Variation in the tyrosinase gene associated with a white humpback whale (Megaptera novaeangliae)

Analysis of the genetic loci of pigment pattern evolution in vertebrates

Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.

Ghost rodents: Albinism in Australian rodent species

While almost half of all mammal species are rodents, records of albinism in free‐ranging rodents are very rare. Australia has a large and diverse assemblage of native rodent species, but there are no records of free‐ranging albino rodents in the published literature. In this study, we aim to improve our understanding of the occurrence of albinism in Australian rodent species by collating contemporary and historic records of this condition and providing an estimate of its frequency. We found 23 records of albinism (i.e., a complete loss of pigmentation), representing eight species, in free‐ranging rodents native to Australia, with the frequency of albinism being generally <0.1%. Our findings bring the total number of rodent species in which albinism has been recorded globally to 76. While native Australian species represent only 7.8% of the world's murid rodent diversity, they now account for 42.1% of murid rodent species known to exhibit albinism. We also identified multiple concurrent albino records from a small island population of rakali (Hydromys chrysogaster) and discuss the factors that may contribute to the relatively high frequency (2%) of the condition on this island. We suggest that the small number of native albino rodents recorded in mainland Australia over the last 100 years means that traits associated with the condition are likely deleterious within populations and are thus selected against.

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

Color morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs-Albino, Lavender Albino, and Ultramel-show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.

Fine Mapping and Functional Analysis of the Gene PcTYR, Involved in Control of Cap Color of Pleurotus cornucopiae

Oyster mushrooms have a high biological efficiency and are easy to cultivate, which is why they are produced all over the world. Cap color is an important commercial trait for oyster mushrooms. Little is known about the genetic mechanism of the cap color trait in oyster mushrooms, which limits molecular breeding for the improvement of cap color-type cultivars. In this study, a 0.8-Mb major quantitative trait locus (QTL) region controlling cap color in the oyster mushroom Pleurotus cornucopiae was mapped on chromosome 7 through bulked-segregant analysis sequencing (BSA-seq) and extreme-phenotype genome-wide association studies (XP-GWAS). Candidate genes were further selected by comparative transcriptome analysis, and a tyrosinase gene (PcTYR) was identified as the highest-confidence candidate gene. Overexpression of PcTYR resulted in a significantly darker cap color, while the cap color of RNA interference (RNAi) strains for this gene was significantly lighter than that of the wild-type (WT) strains, suggesting that PcTYR plays an essential role in cap color formation. This is the first report about fine mapping and functional verification of a gene controlling cap color in oyster mushrooms. This will enhance our understanding of the genetic basis for cap color formation in oyster mushrooms and will facilitate molecular breeding for cap color. IMPORTANCE Oyster mushrooms are widely cultivated and consumed over the world for their easy cultivation and high biological efficiency (mushroom fresh weight/substrate dry weight × 100%). Fruiting bodies with dark caps are more and more popular according to consumer preferences, but dark varieties are rarely seen on the market. Little is known about the genetic mechanism of the cap color trait in oyster mushrooms, which limits molecular breeding for the improvement of cap color-type cultivars. A major QTL of cap color in oyster mushroom P. cornucopiae was fine mapped by using bulked-segregant analysis (BSA) and extreme-phenotype genome-wide association study (XP-GWAS) analysis. A candidate gene PcTYR coding tyrosinase was further identified with the help of comparative transcriptome analysis. qPCR analysis and genetic transformation tests proved that PcTYR played an essential role in cap color formation. This study will contribute to revealing the genetic mechanism of cap color formation in mushrooms, thereby facilitating molecular breeding for cap color trait.

Complex intragene deletion leads to oculocutaneous albinism in tanuki (Japanese raccoon dog)

Tanuki (Nyctereutes procyonoides viverrinus), or Japanese raccoon dog, is a canine native to Japan. Tanuki with complete oculocutaneous albinism are relatively frequent in mountainous areas of mainland Japan. Tyrosinase, which is encoded by the TYR gene, is an enzyme essential for the biosynthesis of melanin pigment. We examined the structure and nucleotide sequence of TYR in an albino tanuki and found that the third exon was removed due to a deletion of approximately 11 kb. In addition, two nonsynonymous nucleotide substitutions were found in the fifth exon. These mutations are possible causes of the albino phenotype; however, the order of occurrence is unclear. Even if the 11-kb deletion was not the first of these mutations, it is considered to cause a total loss of the tyrosinase function because the third exon carries codons for one of the two copper-binding sites of tyrosinase and these sites are essential for the enzyme function. Intriguingly, the deletion was not a simple removal of an 11-kb segment: an internal portion was retained as a segment in the reverse orientation. We propose possible formation processes for this mutation that involve multiple DNA scission events, or an inversion followed by a deletion.

Pigmentation formation and expression analysis of tyrosinase in Siniperca chuatsi

Animal pigmentation primarily depends on the presence and mixing ratio of chromatophores, functioning in animal survival and communication. For the benthic and carnivorous Siniperca chuatsi, pigmentation pattern is key to concealment and predation. In this study, the formation, distribution, and main pattern of chromatophores were observed in the embryos, larvae, skins, and visceral tissues from S. chuatsi. Melanophores were firstly visualized in the yolk sac at segmentation stage, and then they were migrated to the whole body and further clustered into the black stripes, bands, and patches. In adult S. chuatsi, the head, black band, and body side skins mainly contained melanophores, showing as deep or light black. The abdomen skin mainly contained iridophores, showing as silvery. In the eye, the pigment layers were located in the epithelial layers of iris and retina and shown as black. Then, the pigmentation-related gene, tyrosinase gene from S. chuatsi (Sc-tyr) was analyzed by bioinformatics and quantitative methods. The Sc-tyr gene encoded a protein with 540 amino acids (Sc-TYR). The Sc-TYR contained two copper ion binding sites, which were coordinated by six conserved histidines (H182, H205, H214, H366, H370, H393) and necessary for catalytic activity. The Sc-TYR was well conserved compared with TYR of various species with higher degree of sequence similarity with other fishes (77.6-98.3%). The qRT-PCR test showed that the Sc-tyr mRNA reached the peak value at segmentation stage in the embryo development, the black skins displayed a higher expression level than that in silvery skin, and the eye had the highest expression level compared with other tissues. Further research on enzyme activity showed that the expression patterns of tyrosinase activity were similar to that of the Sc-tyr mRNA. Comparing with the results of molecular and phenotype, it was found that the temporal and spatial distributions of tyrosinase corresponded well with changes in pigmentation patterns and the intensity of skin melanization. This study initially explored the pigmentation formation and tyrosinase expression, which served as a foundation for further insight into the genetics mechanism of body color formation in S. chuatsi.

A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population

Background

Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with albinism. In order to facilitate the conservation of the animals, it should be determined whether and to what extent brown animals carry the white gene. For this purpose, samples of one white hind and her brown calf were available for whole genome sequencing to identify the single nucleotide polymorphism(s) responsible for the white phenotype. Subsequently, samples from 194 brown and 11 white animals were genotyped.

Results

Based on a list of colour genes of the International Federation of Pigment Cell Societies, a non-synonymous mutation with exchange of a glycine residue at position 291 of the tyrosinase protein by arginine was identified as the cause of dilution of the coat colour. A gene test led to exactly matching genotypes in all examined animals. The study showed that 14% of the brown animals carry the white gene. This provides a simple and reliable way of conservation for the white animals. However, results could not be transferred to another, unrelated red deer population with white animals. Although no brown animals with a white tyrosinase genotype were detected, the cause for the white colouring in this population was different.

Conclusions

A gene test for the conservation of white red deer is available for the population of the Reinhardswald. While mutations in the tyrosinase are commonly associated with oculocutaneous albinism type 1, the amino acid exchange at position 291 was found to be associated with coat colour dilution in Cervus elaphus.

Albinism in Dasyurus species – a collation of historical and modern records

A new record of an albino marsupial, the northern quoll (Dasyurus hallucatus), is described and placed in the context of 10 records since 1874 from all four Australian quoll species. Of the 10 previous records, one was D. hallucatus, seven are likely to be D. viverrinus, one D. maculatus and one unknown. The recent record comprises the live capture of a healthy adult female northern quoll from the Pilbara region of Western Australia. Despite the rarity and likely deleterious nature of the albino condition, this animal appeared to be in good health, carrying eight pouch young, and was released at location of capture following tissue sampling for DNA analysis.

