In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a “hotspot” locus, repeatedly implicated in generating intraspecific melanic wing color polymorphisms across 100 million years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. We show that none of the four candidate protein-coding genes within this locus, including cortex , serve as major effectors. Instead, a microRNA (miRNA), mir-193 , serves as the major effector across three deeply diverged lineages of butterflies, and its role is conserved in Drosophila . In Lepidoptera, mir-193 is derived from a gigantic primary long noncoding RNA, ivory , and it functions by directly repressing multiple pigmentation genes. We show that a miRNA can drive repeated instances of adaptive evolution in animals.

Butterfly wings display a diversity of cell types, including large polyploid scale cells, yet the molecular basis of such diversity is poorly understood. To explore scale cell diversity at a transcriptomic level, we employ single-cell RNA sequencing of ∼5,200 large cells (>6 μm) from 22.5- to 25-h male pupal forewings of the butterfly Bicyclus anynana. Using unsupervised clustering, followed by in situ hybridization, immunofluorescence, and CRISPR-Cas9 editing of candidate genes, we annotate various cell types on the wing. We identify genes marking non-innervated scale cells, pheromone-producing glandular cells, and innervated sensory cell types. We show that senseless, a zinc-finger transcription factor, and HR38, a hormone receptor, determine the identity, size, and color of different scale cell types and are important regulators of scale cell differentiation. This dataset and the identification of various wing cell-type markers provide a foundation to compare and explore scale cell-type diversification across arthropod species.

Localizing multiple RNA molecules simultaneously in intact tissues and organs is valuable for gaining insights into possible gene-regulatory interactions underlying cell differentiation. Existing technologies for multiplexed RNA localization are expensive, computationally complex, have elaborate sample preparation steps, have size limitations, and require weeks of processing time. This limits the widespread use of such techniques in most labs. Here we describe a cost-effective methodology, Rapid Amplified Multiplexed-FISH (or RAM-FISH), based on Hybridization Chain Reaction 3.0 for localizing dozens of transcripts in the same sample. This methodology achieves multiplexing by localizing 3 genes per cycle to detect 30 or more genes within a few days. The method can be applied to fixed tissue sections, entire organs, or whole organisms such as larval Danio rerio, without extensive sample preparation steps. The automation used here can also be adapted to perform other amplification-based FISH. Here, we demonstrate its utility, flexibility, and versatility for gene expression analysis in two very different types of samples, Bicyclus anynana butterfly larval wings and intact 10-day-old Danio rerio fish larvae. ### Competing Interest Statement A provisional patent involving the arc chamber, and the automation system mentioned in the present methodology has been filed.

Alcohol use disorders (AUDs) are complex phenomena governed by genetics, neurophysiology, environment, and societal structures. New methods to understand the underlying neurogenetics are valuable for designing better prevention and interventional strategies. Here, we used a novel, two-choice self-administration zebrafish assay (SAZA) to isolate the function of nicotinic acetylcholine receptor (nAChR) subunit alpha3 ( chrna3 ) in alcohol response. Juvenile zebrafish exhibited a biphasic response when self-administering alcohol that transitioned from attraction to aversion within minutes, suggesting they can regulate exposure to alcohol. This inverted U-shaped self-administration mirrored the effect alcohol has on shoaling behaviour. Exposure to low concentration of alcohol reduced anxiety-like behaviours characterised by decrease in shoal cohesion, while sedative effects became prominent at higher concentrations resulting in reduced locomotion and uncoordinated swimming. In contrast, chrna3 mutants displayed blunted responses, exhibiting prolonged alcohol self-administration, and increased gregariousness when compared to wild-type fish. These findings suggest that chrna3 dysfunction increased tolerance to alcohol. In humans, genetic variants that decrease CHRNA3 function may increase the likelihood of developing alcohol dependence. Thus, our results provide new insights into chrna3 function, as a potential target for pharmacological manipulation, and highlight the use of non-rodent alternatives to study the neurogenetics of development of AUD. ### Competing Interest Statement The authors have declared no competing interest.

Previous studies have shown that Optix regulates lower lamina thickness and the type of pigment that is produced in wing scales of a few butterfly species. However, the role of Optix in regulating pigment production across species, and in regulating additional aspects of scale morphology remains to be investigated. By combining microspectrophotometry, scanning electron microscopy, and focused ion beam technology on wild-type and Optix Bicyclus anynana crispants, we show that Optix regulates the production of orange pigments (ommochromes), represses the production of brown pigments (melanins), and regulates the morphology of the lower and upper surface of orange scales. Our findings suggest a conserved role of Optix as a switch gene that activates ommochrome and represses melanin synthesis across butterflies. By comparing these effects with other mutations, where only melanin is removed from scales, we propose that pigmentary changes, alone, affect the way that chitin polymerizes within a scale, changing lower lamina thickness as well as multiple intricate structures of the upper surface.

