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.
Tipo de recurso
artículo
Estado
Versión publicada
Año de publicación
2013
País
Argentina
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio
CONICET Digital (CONICET)
Descripción
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.
Idioma
inglés
OAI Identifier
oai:ri.conicet.gov.ar:11336/19361
Enlace del recurso
http://hdl.handle.net/11336/19361
Nivel de acceso
Acceso abierto
Materia
Normalized ESTs
Allele clustering
Yellow starthistle
Invasive species
454 GS FLX Titanium
Genética y Herencia
Ciencias Biológicas
CIENCIAS NATURALES Y EXACTAS