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

• Autores: Dlugosch, Katrina M.; Lai, Zhao; Bonin, Auélie; Hierro, Jose Luis; Rieseberg, Loren H.
• Año de publicación: 2013
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: Normalized ESTs; Allele clustering; Yellow starthistle; Invasive species; 454 GS FLX Titanium
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

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 genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.
Fil: Dlugosch, Katrina M.. University of British Columbia; Canadá
Fil: Lai, Zhao. Indiana University; Estados Unidos
Fil: Bonin, Auélie. Indiana University; Estados Unidos
Fil: Hierro, Jose Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; Argentina
Fil: Rieseberg, Loren H.. University of British Columbia; Canadá. Indiana University; Estados Unidos