Fig 1.
RNA-Seq of G. hirsutum under whitefly-mediated CLCuD stress.
(A) Sketch of CLCuD infestation of three-week-old cotton plant with viruliferous whitefly. (B) Control (top) and CLCuD infected (bottom) leaf of G. hirsutum used for RNA-Seq, arrows are showing vein thickening in CLCuD infected leaf, (C) RNA-Seq data analysis methodology.
Fig 2.
Data quality analysis and mapping to reference genome.
(A) RNA-seq raw vs mapped reads where number of samples and reads lie on x and y-axis, respectively, (B) Data (Log10 FPKM) among the biological replicates, where q1 and q2 represent control and infected samples, moreover q1_0, q1_1, q1_2 symbolize three biological replicates of controls, q2_0, q2_1, q2_2 denote three biological replicates of infected samples. (C-E) Gene dispersion, density and DEGs in the dataset.
Fig 3.
Hierarchical clustering heatmap of cotton DEGs under whitefly-mediated CLCuD.
R-based Heatmap 2.0 package was implemented to make a heat map of G. hirsutum DEGs under whitefly-mediated CLCuD stress (A). Heatmap of 468 DEGs and (B). Hub genes identified by WGCNA.
Table 1.
List of some significant differentially expressed genes in the transcriptomic data of G. hirsutum under whitefly-mediated CLCuD infection.
Fig 4.
RT-qPCR Validation of transcriptomic data in Karishma cultivar.
(A) R-based heat map of 10 selected DEGs for RT-qPCR. (B) Relative expression levels of selected ten genes and 18S as an internal reference detected by RT-qPCR in control and symptomatic leaves. Error bars symbolized standard error of three biological replicates and * shows significance determined by Student’s t-test.
Fig 5.
RT-qPCR Validation of transcriptomic data in MNH786 cultivar.
Relative expression levels of selected ten genes and 18S as an internal reference detected by RT-qPCR in control and symptomatic leaves. Error bars symbolized standard error of three biological replicates and * shows significance determined by Student’s t-test.
Fig 6.
GO term annotation of G. hirsutum differentially expressed genes under CLCuD stress.
Fig 7.
WGCNA for identification of hub genes among CLCuD-responsive DEGs in G. hirsutum.
(A). TOM heatmap on 468 DEGs. Pink and green colors denote high and no strength, respectively, while dendrogram lines represent genes. DEGs with similar expression regulation patterns have been clustered and referred as modules. (B). Weighted correlations within the network deciphered six modules with a threshold of ≥ 0.85. The network nodes having more than 50 connections were denoted as highly connected hub genes (C). GO term annotation of CLCuD responsive hub genes revealed by WGCNA.