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Genome assembly of the flour beetle Tribolium castaneum

ABSTRACT: Long-read genome assembly of the insect model organism Tribolium castaneum

PROVIDER: PRJEB61413 | ENA |

REPOSITORIES: ENA

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Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

Project description:Evolution of cis-properties (such as enhancers) often plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods to study enhancers in species outside of established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum. To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium via FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and stage. Second, we established the first reporter assay system that works in both Drosophila and Tribolium, using nubbin in the wing and hunchback in the embryo as case studies. Together, these advances will be useful to study the evolution of cis-language and morphological diversity in Tribolium and other insects.

2017-10-03 | GSE104495 | GEO

Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

Project description:Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

2010-05-27 | GSE18087 | GEO

Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

Project description:Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle Four biological replicates for male and female beetles with 20 individuals per replicate. Two technical replicates, one replicate per sex. 16,434 genes/expressed non-coding regions represented twice on each array. Three 60 mer probes for most exons/expressed non-coding regions. 167,538 unique genomic probes replicated twice per array.

2010-05-26 | E-GEOD-18087 | biostudies-arrayexpress

Deep sequencing of small RNAs from Tribolium castaneum

Project description:Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries. Sequencing of Tribolium small RNAs from adults and embryos.

2010-12-29 | E-GEOD-26036 | biostudies-arrayexpress

Deep sequencing of small RNAs from Tribolium castaneum

Project description:Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries.

2010-12-29 | GSE26036 | GEO

Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum

Project description:Epigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set of Dnmts. But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. The red flour beetle, Tribolium castaneum, lacks Dnmt3 but possesses Dnmt1 and it has been controversial whether it has a functional DNA methylation system. Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we found Dnmt1 expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown of Dnmt1 caused a developmental arrest in offspring embryos. We show that Dnmt1 plays an essential role in T. castaneum embryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.

2018-11-14 | GSE120735 | GEO

Tribolium castaneum

Project description:Tribolium castaneum Proteome

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Project description:Tribolium castaneum phosphine

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Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum

Project description:Using a tiled whole-genome microarray, we found that 58.2% of Tribolium castaneum genes are maternally loaded into eggs. Comparison of known Drosophila melanogaster maternal genes to our results showed widespread conservation of maternal function with T. castaneum. We also found many T. castaneum genes with previously identified gender or tissue specific expression were also maternally loaded into eggs. The microarray design also allowed the detection of 2315 and 4060 novel transcriptionally active regions greater in length than 100 bp in unfertilized and fertilized T. castaneum eggs, respectively. The primary objective of this study was to identify expressed regions of the Tribolium castaneum genome in unfertilized and fertilized eggs using a whole-genome tiled microarray. The whole RNA of 3 samples of virgin laid eggs and 3 samples of fertilized eggs were compaired.

2013-05-06 | E-GEOD-38245 | biostudies-arrayexpress

Tribolium castaneum experimental evolution

Project description:We report Illumina-generated RNASeq data of several populations of Tribolium castaneum larvae selected for higher or lower immune priming specificity as well as unselected control populations. From each of these populations, we injected groups of 20 larvae with either one of three bacteria species or left them untreated as controls. Whole body samples were taken 6h after injection and used for RNASeq Analysis.

2019-09-11 | GSE133892 | GEO

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