异源多倍化发生初期是形成多倍体的关键时期，此时期发生的基因组变化最终决定异源多倍体子代能否成功繁衍成为新物种。用鲫鱼和普通鲤鱼杂交获得的鲫鲤杂交体系，是目前世界上仅存的亲本背景清晰且杂交后代能稳定遗传的多倍化体系(F1-F21)。本项目拟综合应用新一代测序技术和生物信息学等手段，补充构建并测定mate-pair文库，继续完成获得雌核发育红鲫全基因组草图，以此为参考基因组，对鲫鲤杂交体系中亲本与多倍化初期不同世代(F1-F3; F18; F21)的重要组织进行转录本分析，全面而系统地分析研究异源多倍化发生后子代中的遗传水平改变规律，如重组、子代特异性改变等变化在不同世代中的规律，同时这些改变对基因网络改变的作用和对相关性状改变的贡献，以期了解脊椎动物异源多倍化初期发生的改变规律如何贡献于脊椎动物演化这一重要理论问题提供有意义的线索，也为渔业中更好地利用此现象奠定理论基础。

Allopolyploidizaiton ocurrs recurrently in plants and lower vertebrates, and it can result in instantaneous speciation. Because new polyploids are immediately reproductively isolated from their non-polyploid congeners, polyploidization has played an important role in the diversification of the flowering plants and some vertebrates. Newly formed polyploids must respond to this instantaneous genomic change, which resembles “genome shock” syndrome, to survive and to reproduce successfully. Polyploidy cyprinids are useful models in vertebrate polyploidization investigations and in fisheries. In our recent work, we haved used the first sucessful allopolyploidy system in vertebrate, which was generated by goldfish (maternal) x common carp (parternal), as a model, to inverstigate early stage modifications in their genomes and gene pathways of the polyploidy offsprings with transcriptome data. We have found intriguingly high percentage of recombination rate and even mutation rate in the offspring. In order to fully use the obtained data and to conduct further work in this allopolyploidy system, we start sequencing its materal genome,the goldfish in our pilot work. First we have obtained gynogenetic tetraploid goldfish,by using normal goldfish eggs and stimulate them by heterologous sperms and cold shock. The gynogenetic goldfish has decreased heterozygosity comparing to that of the normal goldfish. After we obtained gynogenetic tetraploid goldfish, its genome were sequenced using the next generation sequencing techniques. We have obtained sequencing results from four short fragment pair-end libraries, and we conducted primitive assembly, In this project, firstly, we will add more longer fragment sequencing results from mate-pair libraries in order to obtain genome draft. Besides, to increase assembly rate and reliability for the tetraploid genome, new algorithms and programs will be developed. Secondly, based on the available goldfish genome, we plan to analyze both the obtained transcriptome data in our pilate work and additional transcriptome data from different tissues of the allopolyploidy offsprings comparing to their progenitors, and to identify the hot-change regions and pathways in the polyploidy offspring. We expect to find out possible key regions in the genomes and key changes in the gene pathways which are important to the formation of allopolyploidization. Lastly, we will also estimate recombination rate, genomic structural variation rate in the offsprings according to the genomes of two progenitors’. Thus, to find clues how of the vertebrate divercification is benefited from allopolyploidization, and in turn, how this process can be applied to fisheries more efficiently.