Analysis of sea-island cotton and upland cotton in response to Verticillium dahliaeinfection by RNA sequencing

Abstract

BackgroundCotton Verticillium wilt is a serious soil-borne vascular disease that causes great economic loss each year. However, due to the lack of resistant varieties of upland cotton, the molecular mechanisms of resistance to this disease, especially to the pathogen Verticillium dahliae, remain unclear.ResultsWe used the RNA-seq method to research the molecular mechanisms of cotton defence responses to different races of Verticillium dahliae by comparing infected sea-island cotton and upland cotton. A total of 77,212 unigenes were obtained, and the unigenes were subjected to BLAST searching and annotated using the GO and KO databases. Six sets of digital gene expression data were mapped to the reference transcriptome. The gene expression profiles of cotton infected with Verticillium dahliae were compared to those of uninfected cotton; 44 differentially expressed genes were identified. Regarding genes involved in the phenylalanine metabolism pathway, the hydroxycinnamoyl transferase gene (HCT) was upregulated in upland cotton whereas PAL, 4CL, CAD, CCoAOMT, and COMT were upregulated in sea-island cotton. Almost no differentially expressed genes in this pathway were identified in sea-island cotton and upland cotton when they were infected with V. dahliae V991 and V. dahliae D07038, respectively.ConclusionsOur comprehensive gene expression data at the transcription level will help elucidate the molecular mechanisms of the cotton defence response to V. dahliae. By identifying the genes involved in the defence response of each type of cotton to V. dahliae, our data not only provide novel molecular information for researchers, but also help accelerate research on genes involved in defences in cotton.

Characterization, Expression, and Functional Analysis of a Novel NAC Gene Associated with Resistance to Verticillium Wilt and Abiotic Stress in Cotton

“…A 1159 bp unigene containing a NAM domain was obtained through screening differentially expressed genes involved in the cotton defense response to V. dahliae (Sun et al 2013b). The assembled sequence obtained after in silico cloning was the same as the original unigene sequence.…”

“…Based on the previous transcriptome sequencing of sea-island cotton in response to V. dahliae (Sun et al 2013b), we identified the differential expression of a unigene fragment (designated as GbNAC1 ). GbNAC1 encodes a NAC protein with 180 amino acids containing three NAC substructure domains (C–E) (Figure 1A and Figure 2).…”

Large-scale transcriptome comparison of sunflower genes responsive to Verticillium dahliae

“…Furthermore, some studies have speculated that a miR482-mediated silencing cascade is involved in the regulation of potato resistance against V. dahliae infection and in the counter defense action of plants in response to pathogen infection [17]. In studies on cotton responses to V. dahliae , Sun et al used the RNA-Seq method to identify 44 differentially expressed genes involved in cotton defense responses [18]. Using the same method, a total of 3027 unigenes were determined as be homologous to known defense-related genes in other plants [19].…”

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

“…qRT-PCR analyses of SiWRKY gene expression in response to waterlogging and drought stresses RNA was extracted from the roots of each of the four cultivars using the EASYspin Plus Plant RNA Kit (Aidlab Biotechnologies, Beijing, China) [60] according to the manufacturer's instructions. The RNA was quantified using a BIOMATE 3 spectrophotometer (Thermo Scientific, Worcester, MA, USA) and its integrity was confirmed using 1% agarose gel electrophoresis.…”