Genome-Wide Identification and Expression Analyses of the Cotton AGO Genes and Their Potential Roles in Fiber Development and Stress Response

Abstract

Argonaute proteins (AGOs) are indispensable components of RNA silencing. However, systematic characterization of the AGO genes have not been completed in cotton until now. In this study, cotton AGO genes were identified and analyzed with respect to their evolution and expression profile during biotic and abiotic stresses. We identified 14 GaAGO, 14 GrAGO, and 28 GhAGO genes in the genomes of Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum. Cotton AGO proteins were classified into four subgroups. Structural and functional conservation were observed in the same subgroups based on the analysis of the gene structure and conserved domains. Twenty-four duplicated gene pairs were identified in GhAGO genes, and all of them exhibited strong purifying selection during evolution. Moreover, RNA-seq analysis showed that most of the GhAGO genes exhibit high expression levels in the fiber initiation and elongation processes. Furthermore, the expression profiles of GhAGO genes tested by quantitative real-time polymerase chain reaction (qPCR) demonstrated that they were sensitive to Verticillium wilt infection and salt and drought stresses. Overall, our results will pave the way for further functional investigation of the cotton AGO gene family, which may be involved in fiber development and stress response.

Molecular Characterization of the Acyl-CoA-Binding Protein Genes Reveals Their Significant Roles in Oil Accumulation and Abiotic Stress Response in Cotton

“…The chromosomal location information of ACBP genes was extracted from GFF gene annotation files and then visualized with the MapChart software [ 22 ]. The duplication pattern for each ACBP gene was analyzed by the method reported in the pear sugar transporter family genes [ 23 ]. For example, the 70,199 genes from the G. hirsutum genome were aligned using an all-vs-all local BLAST search with an e-value < 1 × 10 −10 .…”

Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp.

“…A. thaliana encodes ten AGO proteins [20], and the number of AGOs is even greater in other flowering plants. For example, there are 12 AGO proteins in pepper [21]; 13 in grape, sweet orange, and banana [22][23][24]; 15 in tomato and poplar [25,26]; 17 in maize [27]; 18 in rice and tea [28,29]; 19 in foxtail millet [30]; 21 in sugarcane [31]; 27 in tetraploid oilseed rape (Brassica napus) [32]; 28 in allotetraploid cotton (Gossypium hirsutum) [33]; and 69 TaAGO genes in the hexaploid bread wheat [34]. These proteins are ~100 kD and are shared with four domains, including ArgoN, PIWI-ARGONAUTE-ZWILLE (PAZ), ArgoMid, and a C-terminal PIWI domain [35,36].…”

“…Five and eight DCLs have been reported in the grain crops, including rice [37], maize [27], and foxtail millet [30], respectively. For vegetable crops, seven DCLs have been identified in tomato [25], four in pepper [21], six in common bean [61], eight in Brassica napus [33], and eleven in allotetraploid cotton [62]. Moreover, DCLs were also found in the fruit crops, including grape (four DCLs) [22], sweet orange (five DCLs) [23], banana (three DCLs) [24], and peach (eight DCLs) [63].…”