Nature's Palette: Characterization of Shared Pigments in Colorful Avian and Mollusk Shells

Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis

Noncoding RNAs (ncRNAs) have gained significant attention in recent years due to their crucial roles in various biological processes. However, our understanding of the expression and functions of ncRNAs in Cyclina sinensis, an economically important marine bivalve, remains limited. This study aimed to address this knowledge gap by systematically identifying ncRNAs in the mantles of C. sinensis with purple and white shells. Through our analysis, we identified a differential expression of 1244 mRNAs, 196 lncRNAs, 49 circRNAs, and 23 miRNAs between purple- and white-shell clams. Functional enrichment analysis revealed the involvement of these differentially expressed ncRNAs in biomineralization and pigmentation processes. To gain further insights into the regulatory mechanisms underlying shell color formation, we established competitive endogenous RNA (ceRNA) networks. These networks allowed us to identify targeted differentially expressed miRNAs (DEMis) and genes associated with shell color formation. Based on the ceRNA networks, we obtained an up-down-up lncRNA-miRNA-mRNA network consisting of 13 upregulated lncRNAs and a circRNA-miRNA-mRNA network comprising three upregulated circRNAs (novel_circ_0004787, novel_circ_0001165, novel_circ_0000245). Through these networks, we identified and selected an upregulated novel gene (evm.TU.Hic_asm_7.988) and a downregulated sponge miRNA (hru-miR-1985) as potential contributors to shell color regulation. In summary, the present investigation offers a comprehensive analysis of ncRNA catalogs expressed in the clam mantle of C. sinensis. The findings enhance our comprehension of the molecular mechanisms governing shell coloration and offer new perspectives for selective breeding of C. sinensis in the future.

Plumage and eggshell colouration covary with the level of sex-specific parental contributions to nest building in birds

Interspecific variation in sex-specific contributions to prenatal parental care, including avian nest building, is becoming increasingly better understood as we amass more information on more species. We examined whether sex-specific nest building contributions covary with the colouration of parents and their eggs in 521 species of Western Palearctic birds. Having colourful plumage and laying colourful eggs are costly because of the deposition of pigments in feathers and eggs and/or forming costly nanostructural substrates in feathers, and so it might be expected that those costs covary with the costs of nest building at the level of individuals and/or across species to produce of a suite of codivergent traits. Using a phylogenetically informed approach, we tested the hypothesis that species in which females alone invest energy building nests exhibit less sexual plumage dichromatism. However, we found comparative support for the opposite of this prediction. We then tested that species in which females alone build nests lay more colourful, and costlier, eggs because the dual costs of building nests and laying colourful eggs can only be borne by higher quality individuals. As expected, we found that species in which females build nests alone or together with males are more likely to lay colourfully pigmented eggs relative to species in which only males build nests. Finally, stochastic character mapping provided evidence of the repeated evolution of female-only nest building. Interspecific sex differences in plumage colouration therefore covary in a complex manner with female pre- (nest building) and post-copulatory (egg production) investment in reproduction.

Outer fold is sole effective tissue among three mantle folds with regard to oyster shell colour

Molluscs constitute the second largest phylum of animals in the world, and shell colour is one of their most important phenotypic characteristics. In this study, we found among three folds on the mantle edge of oyster, only the outer fold had the same colour as the shell. Transcriptome and mantle cutting experiment indicated that the outer fold may be mainly reflected in chitin framework formation and biomineralisation. There were obvious differences in SEM structure and protein composition between the black and white shell periostraca. The black shell periostraca had more proteins related to melanin biosynthesis and chitin binding. Additionally, we identified an uncharacterized protein gene (named as CgCBP) ultra-highly expressed only in the black outer fold and confirmed its function of chitin-binding and CaCO₃ precipitation promoting. RNAi also indicated that CgCBP knockdown could change the structure of shell periostracum and reduce shell pigmentation. All these results suggest that the mantle outer fold plays multiple key roles in shell periostraca bioprocessing, and shell periostracum structure affected by chitin-binding protein is functionally correlated with shell pigmentation. The investigation of oyster shell periostracum structure and shell colour will provide a better understanding in pigmentation during biological mineralisation in molluscs.

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

BACKGROUND

Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation.

RESULTS

In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the "gold standard" of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in ^mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop.

CONCLUSIONS

This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.

