Identification and characterization of alternative splicing in parasitic nematode transcriptomes

Particle and Fibre Toxicology

Makedonka Mitreva¹  Bruce A Rosa²  Samantha N McNulty²  Sahar Abubucker² 

[1] Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA;The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA

关键词: Next-generation sequencing;    Alternative splicing;    Transcriptomes;    Parasitic nematodes;   

Others  :  807455
DOI  :  10.1186/1756-3305-7-151

 received in 2014-01-17, accepted in 2014-03-14,  发布年份 2014

【 摘 要 】

Background

Alternative splicing (AS) of mRNA is a vital mechanism for enhancing genomic complexity in eukaryotes. Spliced isoforms of the same gene can have diverse molecular and biological functions and are often differentially expressed across various tissues, times, and conditions. Thus, AS has important implications in the study of parasitic nematodes with complex life cycles. Transcriptomic datasets are available from many species, but data must be revisited with splice-aware assembly protocols to facilitate the study of AS in helminthes.

Methods

We sequenced cDNA from the model worm Caenorhabditis elegans using 454/Roche technology for use as an experimental dataset. Reads were assembled with Newbler software, invoking the cDNA option. Several combinations of parameters were tested and assembled transcripts were verified by comparison with previously reported C. elegans genes and transcript isoforms and with Illumina RNAseq data.

Results

Thoughtful adjustment of program parameters increased the percentage of assembled transcripts that matched known C. elegans sequences, decreased mis-assembly rates (i.e., cis- and trans-chimeras), and improved the coverage of the geneset. The optimized protocol was used to update de novo transcriptome assemblies from nine parasitic nematode species, including important pathogens of humans and domestic animals. Our assemblies indicated AS rates in the range of 20-30%, typically with 2-3 transcripts per AS locus, depending on the species. Transcript isoforms from the nine species were translated and searched for similarity to known proteins and functional domains. Some 21 InterPro domains, including several involved in nucleotide and chromatin binding, were statistically correlated with AS genetic loci. In most cases, the Roche/454 data explored in this study are the only sequences available from the species in question; however, the recently published genome of the human hookworm Necator americanus provided an additional opportunity to validate our results.

Conclusions

Our optimized assembly parameters facilitated the first survey of AS among parasitic nematodes. The nine transcriptome assemblies, their protein translations, and basic annotations are available from Nematode.net as a resource for the research community. These should be useful for studies of specific genes and gene families of interest as well as for curating draft genome assemblies as they become available.

【 授权许可】

   
2014 Abubucker et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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