Phenotypic screen and transcriptomics approach complement each other in functional genomics of defensive stink gland physiology.

Background: Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before.

Results: Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum.

The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution.

The red flour beetle Tribolium castaneum has emerged as an important insect model system for a variety of topics. With respect to studying gene function, it is second only to the vinegar fly D. melanogaster.

Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes.

Background: Most of the known genes required for developmental processes have been identified by genetic screens in a few well-studied model organisms, which have been considered representative of related species, and informative-to some degree-for human biology. The fruit fly Drosophila melanogaster is a prime model for insect genetics, and while conservation of many gene functions has been observed among bilaterian animals, a plethora of data show evolutionary divergence of gene function among more closely-related groups, such as within the insects. A quantification of conservation versus divergence of gene functions has been missing, without which it is unclear how representative data from model systems actually are.

Enhanced genome assembly and a new official gene set for Tribolium castaneum.

Background: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models.

The mlpt/Ubr3/Svb module comprises an ancient developmental switch for embryonic patterning.

Unlabelled: Small open reading frames (smORFs) encoding 'micropeptides' exhibit remarkable evolutionary complexity. Conserved peptides encoded by are essential for embryo segmentation in but, in , function in terminal epidermal differentiation and patterning of adult legs. Here, we show that a molecular complex identified in epidermal differentiation, comprising Mlpt peptides, ubiquitin-ligase Ubr3 and transcription factor Shavenbaby (Svb), represents an ancient developmental module required for early insect embryo patterning.

A re-inducible gap gene cascade patterns the anterior-posterior axis of insects in a threshold-free fashion.

Gap genes mediate the division of the anterior-posterior axis of insects into different fates through regulating downstream hox genes. Decades of tinkering the segmentation gene network of led to the conclusion that gap genes are regulated (at least initially) through a threshold-based mechanism, guided by both anteriorly- and posteriorly-localized morphogen gradients. In this paper, we show that the response of the gap gene network in the beetle upon perturbation is consistent with a threshold-free 'Speed Regulation' mechanism, in which the speed of a genetic cascade of gap genes is regulated by a posterior morphogen gradient.

Double abdomen in a short-germ insect: Zygotic control of axis formation revealed in the beetle .

The distinction of anterior versus posterior is a crucial first step in animal embryogenesis. In the fly , this axis is established by morphogenetic gradients contributed by the mother that regulate zygotic target genes. This principle has been considered to hold true for insects in general but is fundamentally different from vertebrates, where zygotic genes and Wnt signaling are required.

The orphan genes are required for limb bud eversion in the embryo.

Background: Unlike but similar to other arthropod and vertebrate embryos, the flour beetle develops everted limb buds during embryogenesis. However, the molecular processes directing the evagination of epithelia are only poorly understood.

Results: Here we show that the newly discovered genes and are involved in regulating the directional budding of appendages.

Speed regulation of genetic cascades allows for evolvability in the body plan specification of insects.

During the anterior-posterior fate specification of insects, anterior fates arise in a nonelongating tissue (called the "blastoderm"), and posterior fates arise in an elongating tissue (called the "germband"). However, insects differ widely in the extent to which anterior-posterior fates are specified in the blastoderm versus the germband. Here we present a model in which patterning in both the blastoderm and germband of the beetle is based on the same flexible mechanism: a gradient that modulates the speed of a genetic cascade of gap genes, resulting in the induction of sequential kinematic waves of gap gene expression.

The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.

Genetic screens are powerful tools to identify the genes required for a given biological process. However, for technical reasons, comprehensive screens have been restricted to very few model organisms. Therefore, although deep sequencing is revealing the genes of ever more insect species, the functional studies predominantly focus on candidate genes previously identified in Drosophila, which is biasing research towards conserved gene functions.

iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum.

The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen).

Tc-knirps plays different roles in the specification of antennal and mandibular parasegment boundaries and is regulated by a pair-rule gene in the beetle Tribolium castaneum.

Background: The Drosophila larval head is evolutionarily derived at the genetic and morphological level. In the beetle Tribolium castaneum, development of the larval head more closely resembles the ancestral arthropod condition. Unlike in Drosophila, a knirps homologue (Tc-kni) is required for development of the antennae and mandibles.

Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters.

Background: The red flour beetle Tribolium castaneum has developed into an insect model system second only to Drosophila. Moreover, as a coleopteran it represents the most species-rich metazoan taxon which also includes many pest species. The genetic toolbox for Tribolium research has expanded in the past years but spatio-temporally controlled misexpression of genes has not been possible so far.