If the same pigment is found in different tissues in a body, it is natural to assume that the same metabolic pathways are deployed similarly in each tissue. Here we show that this is not the case for ommochromes, the red and orange pigments found in the eyes and wings of butterflies. We tested the expression and function of vermilion and cinnabar, two known fly genes in the ommochrome pathway, in the development of pigments in the eyes and in the wings of Bicyclus anynana butterflies, both traits having reddish/orange pigments. By using fluorescent in-situ hybridization (HCR3.0) we localized the expression of vermilion and cinnabar in the cytoplasm of pigment cells in the ommatidia but observed no clear expression for either gene on larval and pupal wings. We then disrupted the function of both genes, using CRISPR-Cas9, which resulted in the loss of pigment in the eyes but not in the wings. Using thin-layer chromatography and UV-vis spectroscopy we identified the presence of ommochrome and ommochrome precursors in the orange wing scales and in the hemolymph of pupae. We conclude that the wings either synthesize ommochromes locally, with yet unidentified enzymes or incorporate these pigments synthesized elsewhere from the hemolymph. Different metabolic pathways or transport mechanisms, thus, lead to the presence of ommochromes in the wings and eyes of B. anynana butterflies.

Wnt signaling members are involved in the differentiation of cells associated with eyespot and band color patterns on the wings of butterflies, but the identity and spatio-temporal regulation of specific Wnt pathway members remains unclear. Here, we explore the localization and function of Armadillo/β-catenin dependent (canonical) and Armadillo/β-catenin independent (noncanonical) Wnt signaling in eyespot and band development in Bicyclus anynana by localizing Armadillo (Arm), the expression of all eight Wnt ligand and four frizzled receptor transcripts present in the genome of this species and testing the function of some of the ligands and receptors using CRISPR-Cas9. We show that distinct Wnt signaling pathways are essential for eyespot and band patterning in butterflies and are likely interacting to control their active domains.

Two genes, Distal-less (Dll) and spalt (sal), are known to be involved in establishing nymphalid butterfly wing patterns. They function in several ways: in the differentiation of the eyespot's central signalling cells, or foci; in the differentiation of the surrounding black disc; in overall scale melanisation (Dll); and in elaborating marginal patterns, such as parafocal elements. However, little is known about the functions of these genes in the development of wing patterns in other butterfly families. Here, we study the expression and function of Dll and sal in the development of spots and other melanic wing patterns of the Indian cabbage white, Pieris canidia, a pierid butterfly. In P. canidia, both Dll and Sal proteins are expressed in the scale-building cells at the wing tips, in chevron patterns along the pupal wing margins, and in areas of future scale melanisation. Additionally, Sal alone is expressed in the future black spots. CRISPR knockouts of Dll and sal showed that each gene is required for the development of melanic wing pattern elements, and repressing pteridine granule formation, in the areas where they are expressed. We conclude that both genes likely play ancestral roles in organising distal butterfly wing patterns, across pierid and nymphalid butterflies, but are unlikely to be differentiating signalling centres in pierids black spots. The genetic and developmental mechanisms that set up the location of spots and eyespots are likely distinct in each lineage.

The assignment of specific patterns of gene expression to specific cells in a complex tissue facilitates the connection between genotype and phenotype. Single-cell sequencing of whole tissues produces single-cell transcript resolution but lacks the spatial information of the derivation of each cell, whereas techniques such as multiplex FISH localize transcripts to specific cells in a tissue but require a priori information of the target transcripts to examine. Laser dissection of tissues followed by transcriptome analysis is an efficient and cost-effective technique that provides both unbiased gene expression discovery together with spatial information. Here, we detail a laser dissection protocol for total RNA extraction from butterfly larval and pupal wing tissues, without the need of paraffin embedding or the use of a microtome, that could be useful to researchers interested in the transcriptome of specific areas of the wing during development. This protocol can bypass difficulties in extracting high quality RNA from thick fixed tissues for sequencing applications.

