisms mediating ROS production during ABA signaling remain unknown. Here, we report identification of two partially redundant Arabidopsis guard cell-expressed NADPH oxidase catalytic subunit genes, AtrbohD and AtrbohF, in which gene disruption impairs ABA signaling. atrbohD/F double mutations impair ABA-induced stomatal closing, ABA promotion of ROS production, ABA-induced cytosolic Ca(2+) increases and ABA- activation of plasma membrane Ca(2+)-permeable channels in guard cells. Exogenous H(2)O(2) rescues both Ca(2+) channel activation and stomatal closing in atrbohD/F. ABA inhibition of seed germination and root elongation are impaired in atrbohD/F, suggesting more general roles for ROS and NADPH oxidases in ABA signaling. These data provide direct molecular genetic and cell biological evidence that ROS are rate-limiting second messengers in ABA signaling, and that the AtrbohD and AtrbohF NADPH oxidases function in guard cell ABA signal transduction.

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Author and article information

Contributors

Xu Yang: (View ORCID Profile)

Journal

Journal ID (publisher-id): GENEG9

Title: Genes

Abbreviated Title: Genes

Publisher: MDPI AG

ISSN (Electronic): 2073-4425

Publication date Created: September 2023

Publication date (Electronic): August 23 2023

Volume: 14

Issue: 9

Page: 1665

Article

DOI: 10.3390/genes14091665

PubMed ID: 37761805

SO-VID: b59dce21-b469-4ad7-8afa-072a53e22fb6

License:

https://creativecommons.org/licenses/by/4.0/

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