Methodological aspects of read mapping and assembly of transcriptomes derived from the brain tissue samples of Rattus norvegicus

Autor: N. N. Dygalo, P. N. Menshanov
Rok vydání: 2015
Předmět:
Zdroj: Russian Journal of Genetics: Applied Research. 5:401-406
ISSN: 2079-0600
2079-0597
DOI: 10.1134/s2079059715040097
Popis: Identification of all transcripts expressed in the sample and quantification of transcript levels are two major objectives of each transcriptome research study. These objectives are particularly challenging in the case of CNS transcriptomes, since the alternative splicing is widespread in the brain. This paper defines and analyzes several problems associated with the read mapping and the subsequent assembly of transcriptomes derived from samples of CNS tissue, in particular: an unambiguous read identification, the read size, and incomplete reference annotations available for both model and nonmodel species. It was shown that the relative abundance of interexonic reads in the transcriptomes derived from CNS tissues is lower than in those derived from nonCNS tissues in case of identical procedures of the read sequencing, the genomic mapping, and transcriptome assembly are applied. The underrepresentation of interexonic reads in the transcriptomes derived from CNS vs. nonCNS tissues appears to be indicative of the existence of a large number of transcripts with novel sites of splicing not yet annotated. The cost-benefit analysis supports the superiority of sequencing technologies that generate reads with lengths ≥75 bp. For genomic mapping of reads and subsequent transcriptome assembly, it is advisable to use genomic annotations that include both known and ab initio predicted transcripts, such as Ensemble transcriptome annotations.
Databáze: OpenAIRE
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