Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Abstract

Since transcriptome analysis provides genome-wide sequence and gene expression infor- mation, transcript reconstruction using RNA-Seq sequence reads has become popular dur- ing recent years. For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding to coding or non-coding, but expressed, part of genome. In spite of immense potential of RNA-Seq–based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures to be taken in a step-by-step manner. In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) qual- ity check and pre-processing of raw reads, (ii) the pros and cons of de novo transcriptome assemblers, (iii) generating non-redundant transcript data, (iv) current quality assessment tools for de novo transcriptome assemblies, (v) approaches for transcript abundance and differential expression estimations and finally (vi) further mining of transcriptomic data for particular biological questions. Our intention is to provide an overview and practical guidance for choosing the appropriate approaches to best meet the needs of researchers in this area and also outline the strategies to improve on-going projects.