Abstract
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.
Highlights
Poplars (Populus spp.) are widely used as a model system for tree biology research due to their rapid growth, ease of cloning and genetic transformation, moderate genome size, and extensive genetic diversity (Bradshaw et al, 2000; Jansson and Douglas, 2007)
Six single molecular real-time (SMRT) cells generated a total of 121,487, 138,596, and 60,387 reads of inserts (ROIs) from these three libraries respectively, the length distribution of which were consistent with their expected insert size (Table 1; Figure S2)
Low-quality sequences, and short sequences (< 50 bp), a total of 319,689 sub-reads were remained, and more than 74% (235,627) of them were identified as full-length non-chimeric (FLNC) reads with the entire transcript region from the 5' to the 3' end based on the inclusion of barcoded primers and the 3' poly(A) tails
Summary
Poplars (Populus spp.) are widely used as a model system for tree biology research due to their rapid growth, ease of cloning and genetic transformation, moderate genome size, and extensive genetic diversity (Bradshaw et al, 2000; Jansson and Douglas, 2007). Recent researches have shown that the post-transcriptional regulation including alternative splicing (AS) and alternative polyadenylation (APA) contribute significantly to enhance transcriptome diversity in eukaryotic organisms (Reddy, 2007; Kalsotra and Cooper, 2011; Elkon et al, 2013) This transcriptome complexity plays an important role in regulating gene expression during development or in responses to environmental stress (Barbazuk et al, 2008; Chamala et al, 2015; Sun et al, 2016). The identification of full-length splice isoforms, as well as accurate and complete annotation of genome are essential for a deep understanding of the transcriptome complexity and its potential role in gene regulation
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