Limits...
We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects.

Oppenheim SJ, Baker RH, Simon S, DeSalle R - Insect Mol. Biol. (2014)

Bottom Line: Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa.Increasingly, studies are using a comparative approach (across species, sexes and life stages) that examines the transcriptional basis of phenotypic diversity within an evolutionary context.In the present review, we summarize much of this research, focusing in particular on three critical aspects of insect biology: morphological development and plasticity; physiological response to the environment; and sexual dimorphism.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.

Show MeSH
(A) Compilation of studies using transcriptomics in non-model (i.e. non Droosophila melanogaster) insects. The graph is a cumulative count of number of insect transcriptomes analyzed by year since 2001. Blue indicates clone and sequence expressed sequence tag studies, red indicates microarray studies and green inidicates the number of RNA-Seq studies done with next generation sequencing. (B) Bar graph showing the number of insect transcriptomes analyzed and the category of research the transcriptome was generated for.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383654&req=5

fig02: (A) Compilation of studies using transcriptomics in non-model (i.e. non Droosophila melanogaster) insects. The graph is a cumulative count of number of insect transcriptomes analyzed by year since 2001. Blue indicates clone and sequence expressed sequence tag studies, red indicates microarray studies and green inidicates the number of RNA-Seq studies done with next generation sequencing. (B) Bar graph showing the number of insect transcriptomes analyzed and the category of research the transcriptome was generated for.

Mentions: RNA-Seq (also known as whole-transcriptome shotgun sequencing) technology now permeates numerous fields in evolutionary biology and has been used to address questions concerning differential gene expression, phylogenetic relationships, gene creation and gene family evolution, rates of protein evolution, genotype–phenotype association, chromosome organization and the regulation of development. To quantify the escalation of studies examining insect transcriptomes we conducted a literature search using the terms ‘expressed sequence tags’ (‘EST’), ‘microarray’, ‘RNA-Seq’ and ‘transcriptome’. We excluded marker-based analyses such as phylogenomic and population genomic studies from our survey and instead focused on research that examines changes in transcriptional profiles associated with phenotypic differences. This search revealed that most branches of insect diversity research now use transcriptome analysis (Fig. 1). As shown in Fig. 2A, RNA-Seq technology has quickly supplanted previous genomic approaches (e.g. EST sequencing and microarray cDNA hybridization) as the preferred method to examine gene expression patterns.


We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects.

Oppenheim SJ, Baker RH, Simon S, DeSalle R - Insect Mol. Biol. (2014)

(A) Compilation of studies using transcriptomics in non-model (i.e. non Droosophila melanogaster) insects. The graph is a cumulative count of number of insect transcriptomes analyzed by year since 2001. Blue indicates clone and sequence expressed sequence tag studies, red indicates microarray studies and green inidicates the number of RNA-Seq studies done with next generation sequencing. (B) Bar graph showing the number of insect transcriptomes analyzed and the category of research the transcriptome was generated for.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383654&req=5

fig02: (A) Compilation of studies using transcriptomics in non-model (i.e. non Droosophila melanogaster) insects. The graph is a cumulative count of number of insect transcriptomes analyzed by year since 2001. Blue indicates clone and sequence expressed sequence tag studies, red indicates microarray studies and green inidicates the number of RNA-Seq studies done with next generation sequencing. (B) Bar graph showing the number of insect transcriptomes analyzed and the category of research the transcriptome was generated for.
Mentions: RNA-Seq (also known as whole-transcriptome shotgun sequencing) technology now permeates numerous fields in evolutionary biology and has been used to address questions concerning differential gene expression, phylogenetic relationships, gene creation and gene family evolution, rates of protein evolution, genotype–phenotype association, chromosome organization and the regulation of development. To quantify the escalation of studies examining insect transcriptomes we conducted a literature search using the terms ‘expressed sequence tags’ (‘EST’), ‘microarray’, ‘RNA-Seq’ and ‘transcriptome’. We excluded marker-based analyses such as phylogenomic and population genomic studies from our survey and instead focused on research that examines changes in transcriptional profiles associated with phenotypic differences. This search revealed that most branches of insect diversity research now use transcriptome analysis (Fig. 1). As shown in Fig. 2A, RNA-Seq technology has quickly supplanted previous genomic approaches (e.g. EST sequencing and microarray cDNA hybridization) as the preferred method to examine gene expression patterns.

Bottom Line: Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa.Increasingly, studies are using a comparative approach (across species, sexes and life stages) that examines the transcriptional basis of phenotypic diversity within an evolutionary context.In the present review, we summarize much of this research, focusing in particular on three critical aspects of insect biology: morphological development and plasticity; physiological response to the environment; and sexual dimorphism.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.

Show MeSH