Working group session:
Functional Genomics
Presentation type:
oral
Authors:
Li, Qin; Zhou, Cai-Fen; Zhu, Yu-Xian
Presenter:
Li, Qin
Correspondent:
Zhu, Yu-Xian
Abstract:
Using the recent assembled G. raimondii D5 genome, we performed genome-wide mapping at single base-pair resolution using about 10 Gb RNA-seq data and 0.8 Gb non-coding RNA-seq data from Illumina sequencing platform. About sixty percent of intron-containing genes were alternative spliced in G. raimondii and intron retention was the most frequent (~39%) alternative slicing (AS) event while exon skipping, most commonly found in vertebrates, constituted only 6%. Comparative genomics across nine eukaryote species revealed that AS events profiles were conserved between G. raimondii and Arabidopsis thaliana, but varied from eudicots to monocots and other species. In some KNOX genes previously reported to be involved in leaf development, AS events result in the loss of homeodomain that is essential for the biochemical function of the encoded protein as a transcription factor. Combined with a significantly different expression level during plant leaf development, our data indicates that AS could be a potential regulatory mechanism of morphogenesis in plant. In addition, we identified 562 potential miRNA gene loci on G. raimondii genome, all of which were supported by non-coding RNA-seq data. Using cotton EST and microarray data, we found 463 putative miRNA-target genes and most significant up/down-regulation occurred in 10-20 days post anthesis (DPA), indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. Our study have enhanced the accuracy and diversity of the assembled G. raimondii genome and also provided better understanding of plant ribogenome.