Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris)

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.

程序性DNA消除（Programmed DNA elimination）是一类受发育调控的过程，可引发特定基因组序列的可重复性缺失。该过程可见于单细胞纤毛虫以及涵盖无脊椎动物、脊椎动物的多种后生动物类群。在后生动物中，程序性DNA消除通常发生于早期发育阶段的体细胞中，可使生殖系基因组保持完整。目前尚未有针对发生程序性DNA消除的后生动物的参考基因组。本研究针对可发生程序性DNA消除的猪寄生线虫猪蛔虫（Ascaris suum）与马寄生线虫马副蛔虫（Parascaris univalens），分别构建了二者的生殖系与体细胞参考基因组序列。此外，本研究还针对人类寄生线虫人蛔虫（Ascaris lumbricoides）与犬寄生线虫犬弓首蛔虫（Toxocara canis）的程序性DNA消除开展了深度分析。针对线虫程序性DNA消除的分析结果显示，所有受试物种中，属间存在差异的重复序列以及生殖系表达基因（约占基因总数的1000~2000个，或5%~10%）均会被消除。其中35%的被消除基因在线虫类群中保守存在，由此界定出一类在精子发生过程中优先表达的核心消除基因集。本研究的分析结果支持“线虫的程序性DNA消除可沉默生殖系表达基因”这一论断。猪蛔虫与马副蛔虫之间有超过半数的染色体断裂位点保守，而在亲缘关系更远的犬弓首蛔虫中，仅有10%的断裂位点保守。对染色体断裂区域的分析表明，DNA断裂可能采用序列非依赖型机制，后续伴随端粒愈合过程；且在程序性DNA消除发生前，断裂区域的染色质会形成更为开放的结构。本研究构建的基因组组装与注释数据集，同时为程序性DNA消除研究、寄生虫学研究以及线虫比较基因组与表观基因组研究提供了全面的研究资源。