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

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.

Plant ISOform sequencing database (PISO): a comprehensive repertory of full‐length transcripts in plants

“…Dear Editor, In higher eukaryotes, alternative splicing (AS) and alternative polyadenylation (APA) events can produce multiple transcript isoforms in the majority of genes, which significantly increase the protein-coding potential of a genome (Anvar et al, 2018;Pan et al, 2008). Different transcript isoforms might encode proteins with different functions or affect the mRNA stability and translational capacity, in some sense AS and APA events can dramatically increase the complexity and flexibility of the entire transcriptome and proteome (Feng et al, 2015;Li et al, 2017a;Wang et al, 2017a;Yang et al, 2016). Many databases contained AS events and transcripts in animals are available in some public resources such as ASTD and MAASE (Zheng et al, 2005), whereas there is no database containing full-length transcripts and AS events in plants up to now.…”

“…We employed three pipelines for analysing Iso-Seq data of the above three types of plant species (Figure 1a). Firstly, standard TAPIS pipeline was utilized for nine diploids with reference genomes (Abdelghany et al, 2016;Wang et al, 2017a); secondly, two extra steps, phasing and adjusting, were added into TAPIS pipeline for studying the four allopolyploid species owing to the large number of homoeologous genes from different sub-genomes (Wang et al, 2017b); thirdly, for analysing the other six species without reference genome, high-quality reads were mapped to a pseudo-genome generated by Cogent software .…”

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

“…Pacbio SMRT and RNA-seq (Levin et al, 2010) were performed using whole seedlings grown at different salt concentrations (0, 350, 500, and 800 mM NaCl), as described previously (T. Wang et al, 2017).…”

“…RT-PCR and qRT-PCR experiments were conducted as described in a previous study (T. Wang et al, 2017).…”

“…Li, Dai, Hu, Liu, & Kang, 2017; Sun et al, 2018; B. Wang et al, 2016; T. Wang et al, 2017; Xu et al, 2015).…”