Allele-specific Expression of Ribosomal Protein Genes in Interspecific Hybrid Catfish

Abstract

Interspecific hybridization results in a vast reservoir of allelic variations, which may potentially contribute to phenotypical enhancement in the hybrids. Whether the allelic variations are related to the downstream phenotypic differences of interspecific hybrid is still an open question. The recently developed genome-wide allele-specific approaches that harness high-throughput sequencing technology allow direct quantification of allelic variations and gene expression patterns. In this work, I investigated allele-specific expression (ASE) pattern using RNA-Seq datasets generated from interspecific catfish hybrids. The objective of the study is to determine the ASE genes and pathways in which they are involved. Specifically, my study investigated ASE-SNPs, ASE-genes, parent-of-origins of ASE allele and how ASE would possibly contribute to heterosis. My data showed that ASE was operating in the interspecific catfish system. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5,420 (8.2%) and 13,390 (7.5%) SNPs were identified as significant ASE-SNPs, respectively. With these SNPs, a total of 1,519 and 3,075 ASE-genes have been identified. Gene Ontology analysis has revealed that genes encoding for cytoplasmic ribosomal proteins were highly enriched among ASE genes. Parent-of-origins of imbalanced alleles were determined for 27 and 30 ASE ribosomal protein genes in liver and gill, respectively. Of the 27 ASE ribosomal protein genes in the liver, 13 were of channel catfish origin and 14 were of blue catfish origin. Similarly, of the 30 ASE ribosomal protein genes in the gill, 16 were of channel catfish origin, while 14 were of blue catfish origin. Therefore, it appeared that ASE was not related to selected expression of a set of ribosomal protein genes from a specific parent. However, each RP gene appeared to be almost exclusively expressed from only one parent, indicating that ribosomes in the hybrid catfish were in “hybrid” forms. It’s also observed that the expression percentage of ribosomal protein genes out of total genes in gill was smaller in hybrid catfish (19.75%) than channel catfish (25.31%), indicating that hybrid ribosomes probably worked more efficiently than their homozygous counterparts. My study is the very first of its kind in catfish to determine if ASE exists in the interspecific hybrid system. It provides a new avenue of research to discover the genetic interactions at the transcriptional level and genome scale.