Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
Cell Rep. 2017 Oct 17;21(3):834-844. doi: 10.1016/j.celrep.2017.09.077.
The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P. pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P. pacificus. Despite widespread conservation of synteny between P. pacificus and C. elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C. elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P. pacificus.
秀丽隐杆线虫（Caenorhabditis elegans）是整合进化生物学和比较研究的成熟模式生物。尽管现有基因组草案有助于鉴定控制各种发育过程的几个基因，但它的高度碎片化几乎使所有的基因组分析都变得复杂。在这里，我们从单分子长读测序数据中展示了一个从头组装的基因组，其中包含 135 个秀丽隐杆线虫 P. pacificus 连续片段。当与遗传连锁图谱相结合时，组装的 99%可以被排序并定向到 6 条染色体上。这使我们能够在秀丽隐杆线虫 P. pacificus 中稳健地描述基因密度、重复含量、核苷酸多样性、连锁不平衡和大基因簇的染色体模式。尽管秀丽隐杆线虫 P. pacificus 和秀丽隐杆线虫之间广泛存在基因同线性，但我们在导致秀丽隐杆线虫的谱系中发现了一条从常染色体到性染色体的主要易位。这突出了染色体级组装在未来秀丽隐杆线虫 P. pacificus 基因组研究中的潜力。
