ABSTRACT: Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation reveals in moso bamboo (Phyllostachys edulis)
Project description:Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional regulation mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used single-molecule long-read sequencing technology to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system. In total, 145,522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2,241 mis-annotated genes and identification of 8,091 previously unannotated loci. Markedly, more than 42,280 contiguous exon connectivity were derived from full-length splicing isoforms, including a large number of AS events that associated with rhizome systems. In addition, we characterized 25,069 polyadenylation sites from 11,450 genes, 6,311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements (TEs) within the intronic polyadenylation region. Furthermore, this study provided a quantitative altas of poly(A) usage and identified several hundreds of differential poly(A) sites in rhizome-root system using a combination of polyadenylation site sequencing (PAS-seq) and PacBio reads. Taken together, these results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.
Project description:We adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.
Project description:Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.), ) is one of the most importantessential economic bamboo species in China. However, the woods quality and yield of bamboo shoots were significantly threatened by diverse environmental conditions. significantly threaten the quality of wood and yield of bamboo shoots. In this study, to explore the molecular mechanism of abiotic stress response, we report the RNA-seq analyses of mosoMoso bamboo treated with drought, salt, SA and ABA at three -time courses. A total of 224.4 Gb clean data were generate in to explore the molecular mechanism of the abiotic stress response. The full-length transcriptome sequencing of these four treatments generated a total of 224.4 Gb data after quality trimming, and approximately 5.83Gban average of 6.615 Gb clean data were per sample was generated in per sample. The comparative analyses of the generated transcriptome data in this study will provide a valuable resource for identifying regulatory genes and potential pathways involved in various abiotic stresses in mosoMoso bamboo.
Project description:Moso bamboo is a fast-growing bamboo species with high economic, social and cultural value. The method of transplanting moso bamboo seedlings for afforestation has become a more economical and effective method. The effect of light on the growth of plant seedlings is mainly reflected in the regulation of different light quality on the growth and development of seedlings, including light morphogenesis, photosynthesis and secondary metabolites. Therefore, studying the effects of specific wavelength light on the physiology and proteome of moso bamboo seedlings will play an important role in growing seedlings and seed cultivation of moso bamboo. Here, moso bamboo seeds were germinated in the dark and then were transferred to the blue and red-light conditions. After 14 days, we observed the effects of different light treatments on the growth and development of seedlings, and then compared and analyzed their proteome.
