Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

By J. Cristobal Vera, C. Wheat, H. Fescemyer, M. Frilander, D. Crawford, Ilkka Hanski, James H. Marden. Molecular Ecology, 2008

725 citations recorded by the source corpus.

Subfields: Cellular and Molecular Neuroscience, Genetics

View Paper: https://www.semanticscholar.org/paper/58ca04dfd6c18754cf98ed49f4c3fc429a375013

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In Cellular and Molecular Neuroscience

In Genetics

Citations in the corpus

Genomics of Origin, Domestication and Evolution of Phaseolus vulgaris (2014, background): “These provide powerful tools for the understanding of genome variations in crop species at the DNA, RNA and protein levels, and particularly for nonmodel plant species (Vera et al. 2008).”
What Role Does Heritable Epigenetic Variation Play in Phenotypic Evolution? (2010, background): “The light quality triggers an elongation response and allows for competitive growth in plants from open habitats, whereas plants from shaded environments do not respond as strongly, since they will never grow taller than the canopy plants (Dudley and Schmitt 1995, Donohue et al. 2000, Weinig 2000).”
Adapting to climate change: a perspective from evolutionary physiology (2010, background): “…it has also been widely documented in laboratory studies of responses to environmental temperature and water availability (e.g. Bennett et al. 1992, Cavicchi et al. 1995, Bull et al. 2000, Gibbs et al. 2003, Bubliy & Loeschcke 2005, Driessen et al. 2007, Sørensen et al. 2007, Vera et al. 2008).”
Applications of next-generation sequencing technologies in functional genomics. (2008, methodology): “Further, unlike the shorter reads generated using the Illumina or SOLiD sequencers, the length of the 454 reads allows for interpretation of sequences generated from species lacking a genome sequence or extensive transcriptome sequences for comparison (e.g., [66]).”
Applications of next generation sequencing in molecular ecology of non-model organisms (2011, background): “…genome assembly Reference Wasp (Polistes metricus) 454 X X X Toth et al., 2007 Glanville fritillary butterfly (Melitaea cinxia) 454 X X X X Vera et al., 2008; Wheat, 2010 Garden pea (Pisum sativum) 454 X Bräutigam et al., 2008 Bigmouth bass (Micropterus salmoides) 454 X Garcia-Reyero et…”
Optimization of de novo transcriptome assembly from next-generation sequencing data. (2010, methodology): “…reads have been considered difficult (Schuster 2008), and researchers working on non-model organisms have often turned to the more expensive longer sequence reads (250–450 bp) obtained by the 454 Life Sciences (Roche) technology (Margulies et al. 2005; e.g., Vera et al. 2008; Hale et al. 2009).”
Phylogeography's past, present, and future: 10 years after Avise, 2000. (2010, background): “As genomic data become available for non-model organisms (Vera et al., 2008), comparative phylogeographic studies will allow identification of different locus-specific divergent selection patterns (Ellegren and Sheldon, 2008; Luikart et al., 2003; MacCallum and Hill, 2006) between pairs of…”
Perspective: conservation genetics enters the genomics era (2010, methodology): “The researchers used 454 pyrosequencing to study hundreds of thousands of expressed sequence tags (ESTs) in samples from a metapopulation in Finland (Vera et al. 2008), and integrated the genomic information both with field data on individual dispersal and with physiological parameters related to fl”