Multicomponent shell traits are consistent with an individual recognition function of the appearance of common murre (Uria aalge) eggs: A biological replication study

In dense breeding colonies, and despite having no nest structure, common murres (or guillemots: Uria aalge) are still able to identify their own eggs. Each female murre's egg is thought to be recognized individually by the shell's avian-perceivable traits. This is because the eggshells' visible traits conform to expectations of the identity-signaling hypothesis in that they show both high intraindividual repeatability and high interindividual variability. Identity signaling also predicts a lack of correlation between each of the putative multicomponent recognition traits, yielding no significant relationships between those eggshell traits that are generated by mutually exclusive physiological factors. Using a multivariate analysis across eggshell size and shape, avian-perceivable background coloration, spot (maculation) shape, and spot density, we detected no unexpected statistical correlations between Icelandic common murre egg traits lacking known physiological or mathematical relationships with one another. These results biologically replicate the conclusions of a recent eggshell trait study of Canadian common murres using similar methodology. We also demonstrate the use of static correlations to infer identity signaling function without direct behavioral observations, which in turn may also be applied to rare or extinct species and provide valuable insight into otherwise unknown communicative and behavioral functions.

Evo-devo of shell colour in gastropods and bivalves

Recent technical innovations are revealing surprising patterns in mollusc shell pigmentation, such as an unexpectedly modest role for melanins and rapid divergences in the mix of pigments used to achieve similar colour patterns. The elucidation of the molecular genetic basis of shell pigmentation has been slow, probably because of the high genome complexity of gastropods and bivalves. Recent work within the old field of evolutionary ecology of shell pigmentation allows a greater role for the analysis of large-geographic-scale patterns (sometimes employing citizen-science data), as well as experimental field studies. However, the field remains dominated by land snails as model organisms, while colour pattern evolution in marine gastropods and bivalves, particularly those not exposed to visual predators, remains mysterious.

Chemical evidence of rare porphyrins in purple shells of Crassostrea gigas oyster

The colour of oyster shells is a very diverse characteristic morphotype, forming intriguing vivid patterns both on the inside and outside of the shell. In the present study, we have identified for the first time, the presence of several porphyrins as constituents of the shell pigmentation of the Crassostrea gigas oyster consumed worldwide. The precise molecular structures of halochromic, fluorescent and acid-soluble porphyrins, such as uroporphyrin and turacin, are unambiguously determined by reverse phase liquid chromatography combined with high resolution mass spectrometry. Their presence account for the purple colouration of shells but also for the dark colouration of adductor muscle scars. We have also defined the endogenous origin of these porphyrins, specifically secreted or accumulated by the shell forming tissue. These findings are pioneering analytical proofs of the existence of the haem pathway in the edible oyster Crassostrea gigas, evidenced by the chemical identification of haem side-products and supported by the recent publication of the corresponding oyster genome.

Expanding the eggshell colour gamut: uroerythrin and bilirubin from tinamou (Tinamidae) eggshells

To date, only two pigments have been identified in avian eggshells: rusty-brown protoporphyrin IX and blue-green biliverdin IXα. Most avian eggshell colours can be produced by a mixture of these two tetrapyrrolic pigments. However, tinamou (Tinamidae) eggshells display colours not easily rationalised by combination of these two pigments alone, suggesting the presence of other pigments. Here, through extraction, derivatization, spectroscopy, chromatography, and mass spectrometry, we identify two novel eggshell pigments: yellow–brown tetrapyrrolic bilirubin from the guacamole-green eggshells of Eudromia elegans, and red–orange tripyrrolic uroerythrin from the purplish-brown eggshells of Nothura maculosa. Both pigments are known porphyrin catabolites and are found in the eggshells in conjunction with biliverdin IXα. A colour mixing model using the new pigments and biliverdin reproduces the respective eggshell colours. These discoveries expand our understanding of how eggshell colour diversity is achieved. We suggest that the ability of these pigments to photo-degrade may have an adaptive value for the tinamous.