First record of atypical pigmentation pattern in fin whale Balaenoptera physalus in the Atlantic Ocean

Atypical pigmentation, which is rarely observed in the wild, may influence social interactions between animals and can be detrimental for survival. Hypopigmentation, which is the lack of pigment in a part or on the entire body, is a type of atypical pigmentation pattern that can be either acquired (e.g. vitiligo) or congenital resulting from the inheritance of mutations in pigment-related genes (e.g. albinism, leucism and piebaldism). This study documents atypical pigmentation in a fin whale Balaenoptera physalus off the northwestern coast of the Iberian Peninsula (Atlantic Ocean). Photographic and video data collected between 2016 and 2017 on 30 individual fin whales were examined. One fully-grown fin whale exhibited hypopigmentation. Several white patches of different shapes and sizes were present across the body of the fin whale including on the head, body, dorsal fin, flippers, and flukes. The position, shape, and lack of inflammation of the white patches on the whale observed, along with its body length and condition, might indicate that the depigmentation pattern is due to vitiligo. To our knowledge, this is the first case of atypical pigmentation pattern in fin whales described with photographs and video records. As these observations are rare, especially in highly migratory, long-lived, marine mammal species, this study provides valuable information to better understand the occurrence of this phenomenon. Further studies are needed to determine the ecological and physiological implications of atypical colourations, which might have a significant influence on the animal's survival.

Detection of two non-synonymous SNPs in SLC45A2 on BTA20 as candidate causal mutations for oculocutaneous albinism in Braunvieh cattle

BACKGROUND

Cases of albinism have been reported in several species including cattle. So far, research has identified many genes that are involved in this eye-catching phenotype. Thus, when two paternal Braunvieh half-sibs with oculocutaneous albinism were detected on a private farm, we were interested in knowing whether their phenotype was caused by an already known gene/mutation.

RESULTS

Analysis of genotyping data (50K) of the two albino individuals, their mothers and five other relatives identified a 47.61-Mb candidate haplotype on Bos taurus chromosome BTA20. Subsequent comparisons of the sequence of this haplotype with sequence data from four Braunvieh sires and the Aurochs genome identified two possible candidate causal mutations at positions 39,829,806 bp (G/A; R45Q) and 39,864,148 bp (C/T; T444I) that were absent in 1682 animals from various bovine breeds included in the 1000 bull genomes project. Both polymorphisms represent coding variants in the SLC45A2 gene, for which the human equivalent harbors numerous variants associated with oculocutaneous albinism type 4. We demonstrate an association of R45Q and T444I with the albino phenotype by targeted genotyping.

CONCLUSIONS

Although the candidate gene SLC45A2 is known to be involved in albinism in different species, to date in cattle only mutations in the TYR and MITF genes were reported to be associated with albinism or albinism-like phenotypes. Thus, our study extends the list of genes that are associated with bovine albinism. However, further research and more samples from related animals are needed to elucidate if only one of these two single nucleotide polymorphisms or the combination of both is the actual causal variant.

A novel nonsense mutation in the tyrosinase gene is related to the albinism in a capuchin monkey (Sapajus apella)

Background

Oculocutaneous Albinism (OCA) is an autosomal recessive inherited condition that affects the pigmentation of eyes, hair and skin. The OCA phenotype may be caused by mutations in the tyrosinase gene (TYR), which expresses the tyrosinase enzyme and has an important role in the synthesis of melanin pigment. The aim of this study was to identify the genetic mutation responsible for the albinism in a captive capuchin monkey, and to describe the TYR gene of normal phenotype individuals. In addition, we identified the subject’s species.

Results

A homozygous nonsense mutation was identified in exon 1 of the TYR gene, with the substitution of a cytosine for a thymine nucleotide (C64T) at codon 22, leading to a premature stop codon (R22X) in the albino robust capuchin monkey. The albino and five non-albino robust capuchin monkeys were identified as Sapajus apella, based on phylogenetic analyses, pelage pattern and geographic provenance. One individual was identified as S. macrocephalus.

Conclusion

We conclude that the point mutation C64T in the TYR gene is responsible for the OCA1 albino phenotype in the capuchin monkey, classified as Sapajus apella.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0504-8) contains supplementary material, which is available to authorized users.

Diagnosability and description of a new subspecies of Indo-Pacific humpback dolphin, Sousa chinensis (Osbeck, 1765), from the Taiwan Strait

BACKGROUND

Subspecies recognition can affect how people (scientists and non-scientists alike) view organisms and thus has important implications for research on, as well as the conservation of, these entities. Recently, a small group of Indo-Pacific humpback dolphins was discovered inhabiting the waters off central western Taiwan. This geographically isolated population possesses pigmentation patterns that are subtly, but noticeably, different from their nearest conspecifics in the neighbouring waters of the Jiulong River Estuary and Pearl River Estuary of mainland China. Due to this population's low and declining numbers and the numerous threats it faces, it was assessed as critically endangered by the Red List of Threatened Species of the International Union for Conservation of Nature. The purpose of this study is to examine the degree of differentiation of the Taiwanese population to determine if subspecies recognition iswarranted.

RESULTS

Analysis of the degree of differentiation in pigmentation patterns revealed nearly non-overlapping distributions between dolphins from Taiwanese waters and those from the Jiulong River + Pearl River estuaries of mainland China (the nearest known populations). The Taiwanese dolphins were clearly diagnosable from those of the Jiulong River + Pearl Riverestuaries under the most commonly accepted '75%rule' for subspecies delimitation (with 94% of one group being separable from 99+% of the other). Evidence of geographical isolation and behavioural differences also provided additional support for the distinctiveness of the Taiwanese dolphins.

CONCLUSIONS

Together, the evidence strongly demonstrated that the Taiwanese humpback dolphin population is differentiated at the subspecies level and on an evolutionary trajectory that is independent from that of dolphins from adjacent waters of mainland China (i.e. Jiulong River + Pearl River estuaries). As a result, the taxonomy of Sousa chinensis was revised to include two subspecies: the Taiwanese humpback dolphin, Sousa chinensis taiwanensis subsp. nov., and the Chinese humpback dolphin, Sousa chinensis chinensis (the nominotypical subspecies). These subspecies are described, and the holotype and paratype specimens for S. c. taiwanensis are established.

Epigenetic estimation of age in humpback whales

Age is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as 4 years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed based on age-induced changes in DNA methylation of specific genes. We used information on age-associated DNA methylation in human and mouse genes to identify homologous gene regions in humpbacks. Humpback skin samples were obtained from individuals with a known year of birth and employed to calibrate relationships between cytosine methylation and age. Seven of 37 cytosines assayed for methylation level in humpback skin had significant age-related profiles. The three most age-informative cytosine markers were selected for a humpback epigenetic age assay. The assay has an R(2) of 0.787 (P = 3.04e-16) and predicts age from skin samples with a standard deviation of 2.991 years. The epigenetic method correctly determined which of parent-offspring pairs is the parent in more than 93% of cases. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. This is the first epigenetic age estimation method for a wild animal species and the approach we took for developing it can be applied to many other nonmodel organisms.

Whales use distinct strategies to counteract solar ultraviolet radiation

A current threat to the marine ecosystem is the high level of solar ultraviolet radiation (UV). Large whales have recently been shown to suffer sun-induced skin damage from continuous UV exposure. Genotoxic consequences of such exposure remain unknown for these long-lived marine species, as does their capacity to counteract UV-induced insults. We show that UV exposure induces mitochondrial DNA damage in the skin of seasonally sympatric fin, sperm, and blue whales and that this damage accumulates with age. However, counteractive molecular mechanisms are markedly different between species. For example, sperm whales, a species that remains for long periods at the sea surface, activate genotoxic stress pathways in response to UV exposure whereas the paler blue whale relies on increased pigmentation as the season progresses. Our study also shows that whales can modulate their responses to fluctuating levels of UV, and that different evolutionary constraints may have shaped their response strategies.

A nonsense mutation in the tyrosinase gene causes albinism in water buffalo

Background

Oculocutaneous albinism (OCA) is an autosomal recessive hereditary pigmentation disorder affecting humans and several other animal species. Oculocutaneous albinism was studied in a herd of Murrah buffalo to determine the clinical presentation and genetic basis of albinism in this species.

Results

Clinical examinations and pedigree analysis were performed in an affected herd, and wild-type and OCA tyrosinase mRNA sequences were obtained. The main clinical findings were photophobia and a lack of pigmentation of the hair, skin, horns, hooves, mucosa, and iris. The results of segregation analysis suggest that this disease is acquired through recessive inheritance. In the OCA buffalo, a single-base substitution was detected at nucleotide 1,431 (G to A), which leads to the conversion of tryptophan into a stop codon at residue 477.

Conclusion

This premature stop codon produces an inactive protein, which is responsible for the OCA buffalo phenotype. These findings will be useful for future studies of albinism in buffalo and as a possible model to study diseases caused by a premature stop codon.