Transcriptome Bioinformatical Analysis of Vertebrate Stages of Schistosoma japonicum Reveals Alternative Splicing Events

Abstract

Alternative splicing is a molecular process that contributes greatly to the diversification of proteome and to gene functions. Understanding the mechanisms of stage-specific alternative splicing can provide a better understanding of the development of eukaryotes and the functions of different genes. Schistosoma japonicum is an infectious blood-dwelling trematode with a complex lifecycle that causes the tropical disease schistosomiasis. In this study, we analyzed the transcriptome of Schistosoma japonicum to discover alternative splicing events in this parasite, by applying RNA-seq to cDNA library of adults and schistosomula. Results were validated by RT-PCR and sequencing. We found 11,623 alternative splicing events among 7,099 protein encoding genes and average proportion of alternative splicing events per gene was 42.14%. We showed that exon skip is the most common type of alternative splicing events as found in high eukaryotes, whereas intron retention is the least common alternative splicing type. According to intron boundary analysis, the parasite possesses same intron boundaries as other organisms, namely the classic “GT-AG” rule. And in alternative spliced introns or exons, this rule is less strict. And we have attempted to detect alternative splicing events in genes encoding proteins with signal peptides and transmembrane helices, suggesting that alternative splicing could change subcellular locations of specific gene products. Our results indicate that alternative splicing is prevalent in this parasitic worm, and that the worm is close to its hosts. The revealed secretome involved in alternative splicing implies new perspective into understanding interaction between the parasite and its host.

Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing

“…In accordance with previous studies, SE is the most prevalent AS event, while RI is the least prevalent AS event in Epi and IMMC tumor samples ( 21 , 22 ). A total of 272 genes demonstrated alternative splicing in Epi and IMMC tumor samples, and this may be an indication of the important roles of those genes in the progression of NSCLC.…”

Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis

“…It is known that AS within the same species can be affected by developmental stage, tissue type, and growth conditions. Indeed, a higher AS percentage was obtained in schistosomulum and adult stages of S. japonicum ( Wang et al, 2015 ), compared with the AS percentage in the adult stage only ( Piao et al, 2014 ). Our estimate of AS events in Echinococcus species could be underestimated, since the parasite experiences several distinct environments during its complex life cycle, yet we only sequenced samples for one stage.…”

De novo transcriptomic analysis of the female and male adults of the blood fluke Schistosoma turkestanicum

“…NGS technology, such as Solexa/Illumina platforms, has dramatically improved the efficiency of gene discovery, and is particularly suited to transcriptomics of distinct animal and plant taxa [ 10 – 13 ]. To date, many trematode transcriptomes have been sequenced using the NGS technology, such as Fascioloides magna [ 14 ]; Clonorchis sinensis [ 15 ]; Eurytrema pancreaticum [ 16 ], Schistosoma japonicum [ 17 ], Schistosoma mansoni [ 18 ], Schistosoma haematobium [ 19 ], Opisthorchis felineus [ 20 ], Paramphistomum cervi [ 21 ] and Fasciola hepatica [ 22 ]. In spite of the availability of advances in sequencing technologies and bioinformatic methods, there is still a paucity of knowledge of the complete transcriptome for this zoonotic fluke S. turkestanicum .…”