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dc.contributor.author
Dlugosch, Katrina M.
dc.contributor.author
Lai, Zhao
dc.contributor.author
Bonin, Auélie
dc.contributor.author
Hierro, Jose Luis
dc.contributor.author
Rieseberg, Loren H.
dc.date.available
2017-06-30T21:53:54Z
dc.date.issued
2013-02
dc.identifier.citation
Dlugosch, Katrina M.; Lai, Zhao; Bonin, Auélie; Hierro, Jose Luis; Rieseberg, Loren H.; Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis; Genetics Soc Am; G3: Genes, Genomes, Genetics; 3; 2; 2-2013; 359-367
dc.identifier.uri
http://hdl.handle.net/11336/19361
dc.description.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 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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Genetics Soc Am
dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by/2.5/ar/
dc.subject
Normalized Ests
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Allele Clustering
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Yellow Starthistle
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Invasive Species
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454 Gs Flx Titanium
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Genética y Herencia
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Ciencias Biológicas
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
dc.title
Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2017-06-29T13:57:42Z
dc.identifier.eissn
2160-1836
dc.journal.volume
3
dc.journal.number
2
dc.journal.pagination
359-367
dc.journal.pais
Estados Unidos
dc.journal.ciudad
Bethesda
dc.description.fil
Fil: Dlugosch, Katrina M.. University of British Columbia; Canadá
dc.description.fil
Fil: Lai, Zhao. Indiana University; Estados Unidos
dc.description.fil
Fil: Bonin, Auélie. Indiana University; Estados Unidos
dc.description.fil
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
dc.description.fil
Fil: Rieseberg, Loren H.. University of British Columbia; Canadá. Indiana University; Estados Unidos
dc.journal.title
G3: Genes, Genomes, Genetics
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://www.g3journal.org/content/3/2/359.long
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1534/g3.112.003871
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