Biology subjects

Tomoyasu, Y.

Publications and source records attributed to Tomoyasu, Y..

4 recordsLinked to original sources

bioRxiv2024

Regulatory genome annotation of 33 insect species

Annotation of newly-sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis-regulatory modules--e.g., enhancers and silencers--that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation of insect regulatory sequences, and provide a searchable database resource with enhancer predictions for 33 genomes. Using our previously-developed SCRMshaw computational enhancer prediction method, we predict over 2.8 million regulatory sequences along with the tissues where they are expected to be active, in a set of insect species ranging over 360 million years of evolution. Extensive analysis and validation of the data provides several lines of evidence suggesting that we achieve a high true-positive rate for enhancer prediction. One, we show that our predictions target specific loci, rather than random genomic locations. Two, we predict enhancers in orthologous loci across a diverged set of species to a significantly higher degree than random expectation would allow. Three, we demonstrate that our predictions are highly enriched for regions of accessible chromatin. Four, we achieve a validation rate in excess of 70% using in vivo reporter gene assays. As we continue to annotate both new tissues and new species, our regulatory annotation resource will provide a rich source of data for the research community and will have utility for both small-scale (single gene, single species) and large-scale (many genes, many species) studies of gene regulation. In particular, the ability to search for functionally-related regulatory elements in orthologous loci should greatly facilitate studies of enhancer evolution even among distantly related species.

genomics↗

bioRxiv2021

Butterfly eyespots evolved via co-option of the antennal gene-regulatory network

Butterfly eyespots are beautiful novel traits with an unknown developmental origin. Here we show that eyespots likely originated via co-option of the antennal gene-regulatory network (GRN) to novel locations on the wing. Using comparative transcriptome analysis, we show that eyespots cluster with antennae relative to multiple other tissues. Furthermore, three genes essential for eyespot development (Distal-less (Dll), spalt (sal), and Antennapedia (Antp)) share similar regulatory connections as those observed in the antennal GRN. CRISPR knockout of cis-regulatory elements (CREs) for Dll and sal led to the loss of eyespots and antennae, and also legs and wings, demonstrating that these CREs are highly pleiotropic. We conclude that eyespots likely re-used the ancient antennal GRN, a network previously implicated also in the development of legs and wings.

evolutionary biology↗

bioRxiv2017

Two sets of wing homologs in the crustacean, Parhyale hawaiensis

The origin of insect wings is a biological mystery that has fascinated scientists for centuries. Through extensive investigations performed across various fields, two possible wing origin tissues have been identified; a lateral outgrowth of the dorsal body wall (tergum) and ancestral proximal leg structures1,2. With each idea offering both strengths and weaknesses, these two schools of thought have been in an intellectual battle for decades without reaching a consensus3. Identification of tissues homologous to insect wings from linages outside of Insecta will provide pivotal information to resolve this conundrum. Here, through expression analyses and CRISPR/Cas9-based genome-editing in the crustacean, Parhyale hawaiensis, we show that a wing-like gene regulatory network (GRN) operates both in the crustacean terga and in the proximal leg segments, suggesting that (i) the evolution of a wing-like GRN precedes the emergence of insect wings, and (ii) that both of these tissues are equally likely to be crustacean wing homologs. Interestingly, the presence of two sets of wing homologs parallels previous findings in some wingless segments of insects, where wing serial homologs are maintained as two separate tissues4-7. This similarity provides crucial support for the idea that the wingless segments of insects indeed reflect an ancestral state for the tissues that gave rise to the insect wing, while the true insect wing represents a derived state that depends upon the contribution of two distinct tissues. These outcomes point toward a dual origin of insect wings, and thus provide a crucial opportunity to unify the two historically competing hypotheses on the origin of this evolutionarily monumental structure.

evolutionary biology↗

bioRxiv2017

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

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.

developmental biology↗