Table_1_Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing.docx

Poplars are worldwidely cultivated with ecologically and economically important value. Populus alba var. pyramidalis (= P. bolleana) 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 P. alba var. pyramidalis 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 P. alba var. pyramidalis, 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 P. alba var. pyramidalis, which will be helpful in improving our understanding for the genome annotation and gene structures of P. alba var. pyramidalis.

杨树在全球范围内广泛栽培，兼具重要的生态与经济价值。新疆杨（Populus alba var. pyramidalis，又名P. bolleana）因生长迅速、树干通直且生物量可观，是中国西北干旱区农田防护林体系的主栽树种。然而，目前针对新疆杨的全长信使RNA（messenger RNA，简称mRNA）序列及完整基因结构的研究仍存在空白。本研究依托单分子实时（SMRT）测序与下一代高通量测序（NGS）平台，对新疆杨的叶、根、木质部及韧皮部的转录本进行测序，旨在获取其全长mRNA转录本并注释完整基因结构。本次研究共鉴定得到86327条比对上的全长非嵌合（FLNC）读段，发现705个此前未被注释的基因座、3410个长链非编码RNA（lncRNAs）以及174个融合基因。在7536个基因中检测到可变剪接（AS）事件，其中4652个基因存在多种可变剪接事件。此外，共鉴定到10213个可变多聚腺苷酸化（APA）位点，其中2212个基因拥有2个及以上的APA位点。本研究获得的转录组数据提供了新疆杨的全长序列及转录本异构体，将有助于深化对新疆杨基因组注释及基因结构的认知。