A comprehensive rat transcriptome built from large scale RNA-seq-based annotation

Abstract

The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

“…Notably, the testis possessed the most unique mRNAs and lncRNAs at the gene and transcript level ( Figure 3C ), consistent with the patterns reported in humans ( Djureinovic et al, 2014 ). Many of the tree shrew testis-specific genes were involved in spermatogenesis (Supplementary Figure S2), as also reported in rats ( Ji et al, 2020 ).…”

“…Previous studies using next-generation sequencing (NGS) based on RNA-seq and long-read isoform sequencing (ISO-seq) have revealed the complexity and characteristics of eukaryotic transcriptomes ( Chen et al, 2017 ). Using ortholog and de novo annotations ( Garber et al, 2011 ; Yandell & Ence, 2012 ), transcriptome sequencing has been widely used to annotate the genomes of plants ( Purugganan & Jackson, 2021 ; Wang et al, 2019 ), model animals ( Ji et al, 2020 ; Nudelman et al, 2018 ; Zhang et al, 2020a ), and livestock ( Beiki et al, 2019 ; Foissac et al, 2019 ). In this study, we aimed to provide a more comprehensive tree shrew genome annotation using a wide range of transcriptome sequencing data.…”

Alternative Animal Models of Aging Research

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CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure

“…Within transcriptome reference sets, such as the cDNA databases available from Ensembl representing various species [5], or those that are de novo assembled from short-read RNA-Seq data, non-chimeric sequences are direct representations of transcribed genes, while artificially generated chimeric ones are mosaics of two or more pieces of DNA incorrectly pieced together. The latter occurring during library preparation [6,7], or during the de novo assembly process [8,9], where there is a requirement to traverse paths across graphs constructed from read data that ranges in complexity depending on the nature of the gene families being represented [10][11][12]. Chimeras also occur at a genomic level during de novo assembly, such as when inferring haplotypes [13,14], but the causes, and consequences, at a genomic level are different [15][16][17].…”

“…Contigs produced by genomic assemblers are often utilized within the scope of population studies, in conjunction with mapping of whole genome read data, in order quantify and compare nucleotide variation or to annotate coding regions [ 20 , 21 ]. In transcriptomics, the goal is to quantify tens of thousands of expressed genes, and gene isoforms, that differ in length and expression pattern [ 12 , 22 ]. Differences such as these have lead to a distinction in how algorithms, and data structures, are optimized for either genomic or transcriptomic level assembly.…”