Genome-wide identification, characterisation and expression analysis of the ALAS gene in the Yesso scallop (Patinopecten yessoensis) with different shell colours

Porphyrins, one of the most common shell pigments, are by-products of the haem pathway. 5-Aminolaevulinate synthase (ALAS) is the first and rate-limiting enzyme in this pathway and has been well studied in vertebrate species. However, the function of ALAS in shell colouration has been poorly studied in molluscs, which are renowned for their colourful shells. In the present study, an ALAS gene, named PyALAS, was identified through whole-genome scanning in the Yesso scallop (Patinopecten yessoensis), an economically and evolutionarily important bivalve species in which the shell colour represents polymorphism. Two conserved domains were detected in the PyALAS protein sequence, including a Preseq-ALAS domain and a 5-ALAS domain, confirming the identification of PyALAS. Phylogenetic analysis of the ALAS proteins among various invertebrate and vertebrate species revealed a high consistency between the molecular evolution of ALAS and the species taxonomy. PyALAS was ubiquitously expressed in most adult tissues of the Yesso scallop. The left mantle expressed a significantly higher level of PyALAS than the right side in brown scallops, whereas there was no significant difference in white scallops. Significantly different expression levels of PyALAS was also detected between the two different shell colour strains. These data indicate that PyALAS plays an important role in shell colouration in Yesso scallops and the present study provides new insights into the molecular mechanism of shell colouration in molluscs.

Coculturing of Mosquito-Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis

Anopheles mosquito microbiomes are intriguing ecological niches. Within the gut, microbes adapt to oxidative stress due to heme and iron after blood meals. Although metagenomic sequencing has illuminated spatial and temporal fluxes of microbiome populations, limited data exist on microbial growth dynamics. Here, we analyze growth interactions between a dominant microbiome species, Elizabethkingia anophelis, and other Anopheles-associated bacteria. We find E. anophelis inhibits a Pseudomonas sp. via an antimicrobial-independent mechanism and observe biliverdins, heme degradation products, upregulated in cocultures. Purification and characterization of E. anophelis HemS demonstrates heme degradation, and we observe hemS expression is upregulated when cocultured with Pseudomonas sp. This study reveals a competitive microbial interaction between mosquito-associated bacteria and characterizes the stimulation of heme degradation in E. anophelis when grown with Pseudomonas sp.

Eumelanin and pheomelanin pigmentation in mollusc shells may be less common than expected: insights from mass spectrometry

BACKGROUND

The geometric patterns that adorn the shells of many phylogenetically disparate molluscan species are comprised of pigments that span the visible spectrum. Although early chemical studies implicated melanin as a commonly employed pigment, surprisingly little evidence generated with more recent and sensitive techniques exists to support these observations.

RESULTS

Here we present the first mass spectrometric investigations for the presence of eumelanin and pheomelanin in 13 different molluscan species from three conchiferan classes: Bivalvia, Cephalopoda and Gastropoda. In the bivalve Mytilus edulis we demonstrate that eumelanin mainly occurs in the outermost, non-mineralised and highly pigmented layer of the shell (often referred to as the periostracum). We also identified eumelanin in the shells of the cephalopod Nautilus pompilius and the marine gastropods Clanculus pharaonius and Steromphala adriatica. In the terrestrial gastropod Cepaea nemoralis we verify the presence of pheomelanin in a mollusc shell for the first time. Surprisingly, in a large number of brown/black coloured shells we did not find any evidence for either type of melanin.

CONCLUSIONS

We recommend methods such as high-performance liquid chromatography with mass spectrometric detection for the analysis of complex biological samples to avoid potential false-positive identification of melanin. Our results imply that many molluscan species employ as yet unidentified pigments to pattern their shells. This has implications for our understanding of how molluscs evolved the ability to pigment and pattern their shells, and for the identification of the molecular mechanisms that regulate these processes.

Pigmentation of White, Brown, and Green Chicken Eggshells Analyzed by Reflectance, Transmittance, and Fluorescence Spectroscopy

We report on the reflectance, transmittance and fluorescence spectra (λ=200-1200 nm) of four types of chicken eggshells (white, brown, light green, dark green) measured in situ without pretreatment and after ablation of 20-100 μm of the outer shell regions. The color pigment protoporphyrin IX (PPIX) is embedded in the protein phase of all four shell types as highly fluorescent monomers, in the white and light green shells additionally as non-fluorescent dimers, and in the brown and dark green shells mainly as non-fluorescent poly-aggregates. The green shell colors are formed from an approximately equimolar mixture of PPIX and biliverdin. The axial distribution of protein and colorpigments were evaluated from the combined reflectances of both the outer and inner shell surfaces, as well as from the transmittances. For the data generation we used the radiative transfer model in the random walk and Kubelka-Munk approaches.

