Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis.

ABSTRACT: Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11-430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference

SUBMITTER: Dlugosch KM 

PROVIDER: S-EPMC3564996 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature