Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)
Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)
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DOI：
10.1111/tpj.13597
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发表时间：
2017-08-01
期刊：
影响因子：
7.2
通讯作者：
Gu, Lianfeng
中科院分区：
文献类型：
--
作者：
Wang, Taotao;Wang, Huiyuan;Gu, Lianfeng
毛竹（Phyllostachys edulis）是世界上传播最快的植物之一，部分原因是其发达的根茎系统。然而，竹鞭系统发育的转录后机制尚未得到全面的研究。因此，我们使用单分子长读段测序技术和多聚腺苷酸化位点测序（PAS-seq）的组合来重新注释竹子基因组，并确定基因组范围内的选择性剪接（AS）和选择性多聚腺苷酸化（阿帕）在根茎系统。总共分析了145522个映射的全长非嵌合（FLNC）读段，纠正了2241个错误注释的基因，并鉴定了8091个以前未注释的基因座。值得注意的是，超过42 280个不同的剪接异构体来自128 667个含内含子的全长FLNC读段，包括大量的AS事件与根茎系统。此外，我们还从11 450个基因中鉴定了25 069个多聚腺苷酸化位点，其中6311个具有阿帕位点。对内含子多聚腺苷酸化的进一步分析表明，LTR/Gypsy和LTR/Copia是内含子多聚腺苷酸化区域内的两个主要转座元件。此外，本研究提供了一个定量图谱的聚（A）的使用。几百个差分多聚（A）的网站在根茎根系统进行了鉴定。两者合计，这些结果表明，转录后调控可能有潜在的地下根茎根系统中的重要作用。
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 reannotate 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.