HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species.

ABSTRACT:

Background

Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how expression of parental gene copies (homeologs) responds following genome merger. High throughput RNA sequencing now makes this analysis technically feasible, but tools to determine homeolog expression are still in their infancy.

Results

Here we present HyLiTE - a single-step analysis to obtain tables of homeolog expression in a hybrid or allopolyploid and its parent species directly from raw mRNA sequence files. By implementing on-the-fly detection of diagnostic parental polymorphisms, HyLiTE can perform SNP calling and read classification simultaneously, thus allow

SUBMITTER: Duchemin W 

PROVIDER: S-EPMC4300824 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature