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Plant J. 2017 Aug;91(4):684-699. doi: 10.1111/tpj.13597. Epub 2017 Jun 27.

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

Wang T1,2, Wang H1,2, Cai D1,2, Gao Y1, Zhang H1, Wang Y1, Lin C3, Ma L1, Gu L1.

Author information

1
Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
2
College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
3
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.

Abstract

Moso 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.

KEYWORDS:

Phyllostachys edulis; alternative polyadenylation; alternative splicing; rhizome system; single molecular real-time (SMRT) sequencing

PMID:
28493303
DOI:
10.1111/tpj.13597
[Indexed for MEDLINE]
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