Interactions between mitochondrial and nuclear genomes and co-regulation of mitochondrial and nuclear gene expression in reciprocal intergeneric hybrids between Carassius auratus red var. × Cyprinus carpio L.

Abstract

Genetic interactions between nuclear and mitochondrial genomes always play an important role in growth and development. However, it is not feasible to directly perform these studies in some animals. The reciprocal hybrid fishes obtained from intergeneric hybridization are an effective research model for the same nuclear genome and different mitochondrial genomes. The transcriptomes of embryonic development (Blastula Period, Gastrula Period, Segmentation Period and Hatching Period) were obtained from the two reciprocal hybrids of Carassius auratus red var. (RCC) ​× ​Cyprinus carpio L. (CC) and their parents. Most of the reads (average ​> ​99.90%) in the transcriptome of F1-RC (C. auratus red var. (♀) ​× ​C. carpio L. (♂)) and F1-CR (C. carpio L. (♀) ​× ​C. auratus red var. (♂)) were optimally mapped to the maternal mitochondrial genome (MMG), respectively. Then, the other reads with optimally mapped to paternal mitochondrial genome exhibited that the partial coverages and low-level (<0.4%) expressions of paternal mitochondrial genes were in the four developmental stages of them, especially hatching period, in which paternal mitochondrial DNA (mtDNA) is always eliminated in animals. In the four stages, some changes of 13 mitochondrial gene expressions were occurred in comparisons of the female parents and their hybrid progenies (F1-RC vs. RCC and F1-CR vs. CC), although no significantly differential expression (DE) was detected in them. Moreover, in each embryonic development stages, the positive correlation between the number of differential expression of nuclear-encoded mitochondrial genes and the p-value of differential expression of mitochondrial genes help us understanding how the detail of mitochondrial-nuclear genetic interactions operate in hybrids. The detection of paternal mitochondrial genome fragments in hatching period provides us insight into potential escape mechanisms which may disrupt or inactivate PME in hybrids. These differential expression of nuclear-encoded mitochondrial genes between reciprocal hybrids may help us understanding of the genetic basis of growth in hybrids and used in their breeding project.