Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.

ABSTRACT: Next-generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are align

SUBMITTER: Ockendon NF 

PROVIDER: S-EPMC4982090 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature