Malaria causes >600 thousand fatalities each year, with most cases attributed to the human-infectious Plasmodium falciparum species. Many rodent-infectious Plasmodium species, like Plasmodium berghei and Plasmodium yoelii, have been used as model species that can expedite studies of this pathogen. P. yoelii is an especially good model for investigating the mosquito and liver stages of development because key attributes closely resemble those of P. falciparum. Because of its importance, in 2002 the 17XNL strain of P. yoelii was the first rodent malaria parasite to be sequenced. Although this was a breakthrough effort, the assembly consisted of >5000 contiguous sequences that adversely impacted the annotated gene models. While other rodent malaria parasite genomes have been sequenced and annotated since then, including the related P. yoelii 17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the de facto reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for P. yoelii 17XNL using PacBio DNA sequencing. In addition, we use Nanopore and Illumina RNA sequencing of mixed blood stages to create complete gene models that include coding sequences, alternate isoforms, and UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic framework for studies with this commonly used rodent malaria model species.

疟疾每年造成超过 60 万人死亡，其中大多数病例是由传染人类的恶性疟原虫引起的。许多啮齿动物感染性疟原虫物种，如伯氏疟原虫和约氏疟原虫，已被用作模型物种，可以加快对该病原体的研究。约氏疟原虫是研究蚊子和肝脏发育阶段的特别好的模型，因为其关键属性与恶性疟原虫非常相似。由于其重要性，2002 年，约氏疟原虫17XNL 菌株成为第一个被测序的啮齿动物疟疾寄生虫。尽管这是一项突破性的努力，但组装由超过 5000 个连续序列组成，对注释的基因模型产生了不利影响。虽然此后其他啮齿动物疟原虫基因组已被测序和注释，包括相关的约氏疟原虫17X 菌株，但 17XNL 菌株尚未测序和注释。因此，17X 的基因组数据已成为17XNL 菌株事实上的参考基因组，同时围绕 17XNL 和 17X 基因组之间可能存在的差异留下了悬而未决的问题。在这项工作中，我们使用 PacBio DNA 测序展示了P. yoelii 17XNL的高质量基因组组装。此外，我们使用 Nanopore 和 Illumina RNA 混合血液阶段测序来创建完整的基因模型，其中包括编码序列、替代亚型和 UTR 名称。17X 和新的 17XNL 组件的比较揭示了由于编码序列变体的存在而导致菌株之间具有生物学意义的差异。总而言之，我们的工作为这种常用的啮齿动物疟疾模型物种的研究提供了一个新的基因组框架。