Isolation of Hox Cluster Genes from Insects Reveals an Accelerated Sequence Evolution Rate

Hadrys, Heike; Simon, Sabrina; Kaune, Barbara; Schmitt, Oliver; Schöner, Anja; Jakob, Wolfgang; Schierwater, Bernd

doi:10.1371/journal.pone.0034682

Cited by 7 publications

(6 citation statements)

References 57 publications

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“…We found seven regulatory genes in nine transcripts, namely doublesex , abdominal-a , wingless , decapentapleic , bric-a-brac , ultrabithorax and distal-less (Additional file 1 : Table S12). Extensive pigmentation studies performed on D. melanogaster and other insects have reported a role of some of these regulatory elements in pigmentation patterning with strong links to sexual selection, sexual dimorphism and speciation in these more modern insect groups [ 46 , 68 , 69 ]. In the future, identification of pattering genes can help to answer questions related to sex-specific pigmentation in I. elegans and other odonate species that show genetic colour polymorphisms.…”

Section: Resultsmentioning

confidence: 99%

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes

et al. 2014

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BackgroundThere is growing interest in odonates (damselflies and dragonflies) as model organisms in ecology and evolutionary biology but the development of genomic resources has been slow. So far only one draft genome (Ladona fulva) and one transcriptome assembly (Enallagma hageni) have been published. Odonates have some of the most advanced visual systems among insects and several species are colour polymorphic, and genomic and transcriptomic data would allow studying the genomic architecture of these interesting traits and make detailed comparative studies between related species possible. Here, we present a comprehensive de novo transcriptome assembly for the blue-tailed damselfly Ischnura elegans (Odonata: Coenagrionidae) built from short-read RNA-seq data. The transcriptome analysis in this paper provides a first step towards identifying genes and pathways underlying the visual and colour systems in this insect group.ResultsIllumina RNA sequencing performed on tissues from the head, thorax and abdomen generated 428,744,100 paired-ends reads amounting to 110 Gb of sequence data, which was assembled de novo with Trinity. A transcriptome was produced after filtering and quality checking yielding a final set of 60,232 high quality transcripts for analysis. CEGMA software identified 247 out of 248 ultra-conserved core proteins as ‘complete’ in the transcriptome assembly, yielding a completeness of 99.6%. BLASTX and InterProScan annotated 55% of the assembled transcripts and showed that the three tissue types differed both qualitatively and quantitatively in I. elegans. Differential expression identified 8,625 transcripts to be differentially expressed in head, thorax and abdomen. Targeted analyses of vision and colour functional pathways identified the presence of four different opsin types and three pigmentation pathways. We also identified transcripts involved in temperature sensitivity, thermoregulation and olfaction. All these traits and their associated transcripts are of considerable ecological and evolutionary interest for this and other insect orders.ConclusionsOur work presents a comprehensive transcriptome resource for the ancient insect order Odonata and provides insight into their biology and physiology. The transcriptomic resource can provide a foundation for future investigations into this diverse group, including the evolution of colour, vision, olfaction and thermal adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-808) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes

et al. 2014

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“…Using complete taxa with high number of overlapping characters could then provide the opportunity to find genes and/or functional subgroups that harbors the same evolutionary history along the branches as the species under investigation. In addition, eventually comparative research on regulatory genes may become also helpful for deep phylogenetic studies and might bridge some gaps between description and causal explanations (Hadrys et al 2012). …”

Section: Resultsmentioning

confidence: 99%

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

Simon

Narechania

DeSalle

et al. 2012

Genome Biology and Evolution

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The evolution of the diverse insect lineages is one of the most fascinating issues in evolutionary biology. Despite extensive research in this area, the resolution of insect phylogeny especially of interordinal relationships has turned out to be still a great challenge. One of the challenges for insect systematics is the radiation of the polyneopteran lineages with several contradictory and/or unresolved relationships. Here, we provide the first transcriptomic data for three enigmatic polyneopteran orders (Dermaptera, Plecoptera, and Zoraptera) to clarify one of the most debated issues among higher insect systematics. We applied different approaches to generate 3 data sets comprising 78 species and 1,579 clusters of orthologous genes. Using these three matrices, we explored several key mechanistic problems of phylogenetic reconstruction including missing data, matrix selection, gene and taxa number/choice, and the biological function of the genes. Based on the first phylogenomic approach including these three ambiguous polyneopteran orders, we provide here conclusive support for monophyletic Polyneoptera, contesting the hypothesis of Zoraptera + Paraneoptera and Plecoptera + remaining Neoptera. In addition, we employ various approaches to evaluate data quality and highlight problematic nodes within the Insect Tree that still exist despite our phylogenomic approach. We further show how the support for these nodes or alternative hypotheses might depend on the taxon- and/or gene-sampling.

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“…In contrast, a few hemimetabolous insect species, e.g. Oncopeltus and Gryllus , have become more widely used, but have been investigated only for selected key Drosophila homologs 11 – 16 . Although several studies have extensively examined morphological changes during hemimatabolous embryogenesis 17 – 19 , large-scale embryonic transcriptomic studies are still missing.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans

Simon

Sagasser

Saccenti

et al. 2017

Sci Rep

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Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a “core” set of 6,794 transcripts – shared by all embryonic stages – which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.

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Isolation of Hox Cluster Genes from Insects Reveals an Accelerated Sequence Evolution Rate

Cited by 7 publications

References 57 publications

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans

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