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A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco).

Zou M, Zhang X, Shi Z, Lin L, Ouyang G, Zhang G, Zheng H, Wei K, Ji W - PLoS ONE (2015)

Bottom Line: However, non-synonymous mutations result from single nucleotide substitutions residing in coding regions may not contribute to such differences.Based on the high-throughput expression data generated for the two different types of P. fulvidraco, we found that alterations of expression pattern may be more common than non-synonymous mutations.The transcriptome of P. fulvidraco will be an invaluable resource for subsequent comparative genomics and evolutionary analyses of this economically important fish.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province, Wuhan, Hubei, 430070, China.

ABSTRACT
Body colours are important and striking features for individual survival and reproductive success, in particular in vertebrates where mating behaviour and mate preference may be strongly influenced by non-normal phenotypes. Pigmentation disorders may be generated by disruption of one or many independent genes as well as by environmental factors. The first discovery of albino yellow catfish (Pelteobagrus fulvidraco Richardson) with golden skin colour from fish farms in China provides us valuable material to study the molecular mechanism underlying the abnormalities of pigmentation. In this study, transcriptome sequencing of fin tissues corresponding to the distinct body colours, wild type and mutant albino yellow catfish, were performed using Illumina sequencing technology. Based on next-generation sequencing technology and de novo assembly, we generated a transcriptome of P. fulvidraco. A number of genes differentially expressed between the wild types and albinos were identified, suggesting their contribution to the different phenotypes and fitness. However, non-synonymous mutations result from single nucleotide substitutions residing in coding regions may not contribute to such differences. Based on the high-throughput expression data generated for the two different types of P. fulvidraco, we found that alterations of expression pattern may be more common than non-synonymous mutations. The transcriptome of P. fulvidraco will be an invaluable resource for subsequent comparative genomics and evolutionary analyses of this economically important fish.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed genes between wild and albino types in anal fins and their involvement in the melanogenesis pathway.Genes marked in red are up-regulated and in yellow represented genes are down-regulated in wild type versus in albino type, respectively. Comparison between RNA-Seq results (identified by both edgeR and EBSeq) and qRT-PCR validation results. X-axis shows genes validated in this study; Y-axis shows Log2Ratio of expression of wild versus albino types. “*” indicates a significant difference between the two strains.
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pone.0131504.g005: Differentially expressed genes between wild and albino types in anal fins and their involvement in the melanogenesis pathway.Genes marked in red are up-regulated and in yellow represented genes are down-regulated in wild type versus in albino type, respectively. Comparison between RNA-Seq results (identified by both edgeR and EBSeq) and qRT-PCR validation results. X-axis shows genes validated in this study; Y-axis shows Log2Ratio of expression of wild versus albino types. “*” indicates a significant difference between the two strains.

Mentions: Pathway enrichment analyses of differentially expressed genes identified by EBSeq (S3 Table) revealed that eleven candidates take part in the pathway “Melanogenesis” and most of these genes, including the important tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1), were up-regulated in albino types (Fig 5). This may result from the up-regulation of cystine/glutamate transporter in albino types (slc7a11, S2 Table), which transports cystine into melanocytes, switch off the eumelanin (brown to black pigment) synthesis pathway and promote the synthesis of pheomelanin (yellow to red pigment). The lack of substrates for the synthesis of eumelanin may result in the high level of relevant enzymes and corresponding transcripts and reduce the melanin synthesis, which contribute to the abnormal body colour of the albino strain. The similar results were found in common carp [26]. Moreover, KEGG pathways such as “mismatch repair”, “base excision repair”, etc., were significantly enriched in differentially expressed genes (adjusted P value < 0.05, S3 Table). These are cellular mechanisms that repair damaged DNA. We suggest that without the protection of sufficient melanin, albino fishes were much more easily subject to DNA damage caused by ultraviolet (UV). Exposure to UV will trigger intracellular repair mechanisms with the result that the expression levels of many related genes in albino types were significantly different from those in wild types.


A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco).

