Fig 1.
A detailed workflow performed in identification of DEGs in CGMS, maintainer and restorer lines of Gossypium hirsutum L.
Table 1.
Primer sequences of genes used for validation study using qRT-PCR.
Table 2.
Quality screening and mapping statistics of RNA-Seq data.
Fig 2.
Agri GO analysis of DEGs in floral buds.
Singular enrichment analysis was performed in AgriGO v2 to identify enriched gene ontologies associated with pollen developmental processes. Each box shows the GO term number, the p-value in parenthesis, and GO term. The pair of numerals in the left represents the number of genes in input list associated with that GO term and number of genes in the input list. The pair of numerals in the right represents the number of genes associated with a targeted GO term in the Gossypium database and a total number of Gossypium genes with GO annotations in the Gossypium database. Colour and design of arrow indicate the effect of pathways. Box colors indicate levels of statistical significance: yellow = 0.05; orange = eā5; and red = eā9.
Fig 3.
GO classification of non-redundantly expressed genes in CGMS, maintainer and restorer lines of Gossypium hirsutum L.
Fig 4.
a) Distribution of differentially expressed genes on chromosomes of Gossypium hirsutum L. Distribution of phenogram showing the exact location of DEGs on each chromosome of Gossypium hirsutum L. b) The total number of DEGs present on each chromosome of cotton. A total number of differentially expressed genes on diploid sets of Gossypium genome A and D. The X-axis represents different chromosomes. Y-axis is DEGS numbers on each chromosome.
Fig 5.
a) The number of differentially expressed genes (DEGs) between three different lines of cotton. The green color represented up-regulated, the red color represented down-regulated gene numbers on the X-axis, Y-axis represented the number of deferentially expressed genes. b) The fold change wise distributed numbers of genes under the comparison of three different lines. c) Venn diagram showing the distribution of unique and common DEGs among three comparisons.
Fig 6.
qRT-PCR analysis of gene expression compared with the RNA-seq data.
Expression of 14 transcript as analyzed by quantitative PCR in CGMS and fertile lines of Gossypium hirsutum L. The dots with green colour (thirteen in numbers) indicates concordance whereas, red (one in number) indicates non-concordance of expression profiling in qRT-PCR and RNA-seq.