Studies On The Complete Mitochondrial Genomes And Mitochondra-related Genes In Liver Transcriptome Of Different Polyploid Fish

Mitochondria are double-layered membrane-bound organelles, which are found in nearly all eukaryotic cells. They act as cellular energy suppliers and carry their own genetic material, the mitochondrial genome (mtDNA). As a unique cytoplasmic genetic system, mitochondrial DNA (mtDNA) is a small, self-replicating and diverse genome. The study on mitochondrial genome is significant in many biological issues, such as gene structure and function, gene expression regulation on time and space, nucleo-cytoplasmic interaction, the dynamics of molecular evolution, the origin of mitochondria, the origin and evolution of species, and so on.Artificial polyploidy fish induced by hybridization has been used in aquaculture to produce sterility or improve production. Meanwhile, they are also useful for investigating mechanism of ploidy variation, sex determination, and mode of inheritance of mitochondrial genome as well. Previously, we obtained the allotetraploid crucian carp by hybridization of red crucian carp and common carp, and obtained diploid natural gynogenetic red crucian carps (2nGRCC), triploid hybrids (3nRB) and tetraploid hybrids (4nRB) by hybridization of red crucian carp (RCC) and blunt snout bream (BSB). The point of this work was to analyze the genetic information of the mtDNA sequences of2nGRCC,3nRB and4nRB, and to analyze the expression information of the mitochondria-related genes in transcriptome of the allotetraploid crucian carp liver. Meanwhile, we also obtained and analyzed the complete mitochondrial genomes of two wild fish, Culteral alburnus and Xdnocypris davidi. The major results in this paper were presented as follows:1. We firstly reported the genetic information of the complete mitochondrial genomes in2nGRCC,3nRB and4nRB and compared them with the mitochondrial genomes of RCC and BSB which represented the parental fish. The complete mitochondrial DNA (mtDNA) sequences of these three polyploid hybrids were all16580bp in length, as same as their female origin (RCC). Analysis of mtDNA structures and sequence comparison indicated that the complete mitochondrial genomes of2nGRCC,3nRB and4nRB were all quite similar to that of RCC rather than BSB. The similarity and divergence analysis also showed that the genetic relationship between these hybrids and RCC were closer than that between them and BSB. These results indicated that the mitochondrial genomes of2nGRCC,3nRB and4nRB were still strictly maternal inherited, although they experienced hybridization and polyploidization. Meanwhile, we found that it could not determine the relative relationship between these hybrids and BSB at the mtDNA sequences level, which implied that it should be cautious when using mtDNA as molecular marker in phylogenetic studies.2. The backcross of female tetraploid hybrids of red crucian carp (♀) xblunt snout bream ((?)) and male blunt snout bream generated two kinds of polyploidy hybrids:two triploid hybrids and one pentaploid hybrid. We sequenced the mitochondrial ND2genes of the maternal4nRB and three hybrid offspring including two triploid hybrids (3nRB1and3nRB2) and one pentaploid hybrid (5nRB). The ND2genes of4nRBs,3nRB1,3nRB2and5nRB were all1047bp in length, encoding348amino acids. The similarity and divergence analysis indicated that the mitochondrial ND2genes of backcross hybrid offspring still stringently subjected to the maternal inheritance rule. Additionally, we observed two substitution of A→G in the mitochondrial ND2genes of3nRB1and5nRB, respectively. By comparison, we also found A<>G substitutions in the same sites in other16fish. The results indicated that the mtDNA genes of hybrid offspring couldn't capture mutations at large degree, but they probably captured few mutations at hot mutation sites.3. The transcriptome of the allotetraploid crucian carp, red crucian carp and common carp liver obtained in the previous study gave us an opportunity to explore the coordination between the nuclear genome and the mitochondrial genome in hybrid offspring. In this work, we filtered94contigs including41respiratory-related genes of the allotetraploid crucian carp,136contigs including46respiratory-related genes of of red crucian carp and84contigs including37respiratory-related genes of common carp in their transcriptomes. By building respiratory-related gene database of red crucian carp and common carp transcriptomes and then performing balstn research of the allotetraploid crucian carp respiratory-related genes in the database, we found out39best matches in red crucian carp respiratory-related genes for allotetraploid crucian carp,40best matches in common carp respiratory-related genes. The results indicated that both nuclear genomes of red crucian carp and common carp involved the OXPHOS process of allotetraploid crucian carp. Beside the mitochondrial respiratory-related genes, we also detected some other mitochondria-related genes including some genes encoding proteins located in membrane of mitochondria and some genes encoding enzyme of mitochondria. The analysis of these genes showed the similar results to the previous results of respiratory-related genes.4. Culter alburnus and Xdnocypris davidi Bleeker are both popular fish in aquiculture. This study first reported complete mitochondrial genomes of these two fish. The entire mtDNA sequences of Culter alburnus and Xdnocypris davidi Bleeker were16622and16630bp in length, respectively. Similar to other cyprinidae fish, the complete mitochondrial genomes encoded the37genes consisting of13protein-coding genes, two rRNA genes,22tRNA genes and a non-coding control region. The characters of the molecular structure and gene organization of the mtDNA genomes in these two fish were described in detail including three conserved domains of D-loop regions. On the other hand, the NJ phylogenetic tree based on the complete mitochondrial genome of Culter alburnus, Xdnocypris davidi Bleeker and other40cyprinidae fish with oncorhynchus mykiss as outgroup were built, which showed that Culter alburnus and Xdnocypris davidi Bleeker had very close relationship. This work will provide genetic information for the breeding of these two fish, and will help to understand the further phylogenetic relationship of cultrinae and Xenocyprinae fish.