A two-step method for identifying photopigment opsin and rhodopsin gene sequences underlying human color vision phenotypes.

PurposeTo present a detailed, reliable long range-PCR and sequencing (LR-PCR-Seq) procedure to identify human opsin gene sequences for variations in the long wavelength-sensitive (OPN1LW), medium wavelength-sensitive (OPN1MW), short wavelength-sensitive (OPN1SW), and rhodopsin (RHO) genes.MethodsColor vision was assessed for nine subjects using the Farnsworth-Munsell 100 hue test, Ishihara pseudoisochromatic plates, and the Rabin cone-contrast threshold procedure (ColorDX, Konan Medical). The color vision phenotypes were normal trichromacy (n = 3), potential tetrachromacy (n = 3), dichromacy (n = 2), and unexplained low color vision (n = 1). DNA was isolated from blood or saliva and LR-PCR amplified into individual products: OPN1LW (4,045 bp), OPN1MW (4,045 bp), OPN1SW (3,326 bp), and RHO (6,715 bp). Each product was sequenced using specific internal primer sets. Analysis was performed with Mutation Surveyor software.ResultsThe LR-PCR-Seq technique identified known single nucleotide polymorphisms (SNPs) in OPN1LW and OPN1MW gene codons (180, 230, 233, 277, and 285), as well as those for lesser studied codons (174, 178, 236, 274, 279, 298 and 309) in the OPN1LW and OPN1MW genes. Additionally, six SNP variants in the OPN1MW and OPN1LW genes not previously reported in the NCBI dbSNP database were identified. An unreported poly-T region within intron 5(c.36+126) of the rhodopsin gene was also found, and analysis showed it to be highly conserved in mammalian species.ConclusionsThis LR-PCR-Seq procedure (single PCR reaction per gene followed by sequencing) can identify exonic and intronic SNP variants in OPN1LW, OPN1MW, OPN1SW, and rhodopsin genes. There is no need for restriction enzyme digestion or multiple PCR steps that can introduce errors. Future studies will combine the LR-PCR-Seq with perceptual behavior measures, allowing for accurate correlations between opsin genotypes, retinal photopigment phenotypes, and color perception behaviors

Ultraviolet and yellow reflectance but not fluorescence is important for visual discrimination of conspecifics by Heliconius erato

Toxic Heliconius butterflies have yellow hindwing bars that – unlike those of their closest relatives – reflect ultraviolet (UV) and long wavelength light, and also fluoresce. The pigment in the yellow scales is 3-hydroxy-DL-kynurenine (3-OHK), which is found in the hair and scales of a variety of animals. In other butterflies like pierids with color schemes characterized by independent sources of variation in UV and human-visible yellow/orange, behavioral experiments have generally implicated the UV component as most relevant to mate choice. This has not been addressed in Heliconius butterflies, where variation exists in analogous color components, but moreover where fluorescence due to 3-OHK could also contribute to yellow wing coloration. In addition, the potential cost due to predator visibility is largely unknown for the analogous well-studied pierid butterfly species. In field studies with butterfly paper models, we show that both UV and 3-OHK yellow act as signals for H. erato when compared with models lacking UV or resembling ancestral Eueides yellow, respectively, but attack rates by birds do not differ significantly between the models. Furthermore, measurement of the quantum yield and reflectance spectra of 3-OHK indicates that fluorescence does not contribute to the visual signal under broad-spectrum illumination. Our results suggest that the use of 3-OHK pigmentation instead of ancestral yellow was driven by sexual selection rather than predation

Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies.

BACKGROUND: In a world of chemical cues, smell and taste are essential senses for survival. Here we focused on Heliconius, a diverse group of butterflies that exhibit variation in pre- and post-zygotic isolation and chemically-mediated behaviors across their phylogeny. Our study examined the ionotropic receptors, a recently discovered class of receptors that are some of the most ancient chemical receptors. RESULTS: We found more ionotropic receptors in Heliconius (31) than in Bombyx mori (25) or in Danaus plexippus (27). Sixteen genes in Lepidoptera were not present in Diptera. Only IR7d4 was exclusively found in butterflies and two expansions of IR60a were exclusive to Heliconius. A genome-wide comparison between 11 Heliconius species revealed instances of pseudogenization, gene gain, and signatures of positive selection across the phylogeny. IR60a2b and IR60a2d are unique to the H. melpomene, H. cydno, and H. timareta clade, a group where chemosensing is likely involved in pre-zygotic isolation. IR60a2b also displayed copy number variations (CNVs) in distinct populations of H. melpomene and was the only gene significantly higher expressed in legs and mouthparts than in antennae, which suggests a gustatory function. dN/dS analysis suggests more frequent positive selection in some intronless IR genes and in particular in the sara/sapho and melpomene/cydno/timareta clades. IR60a1 was the only gene with an elevated dN/dS along a major phylogenetic branch associated with pupal mating. Only IR93a was differentially expressed between sexes. CONCLUSIONS: All together these data make Heliconius butterflies one of the very few insects outside Drosophila where IRs have been characterized in detail. Our work outlines a dynamic pattern of IR gene evolution throughout the Heliconius radiation which could be the result of selective pressure to find potential mates or host-plants.This project is funded by a NASA grant (NNX10AM80H and NNX07AO30A) to RP, a NSF-DEB 1257839 to RP, NSF cooperative agreement DBI-0939454 to ADB, and a BBSRC grant H01439X and ERC grant ‘SpeciationGenetics’ to CDJ

