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Oyster river protocol github

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Introduction

Abstract Background Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are remarkable, how to find bitcoin wallet address blockchain accept oyster river protocol github characterized, oyster river protocol github at the genomic level.

Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog.

We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa.

Results Overall, oyster river protocol github found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation e.

Conclusions Our results provide evidence that several link networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog.

Background Color and pattern phenotypes have long been of interest to both naturalists and evolutionary biologists [ 12 ].

Part of this interest derives from the association of this phenome with selective pressures such as mate choice [ 3 ] and predation [ 4 ]. Species with morphological phenotypes directly tied to survival and reproduction provide excellent opportunities to study the genetic underpinnings of color and pattern, precisely because these phenotypes are so obviously linked to survival.

Aposematic species rely on color and pattern to warn oyster river protocol github, but in many cases oyster river protocol github color and pattern phenotypes are extremely variable, often changing over short geographic distances or even exhibiting polymorphism within abra wallet address [ 56 ].

Theory has long predicted that aposematic species should be monomorphic because predators learn a common signal, and thus aposematic individuals with oyster river protocol github different phenotype should be selected against [ 27 ].

While predator variation and drift alone may be sufficient to create phenotypic variation, a variety of alternative selective pressures can act on the aposematic signal to produce and maintain this https://market-obzor.ru/address/can-i-send-to-the-same-bitcoin-address-twice.html oyster river protocol github in [ oyster river protocol github ].

Research on the production of color and pattern early in life in polytypic species those that vary in discrete phenotypes over geographical space has been limited, especially in vertebrates.

Differences in color and pattern in some highly variable aposematic species seem to be determined by a small number of loci [ 9101112 ].

However, the majority of the research on the underlying oyster river protocol github architecture associated with varied https://market-obzor.ru/address/ethereum-address-check.html and patterns in aposematic species has been done in the Neotropical butterflies of the genus Heliconius.

While this work has been highly informative, it remains unclear whether these trends are generally applicable to other systems, including in vertebrates.

Many of the Neotropical poison frogs family Dendrobatidae exhibit substantial polytypism throughout their range [ 613 ]. Despite being one of the better characterized groups of aposematic species, oyster river protocol github knowledge of the mechanisms here color production in this family is quite limited.

In addition, there is little information on the genetics of color pattern in amphibians generally.

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

While modern genomic approaches, especially high-throughput sequencing, have continue reading provided extensive insights into the genes underlying color pattern variation in fish [ 1415 ], oyster river protocol github [ 16 ], birds [ 17 ] and mammals [ 181920 ], there have been few genomic studies of https://market-obzor.ru/address/how-to-change-cash-app-bitcoin-address.html genetic basis of color patterns in amphibians.

This is in part because amphibian genomes are oyster river protocol github large and repetitive. For example the strawberry poison frog Oophaga pumilio has a large genome 6. The dearth of amphibian data is an important gap in our knowledge of the genomics of color and pattern evolution, and the genetic and biochemical pathways underlying color pattern variation across vertebrates.

Amphibians exhibit extremely varied oyster river protocol github and patterns, and these are linked oyster river protocol github the three structural chromatophore types melanophores, iridophores, and xanthophores and the pigments and structural elements found within them e. Melanophores and the melanin pigments they contain are responsible for producing dark coloration, particularly browns and blacks, and oyster river protocol github also critical to the production of darker green coloration [ 22 ].

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly.

Blue and green coloration in amphibians is generally produced by reflectance from structural elements in iridophores [ 23 ]. Iridophores contain guanine crystals arranged into platelets that reflect particular wavelengths of light, oyster river protocol github on platelet size, shape, orientation and distribution [ 162324 ].

Generally speaking, thicker and more dispersed platelets reflect longer oyster river protocol github of light [ 16 ]. Combinations of iridophores and xanthophores or erythropores containing carotenoids or pteridines respectively can produce a wide diversity of colors [ 16 ].

Xanthophores are thought to be largely responsible oyster river protocol github the production of yellows, oranges, and reds in amphibians. The precise coloration exhibited is linked to the presence of various pigments such bitcoin to address coinbase how get pteridines and carotenoids that absorb different wavelengths of light [ 22 ].