Apparent role of Tribolium orthodenticle in anteroposterior blastoderm patterning largely reflects novel functions in dorsoventral axis formation and cell survival.

In the short-germ beetle Tribolium castaneum, the head gap gene orthodenticle (Tc-otd) has been proposed to functionally substitute for bicoid, the anterior morphogen unique to higher dipterans. In this study we reanalyzed the function of Tc-otd. We obtained a similar range of cuticle phenotypes as in previously described RNAi experiments; however, we noticed unexpected effects on blastodermal cell fates.

Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps.

Background: Given its sequenced genome and efficient systemic RNA interference response, the red flour beetle Tribolium castaneum is a model organism well suited for reverse genetics. Even so, there is a pressing need for forward genetic analysis to escape the bias inherent in candidate gene approaches.

Results: To produce easy-to-maintain insertional mutations and to obtain fluorescent marker lines to aid phenotypic analysis, we undertook a large-scale transposon mutagenesis screen.

An ancient anterior patterning system promotes caudal repression and head formation in ecdysozoa.

Posterior expression of Caudal is required for early embryonic development in nematodes, arthropods, and vertebrates. In Drosophila, ectopic Caudal in anterior cells can induce head defects, and in Caenorhabditis the absence of Caudal in anterior embryonic cells is required for proper development. Anterior Caudal repression in these species is achieved through unrelated translational repressors, the homeodomain protein Bicoid and the KH domain factor Mex-3, respectively.

Probing the Drosophila retinal determination gene network in Tribolium (II): The Pax6 genes eyeless and twin of eyeless.

The Pax6 genes eyeless (ey) and twin of eyeless (toy) are upstream regulators in the retinal determination gene network (RDGN), which instructs the formation of the adult eye primordium in Drosophila. Most animals possess a singleton Pax6 ortholog, but the dependence of eye development on Pax6 is widely conserved. A rare exception is given by the larval eyes of Drosophila, which develop independently of ey and toy.

The Tribolium ortholog of knirps and knirps-related is crucial for head segmentation but plays a minor role during abdominal patterning.

Segment formation in the long germ insect Drosophila is dominated by overlapping gap gene domains in the syncytial blastoderm. In the short germ beetle Tribolium castaneum abdominal segments arise from a cellular growth zone, implying different patterning mechanisms. We describe here the single Tribolium ortholog of the Drosophila genes knirps and knirps-related (called Tc-knirps).

The genome of the model beetle and pest Tribolium castaneum.

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes.

Antenna and all gnathal appendages are similarly transformed by homothorax knock-down in the cricket Gryllus bimaculatus.

Our understanding of the developmental mechanisms underlying the vast diversity of arthropod appendages largely rests on the peculiar case of the dipteran Drosophila melanogaster. In this insect, homothorax (hth) and extradenticle (exd) together play a pivotal role in appendage patterning and identity. We investigated the role of the hth homologue in the cricket Gryllus bimaculatus by parental RNA interference.

Maintenance of segment and appendage primordia by the Tribolium gene knödel.

For homeotic and segment-polarity genes in Drosophila, a switch in gene regulation has been described that distinguishes patterning and maintenance phases. Maintenance of segment and organ primordia involves secondary patterning and differentiation steps, as well as survival factors regulating proliferation and organ size. In a screen for embryonic lethal mutations in the flour beetle Tribolium castaneum, we have recovered two alleles of the knödel gene, which result in short, bag-like embryos.

Breakdown of abdominal patterning in the Tribolium Kruppel mutant jaws.

During Drosophila segmentation, gap genes function as short-range gradients that determine the boundaries of pair-rule stripes. A classical example is Drosophila Krüppel (Dm'Kr) which is expressed in the middle of the syncytial blastoderm embryo. Patterning defects in Dm'Kr mutants are centred symmetrically around its bell-shaped expression profile.

Tribolium mae expression suggests roles in terminal and midline patterning and in the specification of mesoderm.

In Drosophila, the Mae protein ("modulator of the activity of Ets") regulates receptor tyrosine kinase (RTK)-dependent mitogen-activated protein kinase (MAPK) signaling. Mae has been shown to bind the Yan and Pointed-P2 transcription factors, thereby changing their ability to activate or repress target genes. In this work we show that the mae ortholog of the red flour beetle Tribolium castaneum (Tc'mae) is active at the posterior, but not the anterior pole of the blastoderm.