Hu Hongyin, Yang Wenlu, Zheng Zeyu, Niu Zhimin, Yang Yongzhi, Wan Dongshi, Liu Jianquan, Ma Tao
State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Front Genet. 2020 Feb 7;11:48. doi: 10.3389/fgene.2020.00048. eCollection 2020.
Poplars are worldwidely cultivated with ecologically and economically important value. var. (= . ) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to its rapid growth, erect stems, and high biomass production. However, the full-length messenger RNA (mRNA) sequences and complete structure of var. remain unclear. In this study, using single-molecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of var. , to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) sites were identified, with two or more APA sites observed in 2,212 genes. Our transcriptome data provided the full-length sequences and gene isoforms of transcripts for var. , which will be helpful in improving our understanding for the genome annotation and gene structures of var. .
杨树在全球范围内广泛种植，具有重要的生态和经济价值。胡杨变种（= ）是中国西北干旱地区农田防护林体系的主要树种，因其生长迅速、树干挺直且生物量产量高。然而，胡杨变种的全长信使核糖核酸（mRNA）序列和完整结构仍不清楚。在本研究中，我们使用单分子实时（SMRT）和下一代高通量测序（NGS）平台，对胡杨变种的叶、根、木质部和韧皮部的转录本进行测序，以获得全长mRNA转录本并注释其完整结构。总共鉴定出86,327条映射的全长非嵌合（FLNC） reads，发现了705个以前未注释的基因座、3,410个长链非编码RNA（lncRNA）和174个融合基因。在7,536个基因中检测到可变剪接（AS）事件，其中4,652个基因有多个AS事件。总共鉴定出10,213个可变聚腺苷酸化（APA）位点，在2,212个基因中观察到两个或更多的APA位点。我们的转录组数据提供了胡杨变种转录本的全长序列和基因异构体，这将有助于增进我们对胡杨变种基因组注释和基因结构的理解。
