Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications.

Muhammad Ali,Abid Khan,Wen-Xian Gai,Saeed Ul Haq,Guo-Xin Cheng,Izhar Muhammad,De-Xu Luo,Zhen-Hui Gong,Huai-Xia Zhang

doi:10.3390/ijms19082216

Muhammad Ali, Abid Khan + Show 7 more

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https://doi.org/10.3390/ijms19082216

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Abstract

Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (Capsicum annuum L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. Phytophthora capsici post inoculation, most of the CaChi (CaChiI3, CaChiIII1, CaChiIII2, CaChiIII4, CaChiIII6, CaChiIII7, CaChiIV1, CaChiVI1 and CaChiVI2) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the CaChiIII2, CaChiIII7, CaChiVI1 and CaChiVI2 were upregulated by abiotic stress, while CaChiI1, CaChiIII7, CaChiIV1 and CaChiIV2 responded to hormonal treatments. Furthermore, CaChiIV1-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.

Highlights

Plants being sessile organisms are exposed to a number of stresses
The inducible defense responses of plants include synthesis of signaling molecules, such as methyl jasmonate (MeJA), salicylic acid (SA) and ethylene (ET), which work in a complex network interaction that in turn regulates the expression of defense related genes (PR) and molecules such as reactive oxygen species (ROS), phytoalexins, proline, phenylpropanoids and pathogenesis-related genes [2,3]
The SMART results show that Chitin Binding Domain (CBD) was found in all 16 members while additional functional domains such as glycoside hydrolase_19_super family (CaChiI1, CaChiI2, and CaChiI3), chitinase glycoside_hydrolase_19 (CaChiIV1 and CaChiIV2) and Barwin (CaChiVI2 and CaChi3) were found in this gene family (Figure 1 and Table S2)

Summary

Introduction

Plants being sessile organisms are exposed to a number of stresses. External environmental fluctuations, different insect pest and pathogen considerably affect the growth, development, yield and quality [1]. To safe guard themselves against these threats, plants have evolved some sophisticated defense mechanisms. The inducible defense responses of plants include synthesis of signaling molecules, such as methyl jasmonate (MeJA), salicylic acid (SA) and ethylene (ET), which work in a complex network interaction that in turn regulates the expression of defense related genes (PR) and molecules such as reactive oxygen species (ROS), phytoalexins, proline, phenylpropanoids and pathogenesis-related genes [2,3]. Plant defense mechanism consists of two typical interconnecting layers to develop plant immune system designated as effector-triggered immunity (ETI) and pattern-triggered immunity (PTI), participating in signal transduction [6,7]. A set of pathogenesis related (PR-2 and PR-5) genes are involved in PTI and ETI, depending on the magnitude and time of the interacting signaling components [8,9]

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Discussion

Conclusion