Avian malaria parasites are prevalent around the world and infect a wide diversity of bird species. Here, we report the sequencing and analysis of high-quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum. We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species, and using amino acid divergence between species, we estimate the avian- and mammalian-infective lineages diverged in the order of 10 million years ago. Consistent with their phylogenetic position, we identify orthologs of genes that had previously appeared to be restricted to the clades of parasites containing Plasmodium falciparum and Plasmodium vivax, the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show that the avian lineage is remarkable in the extent to which invasion-related genes are evolving. The subtelomeres of the P. relictum and P. gallinaceum genomes contain several novel gene families, including an expanded surf multigene family. We also identify an expansion of reticulocyte binding protein homologs in P. relictum, and within these proteins, we detect distinct regions that are specific to nonhuman primate, humans, rodent, and avian hosts. For the first time in the Plasmodium lineage, we find evidence of transposable elements, including several hundred fragments of LTR-retrotransposons in both species and an apparently complete LTR-retrotransposon in the genome of P. gallinaceum.

禽疟原虫在世界各地普遍存在，感染多种鸟类。在这里，我们报告了两种禽类疟疾物种（残存疟原虫和鸡疟原虫）的高质量基因组序列草图的测序和分析。我们鉴定了 50 个禽类疟疾特有的基因，这些基因位于基因组的保守核心中，与所有其他已测序的疟疾基因组共享基因同线性。系统发育分析表明，鸟类疟疾物种形成了哺乳动物疟原虫物种的外类群，并且利用物种之间的氨基酸差异，我们估计鸟类和哺乳动物感染谱系在大约 1000 万年前出现了分歧。与它们的系统发育位置一致，我们鉴定了之前似乎仅限于包含恶性疟原虫和间日疟原虫的寄生虫进化枝的基因的直系同源物，这两种寄生虫对人类健康影响最大。从这些直系同源物中，我们探索了整个属的差异多样化选择，并表明鸟类谱系在入侵相关基因进化的程度上是显着的。 P. relictum和P. gallinaceum基因组的亚端粒包含几个新的基因家族，包括扩展的surf多基因家族。我们还鉴定了P. relictum中网织红细胞结合蛋白同源物的扩展，并且在这些蛋白质中，我们检测到非人类灵长类动物、人类、啮齿动物和鸟类宿主特异的不同区域。 我们首次在疟原虫谱系中发现了转座元件的证据，包括两个物种中的数百个 LTR 逆转录转座子片段以及鸡疟原虫基因组中明显完整的 LTR 逆转录转座子。