Zou M, Zhang X, Shi Z, Lin L, Ouyang G, Zhang G, Zheng H, Wei K, Ji W - PLoS ONE (2015)

Differentially expressed genes between wild and albino types in anal fins and their involvement in the melanogenesis pathway.Genes marked in red are up-regulated and in yellow represented genes are down-regulated in wild type versus in albino type, respectively. Comparison between RNA-Seq results (identified by both edgeR and EBSeq) and qRT-PCR validation results. X-axis shows genes validated in this study; Y-axis shows Log2Ratio of expression of wild versus albino types. “*” indicates a significant difference between the two strains.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482592&req=5

pone.0131504.g005: Differentially expressed genes between wild and albino types in anal fins and their involvement in the melanogenesis pathway.Genes marked in red are up-regulated and in yellow represented genes are down-regulated in wild type versus in albino type, respectively. Comparison between RNA-Seq results (identified by both edgeR and EBSeq) and qRT-PCR validation results. X-axis shows genes validated in this study; Y-axis shows Log2Ratio of expression of wild versus albino types. “*” indicates a significant difference between the two strains.
Mentions: Pathway enrichment analyses of differentially expressed genes identified by EBSeq (S3 Table) revealed that eleven candidates take part in the pathway “Melanogenesis” and most of these genes, including the important tyrosinase (TYR) and tyrosinase-related protein 1 (TYRP1), were up-regulated in albino types (Fig 5). This may result from the up-regulation of cystine/glutamate transporter in albino types (slc7a11, S2 Table), which transports cystine into melanocytes, switch off the eumelanin (brown to black pigment) synthesis pathway and promote the synthesis of pheomelanin (yellow to red pigment). The lack of substrates for the synthesis of eumelanin may result in the high level of relevant enzymes and corresponding transcripts and reduce the melanin synthesis, which contribute to the abnormal body colour of the albino strain. The similar results were found in common carp [26]. Moreover, KEGG pathways such as “mismatch repair”, “base excision repair”, etc., were significantly enriched in differentially expressed genes (adjusted P value < 0.05, S3 Table). These are cellular mechanisms that repair damaged DNA. We suggest that without the protection of sufficient melanin, albino fishes were much more easily subject to DNA damage caused by ultraviolet (UV). Exposure to UV will trigger intracellular repair mechanisms with the result that the expression levels of many related genes in albino types were significantly different from those in wild types.

Bottom Line: However, non-synonymous mutations result from single nucleotide substitutions residing in coding regions may not contribute to such differences.Based on the high-throughput expression data generated for the two different types of P. fulvidraco, we found that alterations of expression pattern may be more common than non-synonymous mutations.The transcriptome of P. fulvidraco will be an invaluable resource for subsequent comparative genomics and evolutionary analyses of this economically important fish.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province, Wuhan, Hubei, 430070, China.

ABSTRACT
Body colours are important and striking features for individual survival and reproductive success, in particular in vertebrates where mating behaviour and mate preference may be strongly influenced by non-normal phenotypes. Pigmentation disorders may be generated by disruption of one or many independent genes as well as by environmental factors. The first discovery of albino yellow catfish (Pelteobagrus fulvidraco Richardson) with golden skin colour from fish farms in China provides us valuable material to study the molecular mechanism underlying the abnormalities of pigmentation. In this study, transcriptome sequencing of fin tissues corresponding to the distinct body colours, wild type and mutant albino yellow catfish, were performed using Illumina sequencing technology. Based on next-generation sequencing technology and de novo assembly, we generated a transcriptome of P. fulvidraco. A number of genes differentially expressed between the wild types and albinos were identified, suggesting their contribution to the different phenotypes and fitness. However, non-synonymous mutations result from single nucleotide substitutions residing in coding regions may not contribute to such differences. Based on the high-throughput expression data generated for the two different types of P. fulvidraco, we found that alterations of expression pattern may be more common than non-synonymous mutations. The transcriptome of P. fulvidraco will be an invaluable resource for subsequent comparative genomics and evolutionary analyses of this economically important fish.

No MeSH data available.


Related in: MedlinePlus