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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

Contig length distribution of the P. fulvidraco transcriptome.
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pone.0131504.g002: Contig length distribution of the P. fulvidraco transcriptome.

Mentions: The number of clean reads (clipped and trimmed reads) obtained was > 20 M from most libraries (Table 1). Integrating these data and using a de novo assembly algorithm, we obtained 310,143 contigs > 200 bp. According to the TransDecoder predictions, there were 106,201 contigs encoding 144,487 proteins longer than 100 amino acids. Identical predicted protein sequences were clustered and the corresponding nucleotide sequences were extracted to form a non-redundant transcriptome, which included 64,398 sequences with the total length reached more than 135 Mb. The lengths of most contigs were < 1,000 bp, but there were also many contigs > 5,000 bp (Fig 2). The N50 contig length, median contig length, and average contig length of the non-redundant transcriptome were 3,087 bp, 1,604 bp and 2,098 bp, respectively.


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)

Contig length distribution of the P. fulvidraco transcriptome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131504.g002: Contig length distribution of the P. fulvidraco transcriptome.
Mentions: The number of clean reads (clipped and trimmed reads) obtained was > 20 M from most libraries (Table 1). Integrating these data and using a de novo assembly algorithm, we obtained 310,143 contigs > 200 bp. According to the TransDecoder predictions, there were 106,201 contigs encoding 144,487 proteins longer than 100 amino acids. Identical predicted protein sequences were clustered and the corresponding nucleotide sequences were extracted to form a non-redundant transcriptome, which included 64,398 sequences with the total length reached more than 135 Mb. The lengths of most contigs were < 1,000 bp, but there were also many contigs > 5,000 bp (Fig 2). The N50 contig length, median contig length, and average contig length of the non-redundant transcriptome were 3,087 bp, 1,604 bp and 2,098 bp, respectively.

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