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

Related in: MedlinePlus

Phylogeny of the Nap1 gene family depicting abundant gene expansion within stalk-eyed flies. Contig sequences homologous to Drosophila Nap1 were extracted from an assembly of a testes transcriptome for each stalk-eyed fly species except Teleopsis dalmanni whose sequence data was derived from a multi-tissue assembly (GenBank accession numbers: KM821168-KM821212). The maximum likelihood tree was generated in PhyML (Guindon and Gascuel 2003) using an LG + G model with 100 bootstrap replicates. Branches with bootstrap values >90 are indicated by an asterisk. Red marks on the branches denote putative duplication events. Gene expression values (FPKM) for each T. dalmanni paralogue are presented to the right of the tree. Tissue abbreviations: L,larva; H, adult head; F, female carcass (whole body with reproductive tissues removed); M, male carcass, O, ovaries; T, testes. Stalk-eyed fly generic abbreviations: D. meigenii, Diasemopsis meigenii; D. apicalis, Diopsis apicalis; E., Eurydiopsis; S., Sphyracephala; T., Teleopsis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig03: Phylogeny of the Nap1 gene family depicting abundant gene expansion within stalk-eyed flies. Contig sequences homologous to Drosophila Nap1 were extracted from an assembly of a testes transcriptome for each stalk-eyed fly species except Teleopsis dalmanni whose sequence data was derived from a multi-tissue assembly (GenBank accession numbers: KM821168-KM821212). The maximum likelihood tree was generated in PhyML (Guindon and Gascuel 2003) using an LG + G model with 100 bootstrap replicates. Branches with bootstrap values >90 are indicated by an asterisk. Red marks on the branches denote putative duplication events. Gene expression values (FPKM) for each T. dalmanni paralogue are presented to the right of the tree. Tissue abbreviations: L,larva; H, adult head; F, female carcass (whole body with reproductive tissues removed); M, male carcass, O, ovaries; T, testes. Stalk-eyed fly generic abbreviations: D. meigenii, Diasemopsis meigenii; D. apicalis, Diopsis apicalis; E., Eurydiopsis; S., Sphyracephala; T., Teleopsis.

Mentions: Another critical feature of transcriptome studies is that they facilitate the identification of lineage-specific genes that have no direct homologue in other insect groups. Novel genes can arise in many ways (e.g. gene duplication, lateral gene transfer, de novo gene creation from noncoding regions of DNA) and may rapidly acquire adaptive functional roles (Ranz & Parsch, 2012; Chen et al., 2013). Studies in Drosophila have shown that novel genes represent a substantial component of male-biased gene expression and play a critical role in spermatogenesis. A recent study in stalk-eyed flies (Baker et al., 2012) highlights the ability of RNA-Seq to uncover novel genetic diversity associated with reproductive proteins. More recently, testes transcriptomes from additional stalk-eyed fly species have been analysed, and numerous lineage-specific novel genes have been found (see Fig. 3 for an example). The gene family represented in Fig. 3 comprises homologues of the D. melanogaster gene, Nucleosome assembly protein 1 (Nap1), an important histone chaperone gene that is expressed in the testes (Kimura, 2013). In Drosophila and the mosquito species, Nap1 is present as a single homologue, while stalk-eyed fly species exhibit as many as nine paralogues of Nap1. Overall, the tree suggests there have been at least 14 duplications of the Nap1 gene within the family, and it appears these new genes function primarily in spermatogenesis. Of the seven paralogous copies in T. dalmanni, the one with the closest homology to the D. melanogaster Nap1 protein is expressed ubiquitously throughout the body, while the other six copies exhibit testes-specific gene expression (Fig. 3). DNA undergoes dramatic condensation during spermatogenesis involving the replacement of histones with protamines (White-Cooper, 2010), so it is possible these new Nap1 proteins play some role in this process. Overall, the use of transcriptomes for gene discovery has some inherent limitations because variation in expression levels across taxa will impact their representation in any gene family analysis. Even with this caveat, transcriptome surveys are an incredibly powerful tool for exploring the genetic diversity that is unique, and therefore of particular relevance, to non-model organism groups.