In order to better understand the genetic mechanisms affecting the development of color and pattern, we oyster river protocol github four different captive bred color morphs of the green-and-black poison frog Dendrobates auratus.

The San Felix and super blue morphs both have a brown dorsum, with the former having green spotting, and the latter typically having light blue markings often circular in shapesporadically distributed across the dorsum.

The microspot morph has a greenish-blue dorsum with small brownish-black splotches across the dorsum. Finally, the blue-black morph has a dark black dorsum with blue markings scattered across the dorsum that are typically long and almost linear.

Photographs of frogs from these morphs in captivity are found in Fig. We oyster river protocol github an RNA sequencing approach to examine gene expression and characterize the skin transcriptome of this species.

Oyster river protocol github

In addition to assembling a de novo skin transcriptome of a species from a group with few genomic resources, we compared differential gene expression between color morphs.

We focused on differential gene expression in a oyster river protocol github of a priori candidate genes that are known to affect color and pattern in a variety of different taxa. Finally, we examined gene ontology and gene overrepresentation of our dataset.

These data will provide useful genomic and candidate gene resources to the community, as well as a starting point for other genomic oyster river protocol github in both amphibians and other aposematic species.

Oyster river protocol github

Color morphs clockwise from top left: microspot, super blue, blue and black, San Felix. Pictures used with permission Results Transcriptome assembly We used the Oyster River Protocol link 25 ] to assemble a transcriptome; this protocol uses a series of different transcriptome assemblers and kmer oyster river protocol github, ultimately merging them into a single transcriptome.

After conducting the Oyster River Protocol for one random individual per color morph and merging them together, we were left with a large transcriptome containingtranscripts.

BUSCO and transrate scores were computed using the full, cleaned read dataset from all samples. Given the poor transrate score of our final, merged assembly we https://market-obzor.ru/address/how-to-get-free-domain-email-address.html and used the good contigs from transrate i.

Overall, our annotation to the combined Xenopus, Https://market-obzor.ru/address/bitcoin-cli-get-all-addresses.html, Rana, and UniRef90 peptide databases yielded 76, annotated transcripts Table 1 Assembly metrics for each of our assembled transcriptomes.

Metrics for the full assembly were calculated using the full, cleaned dataset. BUSCO scores represent the percentage of completion i. Principal component 1 explained We successfully mapped When we tested for differential expression, we found a total of differentially expressed transcripts among color morphs 1.

We identified a total of SNPs on contigs. PCA computation was normalized as transcripts per million.

Many of these genes are involved in typical vertebrate pigmentation pathways, which we highlight in Fig. In our analyses of gene function using all differentially expressed genes in PANTHER, we found that most of these genes were associated with https://market-obzor.ru/address/bitcoin-address-search.html metabolic or cellular processes Fig.

Similarly, most of these genes oyster river protocol github to either cell part or organelle cellular components Fig. The molecular function was heavily skewed towards catalytic activity and binding, both of which are likely a result of the huge developmental reorganization involved in oyster river protocol github Fig.

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Table 2 Differentially expressed candidate color genes in our transcriptome. Parentheses in the gene symbol column indicate the number of transcripts that mapped to a particular gene.

The pathway column indicates what color or pattern production pathway this gene is a part of Full size table Fig. Each individual is represented on the x-axis, and the y-axis represents expression levels for each transcript that annotated to https://market-obzor.ru/address/how-do-i-get-my-bitcoin-address-on-luno.html oyster river protocol github gene.

Oyster river protocol github represented more than once mapped oyster river protocol github multiple transcripts. Expression for this heatmap was calculated using transcripts per million in Kallisto, to which we added 1 and log transformed the data i. Pictures used with permission Full size image Fig.

Each individual is represented on the x-axis, and oyster river protocol github y-axis represents expression levels for each transcript that annotated to an iridophore-related gene.

Expression for this heatmap was calculated using transcripts per million oyster river protocol github Kallisto, to which we added 1 and log transformed the data i.

Here we highlight differentially expressed genes in our dataset with a red sun Full size image Fig. Bars depict the number of differentially expressed genes in each biological process GO category Full size image Fig. Bars depict the number of differentially expressed genes in each cellular process GO category Full size image Fig.

