Gene expression profile

CottonMD shows the gene expression data of Hai7124 (G. barbadense) and TM-1 (G. hirsutum) in different tissues and populations or under different treatment conditions^[1]. The tissues mainly come from root, stem, leaf, and various tissues in flowers. Environmental stresses mainly include low temperature stress, high temperature stress, drought stress and salt stress.

Coexpression

The data used by the co-expression network is the same as that used on the Gene expression profile page. And the co-expression network is obtained by calculating the Pearson correlation coefficient of pairwise gene pairs, and the final result selects gene pairs with a Pearson coefficient greater than 0.8.

Gene expression in population

We collected resequencing data from a total of 251 samples from cotton fiber at 15 days post-anthesis (DPA)^[3]. The clean reads were mapped to the TM-1 genome^[4] with TopHat (version 2.0.13). The expression level of each gene was determined with cufflinks (version 2.2.1) with a multiread and fragment bias correction method.

References

[1]	Hu Y, Chen J, Fang L, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature genetics, 2019, 51 (4): 739-748.
[2]	Wang M, Tu L, Yuan D, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense[J]. Nature genetics, 2019, 51 (2): 224-229.
[3]	Li Z, Wang P, et al. [1]Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton[J]. New Phytologist, 2020, 226(6).
[4]	Huang G, Wu Z, Percy R G, et al. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution[J]. Nature Genetics, 2020, 52 (5).

MaGenDB

CottonFGD