Insect cryptochromes: gene duplication and loss define diverse ways to construct insect circadian clocks

Cryptochrome (CRY) proteins are components of the central circadian clockwork of metazoans. Phylogenetic analyses show at least 2 rounds of gene duplication at the base of the metazoan radiation, as well as several losses, gave rise to 2 cryptochrome (cry) gene families in insects, a Drosophila-like cry1 gene family and a vertebrate-like cry2 family. Previous studies have shown that insect CRY1 is photosensitive, whereas photo-insensitive CRY2 functions to potently inhibit clock-relevant CLOCK:CYCLE-mediated transcription. Here, we extended the transcriptional repressive function of insect CRY2 to 2 orders--Hymenoptera (the honeybee Apis mellifera and the bumblebee Bombus impatiens) and Coleoptera (the red flour beetle Tribolium castaneum). Importantly, the bee and beetle CRY2 proteins are not light sensitive in culture, in either degradation of protein levels or inhibitory transcriptional response, suggesting novel light input pathways into their circadian clocks as Apis and Tribolium do not have CRY1. By mapping the functional data onto a cryptochrome/6-4 photolyase gene tree, we find that the transcriptional repressive function of insect CRY2 descended from a light-sensitive photolyase-like ancestral gene, probably lacking the ability to repress CLOCK:CYCLE-mediated transcription. These data provide an evolutionary context for proposing novel circadian clock mechanisms in insects

Homeotic transformation induced by protein transduction

One of the most fundamental features of living organisms is that cells are separated from their external environment by a thin, but highly complex plasma membrane constituted of a lipid bilayer. Although, the lipid bilayer is only a few nanometers in width, it is impermeable to most molecules apart from small hydrophobic ones. The ability of small molecules to diffuse through a lipid bilayer is related to their lipid solubility. Hydrophilic macromolecular Antennapedia homeodomain peptide has been shown to be able to translocate from extracellular space into the cytoplasm of cells in a receptor-independent manner. Its third α-helix domain, designated as “Penetratin”, was proposed to be the functional transduction domain that is responsible for the translocation, and it is widely used for intracellular delivery of various exogenous proteins. Although Penetratin has been regarded to be the only element conferring the capacity of its parent polypeptide to penetrate through the plasma membrane, we found that the complete Antennapedia homeodomain exhibits an appreciably higher level of translocation efficiency as compared to Penetratin. Pharmacological analysis demonstrated that macropinocytic endocytosis plays a significant role underlying the process of the homeodomain internalization, and this is consistent with the observation that internalized polypeptide co-localizes with a fluid phase dye. Our studies identify macropinocytosis as a major mechanism by which Antennapedia homeodomain obtains the access to the interior of cells. In the process of macropinocytosis, signaling from the plasma membrane is required for actin remodeling to generate mechanical deformation forces; the interaction between positively charged Antennapedia homeodomain and negatively charged extracellular heparan sulfate could trigger the signaling cascade for fluid phase endocytosis. This would presumably explain why positively charged peptides, polymers, and liposomes are able to penetrate cells. As a fluid phase macropinocytosis provides cells with a way to non-selectively internalize large quantities of solute, it represents an effective means for drug delivery into cells. Both of “Penetratin” and Antennapedia homeodomain exploit macropinocytosis to a certain extent, the comparison between them may advance our understanding of the mechanisms triggering macropinocytotic endocytosis

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

<p>Abstract</p> <p>Background</p> <p>The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies.</p> <p>Results</p> <p>Sequences from ultraviolet-sensitive (<it>UVRh</it>), blue-sensitive (<it>BRh</it>), and long-wavelength sensitive (<it>LWRh</it>) opsins,<it>EF-1α </it>and <it>COI </it>were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both <it>BRh </it>and <it>LWRh </it>are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of <it>BRh </it>and <it>LWRh </it>sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly <it>Danaus plexippus </it>and the queen <it>D. gilippus </it>(15.3–35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic <it>Limenitis archippus </it>and red-spotted purple <it>L. arthemis </it>(4.7–13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies <it>Heliconius erato </it>and <it>H. melpomene </it>(13.5–26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84–113 million years for the divergence of all butterfly families.</p> <p>Conclusion</p> <p>These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.</p

Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies

Background: In a world of chemical cues, smell and taste are essential senses for survival. Here we focused on Heliconius, a diverse group of butterflies that exhibit variation in pre- and post-zygotic isolation and chemically-mediated behaviors across their phylogeny. Our study examined the ionotropic receptors, a recently discovered class of receptors that are some of the most ancient chemical receptors. Results: We found more ionotropic receptors in Heliconius (31) than in Bombyx mori (25) or in Danaus plexippus (27). Sixteen genes in Lepidoptera were not present in Diptera. Only IR7d4 was exclusively found in butterflies and two expansions of IR60a were exclusive to Heliconius. A genome-wide comparison between 11 Heliconius species revealed instances of pseudogenization, gene gain, and signatures of positive selection across the phylogeny. IR60a2b and IR60a2d are unique to the H. melpomene, H. cydno, and H. timareta clade, a group where chemosensing is likely involved in pre-zygotic isolation. IR60a2b also displayed copy number variations (CNVs) in distinct populations of H. melpomene and was the only gene significantly higher expressed in legs and mouthparts than in antennae, which suggests a gustatory function. dN/dS analysis suggests more frequent positive selection in some intronless IR genes and in particular in the sara/sapho and melpomene/cydno/timareta clades. IR60a1 was the only gene with an elevated dN/dS along a major phylogenetic branch associated with pupal mating. Only IR93a was differentially expressed between sexes. Conclusions: All together these data make Heliconius butterflies one of the very few insects outside Drosophila where IRs have been characterized in detail. Our work outlines a dynamic pattern of IR gene evolution throughout the Heliconius radiation which could be the result of selective pressure to find potential mates or host-plants.This project is funded by a NASA grant (NNX10AM80H and NNX07AO30A) to RP, a NSF-DEB 1257839 to RP, NSF cooperative agreement DBI-0939454 to ADB, and a BBSRC grant H01439X and ERC grant ‘SpeciationGenetics’ to CDJ.This is the final version of the article. It first appeared from BioMed Central via https://doi.org/10.1186/s12864-016-2572-

Longwing (<i>Heliconius</i>) butterflies combine a restricted set of pigmentary and structural coloration mechanisms

BACKGROUND: Longwing butterflies, Heliconius sp., also called heliconians, are striking examples of diversity and mimicry in butterflies. Heliconians feature strongly colored patterns on their wings, arising from wing scales colored by pigments and/or nanostructures, which serve as an aposematic signal. RESULTS: Here, we investigate the coloration mechanisms among several species of Heliconius by applying scanning electron microscopy, (micro)spectrophotometry, and imaging scatterometry. We identify seven kinds of colored scales within Heliconius whose coloration is derived from pigments, nanostructures or both. In yellow-, orange- and red-colored wing patches, both cover and ground scales contain wavelength-selective absorbing pigments, 3-OH-kynurenine, xanthommatin and/or dihydroxanthommatin. In blue wing patches, the cover scales are blue either due to interference of light in the thin-film lower lamina (e.g., H. doris) or in the multilayered lamellae in the scale ridges (so-called ridge reflectors, e.g., H. sara and H. erato); the underlying ground scales are black. In the white wing patches, both cover and ground scales are blue due to their thin-film lower lamina, but because they are stacked upon each other and at the wing substrate, a faint bluish to white color results. Lastly, green wing patches (H. doris) have cover scales with blue-reflecting thin films and short-wavelength absorbing 3-OH-kynurenine, together causing a green color. CONCLUSIONS: The pigmentary and structural traits are discussed in relation to their phylogenetic distribution and the evolution of vision in this highly interesting clade of butterflies

Female Behaviour Drives Expression and Evolution of Gustatory Receptors in Butterflies

Secondary plant compounds are strong deterrents of insect oviposition and feeding, but may also be attractants for specialist herbivores. These insect-plant interactions are mediated by insect gustatory receptors (Grs) and olfactory receptors (Ors). An analysis of the reference genome of the butterfly Heliconius melpomene, which feeds on passion-flower vines (Passiflora spp.), together with whole-genome sequencing within the species and across the Heliconius phylogeny has permitted an unprecedented opportunity to study the patterns of gene duplication and copy-number variation (CNV) among these key sensory genes. We report in silico gene predictions of 73 Gr genes in the H. melpomene reference genome, including putative CO2, sugar, sugar alcohol, fructose, and bitter receptors. The majority of these Grs are the result of gene duplications since Heliconius shared a common ancestor with the monarch butterfly or the silkmoth. Among Grs but not Ors, CNVs are more common within species in those gene lineages that have also duplicated over this evolutionary time-scale, suggesting ongoing rapid gene family evolution. Deep sequencing (∼1 billion reads) of transcriptomes from proboscis and labial palps, antennae, and legs of adult H. melpomene males and females indicates that 67 of the predicted 73 Gr genes and 67 of the 70 predicted Or genes are expressed in these three tissues. Intriguingly, we find that one-third of all Grs show female-biased gene expression (n = 26) and nearly all of these (n = 21) are Heliconius-specific Grs. In fact, a significant excess of Grs that are expressed in female legs but not male legs are the result of recent gene duplication. This difference in Gr gene expression diversity between the sexes is accompanied by a striking sexual dimorphism in the abundance of gustatory sensilla on the forelegs of H. melpomene, suggesting that female oviposition behaviour drives the evolution of new gustatory receptors in butterfly genomes