Novel organismal traits might reuse ancestral gene-regulatory networks (GRNs) in their development, but data supporting this mechanism are still sparse. Here we show the reuse of an ancestral insect venation gene regulatory subnetwork patterning the sharp and distinct rings of color in butterfly eyespots. Using laser microdissection followed by RNA-Seq we first obtained transcriptional profiles of the anterior and posterior compartment of larval wings, and eyespot and adjacent control tissue in pupal wings of Bicyclus anynana butterflies. We identified key venation patterning genes such as Mothers against dpp 6 (Mad6), thickveins, Optix, spalt, optomotor-blind (omb), aristaless, cubitus interruptus, and patched differentially expressed (DE) across compartments, and a sub-set of these genes also DE across eyespot and non-eyespot samples. Fluorescent in-situ hybridization (HCR3.0) on the jointly DE genes Mad6, Optix, and spalt , as well as dpp showed clear eyespot-center, eyespot-rings, and compartment-specific expression. Knocking out dpp resulted in an individual with venation defects and loss of eyespots, whereas knockouts of Optix and spalt resulted in the loss of orange scales and black scales, respectively. Furthermore, using CRISPR-Cas9 followed by immunostainings, we showed that Spalt represses Optix in the central region of the eyespot, limiting Optix expression to a more peripheral ring, which parallels the regulatory interaction found in venation patterning in the anterior compartment of fly larval wings. These network similarities suggest that part of the venation GRN was co-opted to aid in the differentiation of the eyespot rings. One-sentence summary We showed the reuse of an ancestral insect wing venation GRN in patterning a novel complex trait in butterflies.

Simple spot patterns are proposed to be ancestral to more complex eyespot patterns found on the wings of butterflies. Two genes, Distal-less (Dll) and spalt (sal), are known to be involved in two separate functions in establishing nymphalid butterfly eyespots: in the differentiation of their central signaling cells, or foci, necessary for eyespot ring formation, and in scale melanisation. However, little is known about the functions of these genes in the development of more primitive spot patterns. Here, we study the roles of Dll and sal in the development of spots and other melanic wing patterns of the Indian cabbage white, Pieris canidia, a pierid butterfly. We examined the expression pattern of both genes in developing larval and pupal wings and explored their functions using the CRISPR/Cas9 system. In P. canidia, both Dll and sal are expressed in the tips and along the margin of pupal wings, areas of future scale melanisation. Additionally, sal alone, is expressed in the future black spot patterns. CRISPR knockouts of Dll and sal showed that both genes are required for promoting melanic scales in the areas where they are expressed. Both Dll and sal also function as repressors of the pteridine pigment pathway. We conclude that both genes share a conserved role in promoting scale melanisation, across pierid and nymphalid butterflies, but are unlikely to be involved in differentiating spot centers. The genetic and developmental mechanisms that set up the location of spots and eyespots are likely distinct and independently evolved in each lineage.

optix, a gene essential and sufficient for eye development in Drosophila melanogaster, also plays important roles in the development of both the structure and pigmentation of butterfly wing scales. In particular, optix regulates wing scale lower lamina thickness and ommochrome pigment synthesis. Here we explore the role of optix in wing pattern development of Bicyclus anynana butterflies by examining its expression using immunostainings and testing its function via CRISPR-Cas9. We found Optix to be expressed in multiple domains, most prominently in the orange ring of the eyespots and in other scattered orange scales, and to regulate the pigmentation and the development of the upper lamina of the orange scales. We further explored the interaction of Optix with Spalt, a protein involved in the development of black scales in the eyespots, and expressed adjacent to the Optix domain. CRISPR knockouts of optix or spalt, followed by immunostainings, showed that Spalt represses optix expression in cells of the central black region of the eyespot. This regulatory interaction mimics that found in the anterior compartment of the wing disc where both genes respond to Decapentaplegic (Dpp) signaling and play a role in venation patterning. Using in situ hybridizations we show that dpp is expressed in the center of the eyespots and propose that this same circuit might have been recruited for eyespot development where Decapentaplegic acts as a central morphogen, activating optix and spalt at different concentration thresholds, and where spalt cross-regulates optix resulting in the formation of a sharp boundary between the two eyespot color rings.

The colorful wings of butterflies are emerging as model systems for evolutionary and developmental studies. Some of these studies focus on localizing gene transcripts and proteins in wings at the larval and pupal stages using techniques such as immunostaining and in situ hybridization. Other studies quantify mRNA expression levels or identify regions of open chromatin that are bound by proteins at different stages of wing development. All these techniques require dissection of the wings from the animal but a detailed video protocol describing this procedure has not been available until now. Here, we present a written and accompanying video protocol where we describe the tools and the method we use to remove the larval and pupal wings of the African Squinting Bush Brown butterfly Bicyclus anynana. This protocol should be easy to adapt to other species.

How mechanisms of pattern formation evolve has remained a central research theme in the field of evolutionary and developmental biology. The mechanism of wing vein differentiation in Drosophila is a classic text-book example of pattern formation using a system of positional information, yet very little is known about how species with a different number of veins pattern their wings, and how insect venation patterns evolved. Here, we examine the expression pattern of genes previously implicated in vein differentiation in Drosophila in two butterfly species with more complex venation Bicyclus anynana and Pieris canidia We also test the function of some of these genes in B. anynana We identify both conserved as well as new domains of decapentaplegic, engrailed, invected, spalt, optix, wingless, armadillo, blistered and rhomboid gene expression in butterflies, and propose how the simplified venation in Drosophila might have evolved via loss of decapentaplegic, spalt and optix gene expression domains, via silencing of vein-inducing programs at Spalt-expression boundaries, and via changes in expression of vein maintenance genes.

