Characterization of Liaoning Cashmere Goat Transcriptome: Sequencing, De Novo Assembly, Functional Annotation and Comparative Analysis

Abstract

BackgroundLiaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology.ResultsTranscriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51%) unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17%) unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes.ConclusionThe transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

Genomic analysis of host – Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways

“…Since annotated reference sequence of Capra hircus is unavailable, an integrated, non-redundant and well-annotated reference sequence of Bos taurus was used for further analysis. Bos taurus reference genome was earlier used for comparative analysis and functional annotation of goat transcriptome by several groups [ 15 - 17 ]. Also, the average sequence identity between these two species was estimated to be 82.79%.…”

Comparative and temporal transcriptome analysis of peste des petits ruminants virus infected goat peripheral blood mononuclear cells

“…Capra hircus genome is not well annotated therefore the well-defined B. taurus reference genome was used for mapping reads using TopHat version 2.0.7 (Kim et al, 2013). Bos taurus reference genome has been previously used by many groups for analyzing the goat transcriptome (Liu et al, 2013;Fontanesi et al, 2010). The mapped reads were then assembled using cufflinks, which quantifies the gene expression in terms of FPKM.…”

Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)

“…In recent years, the characteristics of cashmere fiber have received special attention in that they play an obvious role in cashmere quality. Several studies indicated that coding and noncoding genes were associated with the regulation of cashmere growth [3][4][5] . In addition, several important pathways have been demonstrated to be related to the formation of cashmere fiber [6][7][8] , for instance, Wnt, NF-κB, Shh, Notch and other signaling pathways [9][10][11][12][13] .…”