National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Brief Bioinform. 2021 Sep 2;22(5). doi: 10.1093/bib/bbaa399.
With the rapid progress of sequencing technologies, various types of sequencing reads and assembly algorithms have been designed to construct genome assemblies. Although recent studies have attempted to evaluate the appropriate type of sequencing reads and algorithms for assembling high-quality genomes, it is still a challenge to set the correct combination for constructing animal genomes. Here, we present a comparative performance assessment of 14 assembly combinations-9 software programs with different short and long reads of Duroc pig. Based on the results of the optimization process for genome construction, we designed an integrated hybrid de novo assembly pipeline, HSCG, and constructed a draft genome for Duroc pig. Comparison between the new genome and Sus scrofa 11.1 revealed important breakpoints in two S. scrofa 11.1 genes. Our findings may provide new insights into the pan-genome analysis studies of agricultural animals, and the integrated assembly pipeline may serve as a guide for the assembly of other animal genomes.
随着测序技术的快速发展，已经设计了各种类型的测序reads 和组装算法来构建基因组组装。尽管最近的研究试图评估用于组装高质量基因组的适当类型的测序reads 和算法，但为构建动物基因组设置正确的组合仍然是一个挑战。在这里，我们对 14 种组装组合进行了比较性能评估，这些组合是针对杜洛克猪的不同短读长和长读长的 9 种软件程序。基于基因组构建的优化过程的结果，我们设计了一个集成的混合从头组装管道 HSCG，并构建了杜洛克猪的草图基因组。新基因组与 Sus scrofa 11.1 的比较揭示了两个 Sus scrofa 11.1 基因中的重要断点。我们的研究结果可能为农业动物的泛基因组分析研究提供新的见解，而集成的组装管道可以为其他动物基因组的组装提供指导。
