|San francisco, Susan|
Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract only
Publication Acceptance Date: 5/1/2013
Publication Date: N/A
Citation: Interpretive Summary:
Technical Abstract: Cotton fibers are the dominant source of natural fibers used in the textile industry and contribute significantly to the world economy. Adverse environmental conditions negatively affect fiber characteristics, especially when the fibers are in the elongation phase of development. Improvement in the yield and quality of cotton fibers requires the identification of the molecular networks involved in fiber development. In this research, we have analyzed cotton fibers in the early elongation phase using RNA-Seq, to identify the genes involved in the different pathways activated/deactivated during this stage of fiber development. Tru-Seq RNA sample preparation kit was used to prepare cDNA libraries from RNA extracted from Upland cotton cultivar TM-1 cotton fibers samples at 3 and 5 days post-anthesis (DPA). These libraries were sequenced using 150 bp, paired-end Illumina sequencing which produced 6,570,054 sequences and 7,063,378 sequences from 3 DPA and 5 DPA libraries respectively. The de novo assembly of these raw reads with NGen identified 20,270 contigs in 3 DPA and 20,339 contigs in 5 DPA. The raw files were evaluated in ArrayStar to identify the differentially expressed transcripts. A total of 3,177 transcripts were recognized as differentially expressed with 95% probability and at least a 2-fold change between 3 DPA and 5 DPA. These 3,177 transcripts were annotated using Mercator and Blast2Go, revealing several processes linked to fiber development. The up-regulated transcripts at 5 DPA belonged to cell-wall modification, phospholipid and sphingolipid synthesis, solute and water transporters, cytoskeletal elements, phytohormones, signal transducers and transcription factor categories; processes that were involved in cell wall extension, hinting that the fibers at this stage are involved in loosening the cell wall in anticipation of the rapid fiber elongation beyond 5 DPA. In the future, we plan to combine this data with proteomic analysis on the same stages. We have created a reference protein database containing 374,562 possible protein contigs for protein identification from the raw spectra obtained from the mass spectrometry runs. The NGen assembled transcriptomes from 6 stages of fiber development, 3 DPA, 5 DPA, 11 DPA, 17 DPA, 21 DPA and 24 DPA, were assembled using CAP3 assembly software. This assembled transcriptome was six-frame translated using a perl script to create the protein database. This is the first report on the generation of a transcriptome and a proteome of the elongating cotton fibers using RNA-Seq. These databases form a significant source of information, and will contribute towards research on the improvement of cotton fiber characteristics.