Comprehensive profiling of rhizome‐associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)

• DOI: 10.1111/tpj.13597
• Publication Date: 2017-05-10T20:22:45Z
• Authors: Taotao Wang; Huiyuan Wang; Dawei Cai; Yubang Gao; Hangxiao Zhang; Yongsheng Wang; Chentao Lin; Liuyin Ma; Lianfeng Gu
• Keywords: Plant Biology & Botany; Bioinformatics and Computational Biology; Plant Biology; Poaceae; Polyadenylation; alternative splicing; alternative polyadenylation.; 03 medical and health sciences; Genetics; Phyllostachys edulis; Plant biology; 0303 health sciences; single molecular real-time (SMRT) sequencing; Human Genome; alternative polyadenylation; Molecular Sequence Annotation; DNA; Sequence Analysis, DNA; Biological Sciences; 15. Life on land; Introns; Alternative Splicing; Biochemistry and cell biology; rhizome system; Biochemistry and Cell Biology; Poly A; Sequence Analysis; Rhizome; Biotechnology

SummaryMoso bamboo (Phyllostachys edulis) represents one of the fastest‐spreading plants in the world, due in part to its well‐developed rhizome system. However, the post‐transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single‐molecule long‐read sequencing technology and polyadenylation site sequencing (PAS‐seq) to re‐annotate the bamboo genome, and identify genome‐wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full‐length non‐chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis‐annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron‐containing full‐length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome‐root system were identified. Taken together, these results suggest that post‐transcriptional regulation may potentially have a vital role in the underground rhizome‐root system.