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)

Phylogeny of the Nap1 gene family depicting abundant gene expansion within stalk-eyed flies. Contig sequences homologous to Drosophila Nap1 were extracted from an assembly of a testes transcriptome for each stalk-eyed fly species except Teleopsis dalmanni whose sequence data was derived from a multi-tissue assembly (GenBank accession numbers: KM821168-KM821212). The maximum likelihood tree was generated in PhyML (Guindon and Gascuel 2003) using an LG + G model with 100 bootstrap replicates. Branches with bootstrap values >90 are indicated by an asterisk. Red marks on the branches denote putative duplication events. Gene expression values (FPKM) for each T. dalmanni paralogue are presented to the right of the tree. Tissue abbreviations: L,larva; H, adult head; F, female carcass (whole body with reproductive tissues removed); M, male carcass, O, ovaries; T, testes. Stalk-eyed fly generic abbreviations: D. meigenii, Diasemopsis meigenii; D. apicalis, Diopsis apicalis; E., Eurydiopsis; S., Sphyracephala; T., Teleopsis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig03: Phylogeny of the Nap1 gene family depicting abundant gene expansion within stalk-eyed flies. Contig sequences homologous to Drosophila Nap1 were extracted from an assembly of a testes transcriptome for each stalk-eyed fly species except Teleopsis dalmanni whose sequence data was derived from a multi-tissue assembly (GenBank accession numbers: KM821168-KM821212). The maximum likelihood tree was generated in PhyML (Guindon and Gascuel 2003) using an LG + G model with 100 bootstrap replicates. Branches with bootstrap values >90 are indicated by an asterisk. Red marks on the branches denote putative duplication events. Gene expression values (FPKM) for each T. dalmanni paralogue are presented to the right of the tree. Tissue abbreviations: L,larva; H, adult head; F, female carcass (whole body with reproductive tissues removed); M, male carcass, O, ovaries; T, testes. Stalk-eyed fly generic abbreviations: D. meigenii, Diasemopsis meigenii; D. apicalis, Diopsis apicalis; E., Eurydiopsis; S., Sphyracephala; T., Teleopsis.
Mentions: Another critical feature of transcriptome studies is that they facilitate the identification of lineage-specific genes that have no direct homologue in other insect groups. Novel genes can arise in many ways (e.g. gene duplication, lateral gene transfer, de novo gene creation from noncoding regions of DNA) and may rapidly acquire adaptive functional roles (Ranz & Parsch, 2012; Chen et al., 2013). Studies in Drosophila have shown that novel genes represent a substantial component of male-biased gene expression and play a critical role in spermatogenesis. A recent study in stalk-eyed flies (Baker et al., 2012) highlights the ability of RNA-Seq to uncover novel genetic diversity associated with reproductive proteins. More recently, testes transcriptomes from additional stalk-eyed fly species have been analysed, and numerous lineage-specific novel genes have been found (see Fig. 3 for an example). The gene family represented in Fig. 3 comprises homologues of the D. melanogaster gene, Nucleosome assembly protein 1 (Nap1), an important histone chaperone gene that is expressed in the testes (Kimura, 2013). In Drosophila and the mosquito species, Nap1 is present as a single homologue, while stalk-eyed fly species exhibit as many as nine paralogues of Nap1. Overall, the tree suggests there have been at least 14 duplications of the Nap1 gene within the family, and it appears these new genes function primarily in spermatogenesis. Of the seven paralogous copies in T. dalmanni, the one with the closest homology to the D. melanogaster Nap1 protein is expressed ubiquitously throughout the body, while the other six copies exhibit testes-specific gene expression (Fig. 3). DNA undergoes dramatic condensation during spermatogenesis involving the replacement of histones with protamines (White-Cooper, 2010), so it is possible these new Nap1 proteins play some role in this process. Overall, the use of transcriptomes for gene discovery has some inherent limitations because variation in expression levels across taxa will impact their representation in any gene family analysis. Even with this caveat, transcriptome surveys are an incredibly powerful tool for exploring the genetic diversity that is unique, and therefore of particular relevance, to non-model organism groups.

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
Related in: MedlinePlus