Gene duplication events often create genetic redundancy that can either lead to the appearance of pseudogenes or, instead, create opportunities for the evolution of novel proteins that can take on new functions. One of the genes which has been widely studied with respect to gene duplication is engrailed (en). En-family proteins are expressed in a morphological novelty, eyespots (in the center and in the outer gold ring), in the African squinting bush brown butterfly Bicyclus anynana, as well as in a more conserved pattern, the posterior compartment of a wing. In the present study, we used whole-genome sequencing and transcriptome data to show the presence of three en-family genes and their differential expression on the pupal wings of B. anynana using in situ hybridization. The results suggest two duplication events of en-family genes, the first evidence of a two-fold duplication in the Lepidoptera. We propose that all copies initially had posterior wing compartment expression and all copies subsequently gained a novel expression domain associated with eyespot centers. Two copies secondarily lost the posterior compartment expression, and one copy alone gained the outer ring expression domain. By dating the origin of both duplication events, however, we conclude that they predate the origin of eyespots by at least 60 mya, and hence our data does not support the retention of the multiple en gene duplicates in the genome via their involvement with the novel eyespot evolutionary innovation.

Eyespots on the wings of nymphalid butterflies represent colorful examples of pattern formation, yet the developmental origins and mechanisms underlying eyespot center differentiation are still poorly understood. Using CRISPR-Cas9 we re-examine the function of Distal-less (Dll) as an activator or repressor of eyespots, a topic that remains controversial. We show that the phenotypic outcome of CRISPR mutations depends upon which specific exon is targeted. In Bicyclus anynana, exon 2 mutations are associated with both missing and ectopic eyespots, and also exon skipping. Exon 3 mutations, which do not lead to exon skipping, produce only null phenotypes, including missing eyespots, lighter wing coloration and loss of scales. Reaction-diffusion modeling of Dll function, using Wnt and Dpp as candidate morphogens, accurately replicates these complex crispant phenotypes. These results provide new insight into the function of Dll as a potential activator of eyespot development, scale growth and melanization, and suggest that the tuning of Dll expression levels can generate a diversity of eyespot phenotypes, including their appearance on the wing.This article has an associated 'The people behind the papers' interview.

CRISPR-Cas9 is revolutionizing the field of genome editing in non-model organisms. The robustness, ease of use, replicability and affordability of the technology has resulted in its widespread adoption among researchers. The African butterfly Bicyclus anynana is an emerging model lepidopteran species in the field of evo-devo, with a sequenced genome and amenable to germ line transformation. However, efficient genome editing tools to accelerate the pace of functional genetic research in this species have only recently become available with CRISPR-Cas9 technology. Here, we provide a detailed explanation of the CRISPR-Cas9 protocol we follow in the lab. The technique has been successfully implemented to knock-out genes associated with eyespot development and melanin pigmentation.

Franconibacter pulveris strain DJ34, isolated from Duliajan oil fields, Assam, was characterized in terms of its taxonomic, metabolic and genomic properties. The bacterium showed utilization of diverse petroleum hydrocarbons and electron acceptors, metal resistance, and biosurfactant production. The genome (4,856,096bp) of this strain contained different genes related to the degradation of various petroleum hydrocarbons, metal transport and resistance, dissimilatory nitrate, nitrite and sulfite reduction, chemotaxy, biosurfactant synthesis, etc. Genomic comparison with other Franconibacter spp. revealed higher abundance of genes for cell motility, lipid transport and metabolism, transcription and translation in DJ34 genome. Detailed COG analysis provides deeper insights into the genomic potential of this organism for degradation and survival in oil-contaminated complex habitat. This is the first report on ecophysiology and genomic inventory of Franconibacter sp. inhabiting crude oil rich environment, which might be useful for designing the strategy for bioremediation of oil contaminated environment.

Eyespots on the wings of nymphalid butterflies represent colorful examples of the process of pattern formation, yet the developmental origins and the mechanisms behind eyespot differentiation are still not fully understood. Here we re-examine the function of Distal-less (Dll) in eyespot development, which is still unclear. We show that CRISPR-Cas9 induced exon 2 mutations in Bicyclus anynana leads to exon skipping and ectopic eyespots on the wing. Exon 3 mutations, however, lead to null/missense transcripts, missing eyespots, lighter wing coloration, loss of scales, and a variety of other phenotypes implicating Dll in the process of eyespot differentiation. Reaction-diffusion modeling enabled exploration of the function of Dll in eyespot formation, and accurately replicated a wide-range of mutant phenotypes. These results confirm that Dll is a required activator of eyespot development, scale growth and melanization and point to a new mechanism of alternative splicing to achieve Dll over-expression phenotypes.