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Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish

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Abstract

Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE). In this work, we analyzed ASE in F1 hybrid catfish using RNA-Seq datasets. While the vast majority of genes were expressed with both alleles, 7–8 % SNPs exhibited significant differences in allele ratios of expression. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5420 (8.2 %) and 13,390 (7.5 %) SNPs were identified as significant ASE-SNPs, respectively. With these SNPs, a total of 1519 and 3075 ASE-genes were identified. Gene Ontology analysis revealed that genes encoding cytoplasmic ribosomal proteins (RP) were highly enriched among ASE genes. Parent-of-origin was determined for 27 and 30 ASE RP genes in the liver and gill, respectively. The results indicated that genes from both channel catfish and blue catfish were involved in ASE. However, each RP gene appeared to be almost exclusively expressed from only one parent, indicating that ribosomes in the hybrid catfish were in the “hybrid” form. Overall representation of RP transcripts among the transcriptome appeared lower in the F1 hybrid catfish than in channel catfish or blue catfish, suggesting that the “hybrid” ribosomes may work more efficiently for translation in the F1 hybrid catfish.

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Acknowledgments

The authors wish to thank Ludmilla Kaltenboeck and Huseyin Kucuktas for their technical assistance. This project was supported by USDA National Institute of Food and Agriculture through grants from Agriculture and Food Research Initiative Animal Genomics, Genetics and Breeding Program (2015-67015-22907) and Animal Disease Program (2015-67015-22975), and partially supported by USDA Aquaculture Research Program Competitive Grant (2014-70007-22395).

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Authors and Affiliations

  1. The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA

    Ailu Chen, Ruijia Wang, Shikai Liu, Eric Peatman, Luyang Sun, Lisui Bao, Chen Jiang, Chao Li, Yun Li, Qifan Zeng & Zhanjiang Liu

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  1. Ailu Chen
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  2. Ruijia Wang
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  3. Shikai Liu
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  7. Chen Jiang
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  9. Yun Li
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Correspondence to Zhanjiang Liu.

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Communicated by J. Cerdá.

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Chen, A., Wang, R., Liu, S. et al. Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish. Mol Genet Genomics 291, 1083–1093 (2016). https://doi.org/10.1007/s00438-015-1162-z

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