The Plant Journal:福建农大顾连峰与马留银课题组发表毛竹研究成果
2017年5月10日，国际植物学权威期刊《The plant Journal》在线发表了福建农林大学海峡联合研究院林学中心顾连峰课题组与马留银课题组合作题为“Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)”的文章,全面解析了选择性拼接和选择性多聚腺苷酸化在毛竹地下茎组织生长发育中的调控。林学中心研究生王涛涛、王汇源及蔡大伟为共同第一作者，马留银副教授与顾连峰教授为共同通讯作者。
毛竹是生长最快的植物之一，福建是毛竹的主要产区，研究其快速生长机制具有重要的理论意义和实际应用价值。毛竹地下茎系统运输养分是茎秆快速生长的重要保障，但其生长发育的调控机制尚未开展研究。
研究采用PacBio第三代单分子测序，并结合rna-seq和PAS-seq (polyadenylation site sequencing)，对毛竹地下系统几个关键组织的选择性拼接和选择性多聚腺苷酸化进行了全面解析和量化，发现二者相互关联调控转运蛋白、转录因子、纤维素合成酶及翻译调节因子等相关基因，调控毛竹地下茎不同组织生长发育。该研究对毛竹基因进行重注释，并发现一批新的编码基因及非编码RNA，并对富含DNA甲基化的转座子侧翼选择性多聚腺苷酸化的表观遗传学调控进行了初步的探索，该成果为后续研究毛竹转录后调控及表观遗传学与快速生长的关系奠定了重要的前期基础。
原文链接：
Comprehensive profiling of rhizome-associated alteRNAtive splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis
原文摘要：
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 mechanism has not been comprehensively studied for the development of rhizome system in bamboo. 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 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. Several hundreds of differential poly(A) sites in rhizome-root system were identified. Taken together, these results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.
作者：顾连峰与马留银
