The Transcriptome Analysis Of Trichinella Spiralis

Trichinellosis of human and other mammals was caused through the ingestion ofThichinella spiralis contaminated meat. T. spiralis is often referred as one of thelargest intracellular parasites that cause trichinellosis with an estimation of more than10million people infected world-wide. Infections by the parasite can cause clinicaldisease (trichinellosis) in humans that ranges from mild flu-like symptoms to severeinflammatory conditions, which in turn can lead to myocarditis, encephalitis anddeath.Transcriptome is the entire population of RNA transcripts in a species in aspecific developmental stage or physiological condition, which include mRNA,non-coding RNA, tRNA and rRNA. Unlike genome,the transcriptome can vary inrespoding to the internal and external enviromental changes. Thus a transcriptomerepresents a link between information encoded in DNA and phenotypes.Understanding the transcriptome is essential for interpreting the functional elementsof the genome and revealing the molecular constituents of cells and tissues. Here, weanalysed the transcriptome of the parasite Thichinella spiralis in its differentdevelopmental stages with an aim to understand the developmental biology of theparasite. The main results are as follows:1. The transcriptome of small non-coding RNAsSmall non-coding RNAs (sncRNAs) are a large group of small endogenousRNAs that have been widely identified in animals, plants and some viruses. They aregenerally21-23nucleotides in length, which guide various biological processesinvolving sequence-specific silencing through chromatin modification, mRNAdegradation, and translational repression. Based on their origins, structures, associatedproteins and biological roles, sncRNAs are divided into three general categories:miRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs), andpiwi-interacting RNAs (piRNAs). MiRNA and endo-siRNAs have been discovered indiverse animals and plants and considered to be the main sncRNAs for the regulationof gene expression, while piRNAs are found only in germlines in animals. In this study, we identified and analyzed the expression of miRNAs and endo-siRNAs inthree development stages of T. spiralis by using high through-put RNA sequencingtechniques. A total of21conserved miRNAs in13metazoan miRNA familis and213novel miRNAs were identified in the parasite. Some of the miRNAs showed clearstage-specific expression patterns, suggesting a potential regulatory function in thecorresponding developmental stages. The endo-siRNAs were mainly derived fromnatural antisense transcripts and transposible elements (TE). However, endo-siRNAsaccounted for only a minor proportion in the small RNA population identifed in theparasite. And there are no obviously differences in three developmental stages of theparasite.2. The transcriptome of mRNAs and differentially expressed gene of T. spiralisIn this study, we analyzed the global gene expression patterns in the threedevelopmental stages of T. spiralis using RNA-seq analysis. Almost60millionsequence tags were generated with the Illumina RNA-seq technology, producingexpression data for more than13,000genes, covering85%of the genome. Thetranscriptome analysis revealed thousands of differentially expressed genes of thegenome, and a panel of genes encoding functional proteins associated with parasiteinvasion and immuno-modulation were identified. Further, based on gene ontologicalanalysis, over4000genes were functionally categorized and biological pathways inthe three life cycle stage were elucidated. Thousands of novel exon and transcriptswere identified in three developmental stages. The totle number of novel exon andtranscripts in adult parasite (Ad), musule larvae (ML) and new-borne larvae (NBL)were8946and2502,8759and2616,8285and4659, respectively.3. mRNA alternative splicing in T. spiralisIt is the first time to identify the pehomenon of alternative splicing in T. spiralis.Alternative splicing is a widespread means of increasing protein diversity andregulating gene expression in eukaryotes. Since many alternative splicing events aretissue-specific, this process plays an important role in cellular differentiation andorganismal development. In this study, six categories except mutually exclusive exonssplicing were found in T. spiralis. Our RNA-seq analysis has identified3737putativenovel splicing events in2152genes in Ad,6125putative novel splicing events in 3076genes in ML and10996putative novel splicing events in4165genes in NBL.Thus alternative splicing events had been found in more than4000genes accountingfor30%of the total genes of T. spiralis.In summary, this study presents a first deep analysis of the transcriptome of T.spiralis, providing insight information of the parasite biology. Transcriptome analysiswill open a new avenue towards a final dissection of the parasite biology andhopefully facilitate the discovery of potential anti-parasitic drug targets.