Transcriptome dynamics along with expression analysis of key genes involved in fiber development between Gossypium barbadense and Gossypium darwinii

Abstract

The transcriptome profiling for underpinning the role of key genes controlling formation of fiber in cultivated Gossypium barbadense compared to wild allotetraploid cotton Gossypium darwinii which remained less investigated. Owing to excellent fiber quality of both Gossypium barbadense and Gossypium darwinii and information obtained via Simple Sequence Repeat (SSR) markers, two lines: Xh-18 and darwinii 5-7 were selected for transcriptome sequencing during developmental stages i.e., fiber initiation, elongation, and secondary cell wall (SCW) biosynthesis followed by 0 day after anthesis (DPA), 5DPA, 10DPA, 15DPA and 25DPA, respectively. Twelve libraries of RNA-seq were generated and sequenced individually generating approximately 818 million clean reads of Gossypium darwinii. However, for Gossypium barbadense more than 844 million clean reads were recorded. The Pearson Correlation Coefficient (PCC) analysis results indicated that gene expressions for both Gossypium barbadense and Gossypium darwinii indicated more than 90% of the commonalities at the same stage of fiber growth. However, genes found among Gossypium darwinii at 5, 6 and 7 DPA and XH-18 at 10 and 25 DPA were found disimilar. The expression quantity of RNA sequencing data, 31 genes were found common throughout all stages of DPAs in Gossypium darwinii 5-7 whereas, 377 genes were common in Gossypium barbadense XH-18 at 0, 5, 10, 15, 20, and 25 DPA stages of fiber development. Three genes XLOC_080616 (LTPG2_ARATH/ NLTL2_ARATH; GPI-anchored 2 non-specific lipid transfer protein, similar to At2 g13820), XLOC_065471 (LPAT2_ARATH/LPAT2_BRAOL 1-acyl-sn-glycerol-3-phosphate acyltransferase2), and XLOC_077416 (uncharacterized protein) shown up-regulated expression during 15 and 20 DPA for both Gossypium barbadense and Gossypium darwinii. It will also explore the possible role Gossypium barbadense DNA segment associated with development of fiber quality. Furthermore, this research will decipher the underlying process of fiber development and the possible role of genes for fiber formation in both Sea Island and wild cotton species.

Keywords: DPAs; Fiber development; Gene Functions; Single sequence repeats; Transcriptome profile.

Fig. 1

A heat map of Comparative DEGs from 12 samples in three replicates in darwinii 5–7 and XH-18 at different stages of DPAs like 0DPA, 5DPA, 10DPA, 15DPA, 20DPA and 25DPA, respectively

Fig. 2

GO terms annotation of 32,539 DEGs

Fig. 3

GO terms annotation of 14,584 up regulated DEGs

Fig. 4

GO terms annotation of 17,955 down regulated DEGs

Fig. 5

Comparative study of gene distribution at 0DPA between darwinii 5–7 and XH-18

Fig. 6

Comparative study of gene distribution in KEGG pathways between darwinii 5–7 and XH-18

Fig. 7

Expression patterns of various genes in the form of clusters between two lines. Each cluster indicate a trend of gene expression patterns. The top number specifies the profile ID number as well as the number of genes in that profile

Fig. 8

Ven diagrams comparing novel gene expression patterns between the two lines at the same fiber development stage

Fig. 9

A heatmap of 20 randomly selected DEGs involved in fiber development at different DPAs in Gossypium barbadense

Fig. 10

A heatmap 0f 20 randomly selected DEGs involved in fiber development at different DPAs in Gossypium darwinii.

Fig. 11

A heatmap 0f 20 randomly selected DEGs involved in fiber development at different DPAs in Gossypium darwinii.