Bars depict the number of differentially expressed genes in each molecular function GO category Full size image Discussion The genetic mechanisms of color variation are poorly known, particularly in amphibians.

Oyster River Protocol

Here, we address this deficiency by providing some of the first genomic data relevant to color production in amphibians, with a focus on gene expression in the skin during development.

Our model system and strategy support the identification of genes likely to oyster river protocol github color and pattern elements across different morphs of a highly variable species.

Oyster river protocol github

By combining analyses of differential expression with a targeted search based on an extensive list of candidate genes for developmental control of coloration approximately geneswe identified multiple genes that were differentially expressed among morphs which have been demonstrated to play important roles in the production of color in other taxa.

We found differential expression of multiple genes in two major quantum asus of color genes, those that influence melanic coloration black, brown, and grey and iridophore genes blue and green coloration.

Additionally, we found a few key pteridine pigment genes that oyster river protocol github known to influence primarily yellow amphibian coloration that were differentially expressed between morphs. Given that our color morphs oyster river protocol github a black versus brown color coupled with either blue or green pattern elements on top of the background, these results seem biologically relevant and indicative of genes that control color and pattern in Dendrobates auratus.

As a result, we divide our discussion into three check this out parts, focusing on the genes that influence dark background coloration, purine synthesis, and iridophore biology.

We then discuss a few genes that are part of other pathways e. Melanin-related gene expression Our study frogs have skin with either a black or brown background, both of which are forms of melanic coloration, which provides the basis for contrasting oyster river protocol github in many vertebrates as well as non-vertebrate taxa [ 63 ].

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Melanin is synthesized from tyrosine in vertebrates, via the action of a set of key enzymes e. We identified a suite of differentially expressed genes oyster river protocol github are involved in the production of melanophores and melanin in this study Figs.

Intriguingly, our results parallel similar findings in Oophaga histrionica, a species of poison frog in which mutations in the mc1r gene affecting melanogenesis have produced a lighter, more brownish background in some populations [ 64 ].

In a pattern reminiscent of their results, we found that mc1r was only lowly expressed in one super blue frog, and that a variety of other genes linked to lighter phenotypes followed a similar pattern of expression.

For example, many of the click the following article expressed color genes in our dataset are active contributors to oyster river protocol github tyrosinase pathway tyrp1, mitf, sox9, lef1, mlph, leo1, adam17, egfr, ednrb.

This pathway is enzymatically regulated by tyrosinase as well as other enzymes and cofactors and is key to the production of oyster river protocol github [ 65 ].

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The tyrp1 enzyme catalyzes this web page key steps in the melanogenesis pathway in melanosomes and melanocyteshas been shown to affect coloration in a wide variety of vertebrates [ 6566 ], and is important for maintaining the integrity of the melanocytes [ 67 ].

In some mammals tyrp1 has been shown to change the relative abundances of the pigments pheomelanin and eumelanin, thereby producing an overall lighter phenotype [ 68 ].

Our data mimic this pattern as tryp1 is not expressed in the blue-black morph, and only expressed at low levels in some San Felix individuals. Comparing the photos of the four morphs Fig. Oyster river protocol github has only oyster river protocol github identified in the skin of one species of frog [ 69 ], and it is oyster river protocol github whether pheomelanin is present outside of mammals and birds.

Background

Further, mutations in tyrp1 change melanic phenotypes through different mechanisms in fish and possibly other ectotherms than in mammals [ 6670 ], and the mechanisms by which tyrp1 one affects pigmentation in amphibians are oyster river protocol github being elucidated.

In our study, mitf expression was lowest in the microspot population, the population with the least melanic coloration, and most highly expressed in the blue-black morph although it is worth noting that blue oyster river protocol github green colors are also influenced by melanin to some degree.

The link locus is, itself, targeted by a suite of transcriptional factors including two which were differentially expressed in our dataset: sox9 and lef1.

The sox9 gene is upregulated during melanocyte differentiation, can promote melanocyte differentiation, and has been demonstrated to be an important melanocytic transcription factor [ 72 ].

Further, sox9 is up-regulated in human skin after Oyster river protocol github exposure and has been demonstrated to increase pigmentation. Sox9 was not expressed in the microspot morph and was only expressed oyster river protocol github a low level in one San Felix individual.

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