Working group session:
Functional Genomics
Presentation type:
poster
Authors:
Li, Xihua; Wu, Man; Yu, Jiwen; Pei, Wenfeng; Yu, Shuxun
Presenter:
Li, Xihua
Correspondent:
Yu, Shuxun
Abstract:
Background: Cotton (Gossypium spp.) is the world’s leading natural fiber and the third largest oilseed crop. Cotton fibers are trichomes that terminally differentiate from single cells located in the epidermis of the ovule and a model system for studying cell elongation. To identify differentially expressed genes related to differences in fiber length between two near-isogenic lines that will facilitate the uncovering of the mechanism of fiber elongation, a high-throughput sequencing technology was applied.
Results: Six sequencing libraries were constructed and sequenced of ovules and developing fibers at the early cotton fiber development stages including the initiation stage (0 days post anthesis (DPA), 3 DPA and the fast elongation stage (10 DPA) in two near-isogenic lines differing in fiber length. As a result, 28 G raw data were obtained and then de novo assembled into 98,464 unigenes with a mean length of 896 bp and a N50 length of 1397 bp. Approximately 71.5% of the unigenes were annotated by aligning against the public protein databases including NR, SwissProt, KEGG and COG. Differentially expressed genes (DEGs) were investigated using the FPKM method, leading to identification of 1536 up-regulated genes and 395 down-regulated genes between the two lines at 10 DPA. Based on GO enrichment and metabolic pathway enrichment analysis, a number of candidate genes involved in fiber elongation related pathways were selected and discussed. Moreover, genes related to previous linear cell growth mode were also confirmed in our study.
Conlusion: we investigate the transcriptome profiling of two near-isogenic lines differing in fiber length at fast elongation period using the Illumina RNA-Seq technology. Studies of DEGs involved in fiber elongation related pathways facilitate the discovery of genes related to fiber length and the mechanism of fiber elongation.
Keywords：Gossypium hirsutum, near-isogenic lines, Fiber elongation, de novo, RNA-Seq