Transcriptome profiling of seed developmental stages in Arabidopsis thaliana

Abstract

Seed dormancy and germination are the physiological phenomenon by a capacity between dormancy or germination to grow as the whole plants. These are determined by the narrow range of environments and hormones such as Abscisic acid (ABA) and Gibberellic acid (GA). Also, many studies have found the gene related to seed development such as Delay of germination1 (DOG1), in Arabidopsis thaliana. Recently, Non-coding RNA and long non-coding RNA were identified as the regulators in animals or plants. Using strand-specific RNA sequencing data in this study, I performed that differential expression analysis and gene correlation analysis with Arabidopsis thaliana seed samples in developmental stages. 6121 Protein-coding genes were up-regulated in After-ripening germination seeds, while 2636 protein-coding genes were down-regulated in Freshly harvested seeds. I classified protein-coding genes in developmental stages through expression pattern analysis and GO enrichment analysis. Most genes correlated to each marker gene. I identified 1199 novel lncRNAs in Arabidopsis thaliana seed. Of those, 417 lncRNAs were expressed with high abundance. 366 lncRNAs were expressed the opposite direction of protein-coding genes and correlated or anti-correlated with those. My study provides as guides to measure the criterion for dormancy and germination in seed developmental stages and as the fundamental data to identify the biological mechanism between protein-coding gene and long non-coding RNA in the cell.