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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.

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Phylogenetic tree showing the broad phylogenetic distribution of insect transcriptomes. Tree modified after Bugwood (http://wiki.bugwood.org/Main_Page). The number of transcriptomes for each insect order was compiled from the literature. Each order with transcriptomes generated independent of 1KITE (http://www.1kite.org) and surveyed as part of our literature search (key words: ‘transcriptome’, ‘RNA-Seq’, ‘microarray’, or ‘454’; November 2013) has a pie graph associated with it. The green (dark) section of the graph represents the number of species with transcriptomes generated for that order by 1KITE (http://www.1kite.org/downloads/1KITE_species.txt; November 2013). The blue (light) section represents the number of taxa with transcriptional studies done independently of the 1KITE initiative. The number in small font indicates the number of taxa slated for study by the 1KITE initiative. The number in large font represents the number of 1KITE species examined or slated for examination in a given order, where no studies independent of 1KITE have been done.
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fig01: Phylogenetic tree showing the broad phylogenetic distribution of insect transcriptomes. Tree modified after Bugwood (http://wiki.bugwood.org/Main_Page). The number of transcriptomes for each insect order was compiled from the literature. Each order with transcriptomes generated independent of 1KITE (http://www.1kite.org) and surveyed as part of our literature search (key words: ‘transcriptome’, ‘RNA-Seq’, ‘microarray’, or ‘454’; November 2013) has a pie graph associated with it. The green (dark) section of the graph represents the number of species with transcriptomes generated for that order by 1KITE (http://www.1kite.org/downloads/1KITE_species.txt; November 2013). The blue (light) section represents the number of taxa with transcriptional studies done independently of the 1KITE initiative. The number in small font indicates the number of taxa slated for study by the 1KITE initiative. The number in large font represents the number of 1KITE species examined or slated for examination in a given order, where no studies independent of 1KITE have been done.

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)

Phylogenetic tree showing the broad phylogenetic distribution of insect transcriptomes. Tree modified after Bugwood (http://wiki.bugwood.org/Main_Page). The number of transcriptomes for each insect order was compiled from the literature. Each order with transcriptomes generated independent of 1KITE (http://www.1kite.org) and surveyed as part of our literature search (key words: ‘transcriptome’, ‘RNA-Seq’, ‘microarray’, or ‘454’; November 2013) has a pie graph associated with it. The green (dark) section of the graph represents the number of species with transcriptomes generated for that order by 1KITE (http://www.1kite.org/downloads/1KITE_species.txt; November 2013). The blue (light) section represents the number of taxa with transcriptional studies done independently of the 1KITE initiative. The number in small font indicates the number of taxa slated for study by the 1KITE initiative. The number in large font represents the number of 1KITE species examined or slated for examination in a given order, where no studies independent of 1KITE have been done.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig01: Phylogenetic tree showing the broad phylogenetic distribution of insect transcriptomes. Tree modified after Bugwood (http://wiki.bugwood.org/Main_Page). The number of transcriptomes for each insect order was compiled from the literature. Each order with transcriptomes generated independent of 1KITE (http://www.1kite.org) and surveyed as part of our literature search (key words: ‘transcriptome’, ‘RNA-Seq’, ‘microarray’, or ‘454’; November 2013) has a pie graph associated with it. The green (dark) section of the graph represents the number of species with transcriptomes generated for that order by 1KITE (http://www.1kite.org/downloads/1KITE_species.txt; November 2013). The blue (light) section represents the number of taxa with transcriptional studies done independently of the 1KITE initiative. The number in small font indicates the number of taxa slated for study by the 1KITE initiative. The number in large font represents the number of 1KITE species examined or slated for examination in a given order, where no studies independent of 1KITE have been done.
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