Preliminary Study On The Heterosis Mechanism Of Takifugu With High-throughput Sequencing Technologies

Heterosis refers to the improved biological qualities in the hybrid offspringof two distinct species, which has been used to increase yields and vigor inagricultural production for thousands of years. The mechanism study ofheterosis has been processding since1900’s, however there is stillcontroversy. Jiyan-1is the hybrid offspring of Takifugu rubripes and Takifuguflavidus, which exhibits obvious heterosis in the fields of growth performance,flavor and stress tolerance. In the present study, the genome of T. flavidus wassequenced and assembled, and the characteristic features were also analyzed.In addition, the transcriptomes of Jiyan-1and both parental species werecomparatively studied. The potential mechanisms of heterosis were discussedin the fields of gene action modes, function annotation of differentiallyexpressed transcripts and prediction of novel transcript isoforms.Firstly, three Mate-Pair libraries with different insert sizes were constructedfrom genomic DNA of T. flavidus, and sequenced using SOLiD4platform. Thecombined sequencing length was76.0Gb, and the average sequencing depthwas more than190-fold. The genome was assembled with assisted-assemblywhich generated50,947scaffolds with N50value of305.7kb. The average GCcontent was45.2%, and the proportion of repetive sequences was6.87%ofthe genome, which indicated the genome of T. flavidus was as compact as thegenome of T. rubripes. Sequence comparison of scaffolds showed obvioussynteny between the genomes of T. flavidus and T. rubripes.There were1,253non-coding RNA genes, including649tRNA genes whichwere capable of encoding50anticodons for all species of amino acids. Thenumbers of species and copies of miRNA genes were more than that in the genomes of T. rubripes and T. nigroviridus, indicating the gene expression wasunder more rigorous monitor and the gene expasion had been ongoing afterthe speciation of T. flavidus. There were30,285protein-encoding genes whoseprotein products had an average length of519.9aa. There were average7.2introns per gene, and75%of introns were with length less than543bp. Thelengths of introns in T. flavidus were greater than that of T. rubripes, while nosignificant difference was found for the number of protein-encoding genes andintrons, the sequences of proteins and the length distribution of proteinsbetween T. flavidus and T. rubripes. The phylogenetic analysis of wholeproteomes indicated T. flavidus and T. rubripes were closely allied species.There were16genes related to the biosynthesis of pigment granules and116genes evolved in the microtubule-dependent transport system. The copynumbers of these genes were much more that in the T. rubripes, indicating themicrotubule-dependent transport system might play a role in the color patternvariation during the growth. The T. flavidus genome contained42genesencoding Brinker which was an importance suppressor for Dpp signalingpathway. Besides, the more copy numbers of adiponectin receptor gene andnoradrenaline transporter gene suggested the activities of lipid mobilizationand metabolism were up-regulated in T. flavidus. The genomic level analysiscontributed to better understanding of the relationship between the genotypeand phenotype, and also provided valuable data resource for heterosis studyin transcriptomic level.Whole transcriptomes of Jiyan-1, T. rubripes and T. flavidus weresequenced by SOLiD4platform. The combined sequencing length was12.2Gb. A total of44,305transcripts were identified, among which there were14,148differentially expressed transcripts (DTs). In Jiyan-1,68.7%DTs wereclassified as “above high parent”,19.8%DTs were classified as “low parent” or“high parent”, and4.6%DTs were classified as “mid parent”. The coexistenceof overdominance, dominance, underdominance and additivity was observedin the gene action modes of Jiyan-1. The functional annotation of enriched DTs indicated the metabolism was more activated in Jiyan-1. In addition, therewere35KEGG pathways affiliated by more than3DTs. Among them, thexenobiotics and drug metabolism pathways mediated by cytochrome P450andthe metabolism pathway of carbohydrate, amino acid and triglyceridepotentially gave rise to the high tolerance of hostile environment and fastgrowth rate. The identified novel transcript isoforms in Jiyan-1were likelyinvolved in a variety of biological processes including signal transduction,metabolism, transmembrane transportation and so on, which also underlinedthat heterosis was not originated from one single mechanism, but by theaccumulation of disparities from multiple pathways.