A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.

ABSTRACT: De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental goals. In this study, we explore the utility of 454 and Illumina sequences for de novo transcriptome assembly and downstream RNA-Seq applications in a reproductive gland from a non-model bird species, the Japanese quail (Coturnix japonica). Four transcriptomes composed of either pure 454 or Illumina reads or mixtures of read types were assembled and evaluated for the same cost. Illumina assemblies performed best for de novo transcriptome characterization in terms of contig length, transcriptome co

SUBMITTER: Finseth FR 

PROVIDER: S-EPMC4184788 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature