Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. Here, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum and the horse parasite Parascaris univalens. In addition, we carried out in-depth analyses of DNA elimination in the parasitic nematode of humans, Ascaris lumbricoides, and the parasitic nematode of dogs, Toxocara canis. Our analysis of nematode DNA elimination reveals that in all species, repetitive sequences (that differ among the genera) and germline-expressed genes (approximately 1000–2000 or 5%–10% of the genes) are eliminated. Thirty-five percent of these eliminated genes are conserved among these nematodes, defining a core set of eliminated genes that are preferentially expressed during spermatogenesis. Our analysis supports the view that DNA elimination in nematodes silences germline-expressed genes. Over half of the chromosome break sites are conserved between Ascaris and Parascaris, whereas only 10% are conserved in the more divergent T. canis. Analysis of the chromosomal breakage regions suggests a sequence-independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our genome assemblies and annotations also provide comprehensive resources for analysis of DNA elimination, parasitology research, and comparative nematode genome and epigenome studies.

程序化的DNA消除是一个发育受调控的过程，导致特定基因组序列的可再现丢失。DNA消除发生在单细胞纤毛虫和各种后生动物中，包括无脊椎动物和脊椎动物。在后生动物中，DNA消除通常在早期发育过程中发生在体细胞中，而使种系基因组保持完整。没有经过DNA消除的后生动物的参考基因组。在这里，我们产生种系和DNA消除猪寄生线虫躯体参照基因组序列猪蛔虫和马寄生虫蛔虫univalens。此外，我们对人类寄生线虫Ascaris lumbricoides，和狗的寄生线虫Toxocara cani s。我们对线虫DNA消除的分析表明，在所有物种中，重复序列（属间不同）和种系表达基因（约占1000–2000或基因的5％–10％）被消除了。这些线虫中有35％的这些被消除的基因是保守的，从而定义了一组在精子发生过程中优先表达的被消除的基因的核心。我们的分析支持以下观点：线虫中的DNA消除使种系表达的基因沉默。在染色体断裂点的一半之间保守的蛔虫和蛔虫，而只有10％是在更发散保守犬蛔虫。染色体断裂区域的分析表明DNA断裂的一种独立于序列的机制，随后发生了端粒修复，在DNA消除之前，断裂区域中形成了更多可利用的染色质。我们的基因组组装和注释还为DNA消除分析，寄生虫学研究，比较线虫基因组和表观基因组研究提供了全面的资源。