Analysis of Siamese Crocodile (Crocodylus siamensis) Eggshell Proteome

The proteins and pigment of the eggshell of the Siamese crocodile (Crocodylus siamensis) were analysed. For proteomic analysis, various decalcification methods were used when the two main surface layers were analyzed. These layers are important for antimicrobial defense of egg (particularly the cuticle). We found 58 proteins in both layers, of which 4 were specific for the cuticle and 26 for the palisade (honeycomb) layer. Substantial differences between proteins in the eggshell of crocodile and previously described birds' eggshells exist (both in terms of quality and quantity), however, the entire proteome of Crocodilians has not been described yet. The most abundant protein was thyroglobulin. The role of determined proteins in the eggshell of the Siamese crocodile is discussed. For the first time, the presence of porphyrin pigment is reported in a crocodilian eggshell, albeit in a small amount (about 2 to 3 orders of magnitude lower than white avian eggs).

Eggshells as hosts of bacterial communities: An experimental test of the antimicrobial egg coloration hypothesis

Oviparous animals have evolved multiple defenses to prevent microbes from penetrating their eggs and causing embryo mortality. In birds, egg constituents such as lysozyme and antibodies defend against microbial infestation, but eggshell pigments might also impact survival of bacteria. If so, microbes could exert an important selective pressure on the evolution of eggshell coloration. In a previous lab experiment, eggshell protoporphyrin caused drastic mortality in cultures of Gram positive, but not Gram negative, bacteria when exposed to light. Here, we test this "photodynamic antimicrobial hypothesis" in a field experiment. In a paired experimental design, we placed sanitized brown, protoporphyrin-rich chicken eggs alongside white eggs that lack protoporphyrin. We deployed eggs for 48 hr without incubation, as can occur between laying and incubation, when microbial infection risk is highest. Eggs were placed on the open ground exposed to sunlight and in dark underground storm-petrel burrows. We predicted that the proportion of Gram-positive bacteria on brown eggs should be lower when exposed to sunlight than when kept in the dark, but we expected no such difference for white eggs. Although our data revealed variation in bacterial community composition, the proportion of Gram-positive bacteria on eggshells did not vary by egg color, and there was no interaction between egg color and location. Instead, Gram-positive bacteria were proportionally more common on eggs on the ground than eggs in burrows. Overall, our experiment did not support the photodynamic antimicrobial hypothesis. The diverse range of avian egg colors is generated by just two pigments, but over 10 hypotheses have been proposed for the evolution of eggshell color. If our results are generalizable, eggshell protoporphyrin might not play a substantial role in defending eggs against microbes, which narrows the field of candidate hypotheses for the evolution of avian eggshell coloration.

Identification of Shell Colour Pigments in Marine Snails Clanculus pharaonius and C. margaritarius (Trochoidea; Gastropoda)

Colour and pattern are key traits with important roles in camouflage, warning and attraction. Ideally, in order to begin to understand the evolution and ecology of colour in nature, it is important to identify and, where possible, fully characterise pigments using biochemical methods. The phylum Mollusca includes some of the most beautiful exemplars of biological pigmentation, with the vivid colours of sea shells particularly prized by collectors and scientists alike. Biochemical studies of molluscan shell colour were fairly common in the last century, but few of these studies have been confirmed using modern methods and very few shell pigments have been fully characterised. Here, we use modern chemical and multi-modal spectroscopic techniques to identify two porphyrin pigments and eumelanin in the shell of marine snails Clanculus pharaonius and C margaritarius. The same porphyrins were also identified in coloured foot tissue of both species. We use high performance liquid chromatography (HPLC) to show definitively that these porphyrins are uroporphyrin I and uroporphyrin III. Evidence from confocal microscopy analyses shows that the distribution of porphyrin pigments corresponds to the striking pink-red of C. pharaonius shells, as well as pink-red dots and lines on the early whorls of C. margaritarius and yellow-brown colour of later whorls. Additional HPLC results suggest that eumelanin is likely responsible for black spots. We refer to the two differently coloured porphyrin pigments as trochopuniceus (pink-red) and trochoxouthos (yellow-brown) in order to distinguish between them. Trochopuniceus and trochoxouthos were not found in the shell of a third species of the same superfamily, Calliostoma zizyphinum, despite its superficially similar colouration, suggesting that this species has different shell pigments. These findings have important implications for the study of colour and pattern in molluscs specifically, but in other taxa more generally, since this study shows that homology of visible colour cannot be assumed without identification of pigments.