Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.

中文翻译：

---

不同的生活史影响锈病真菌小麦条锈菌（Puccinia striiformis）中的双核基因组进化，导致小麦出现条锈病。

小麦条锈病，造成专活体营养性真菌条锈菌病菌 小麦是全球小麦生产的主要威胁，估计每年损失10亿美元。长读测序技术和定制组装算法的最新进展使我们能够解开Pst的两个单倍体基因组。这为我们提供了全基因组水平的单倍型特定信息。利用这一新颖信息，我们进行了两个P的全基因组比较基因组学。条锈病f.sp 。小麦与相反的生活史隔离。我们比较了一个古老的欧洲血统（PstS0）的分离株，该病已经无性繁殖了50多年，以及一个从2011年从喜马拉雅地区的性人口新入侵欧洲的战士分离株（PstS7血统）。这种比较提供了证据，表明长期的无性进化导致基因组扩展，转座因子的积累以及单核苷酸，结构和等位基因水平上杂合性的提高。在全基因组水平上，候选效应子没有被区分开并且没有表现出降低的同义水平。然而，我们能够确定候选效应子群体的两个子集。约70％的候选效应子在两个分离株之间是不变的，而30％是高变的。后者可能参与了小麦的寄主适应，并解释了两种分离株的不同表型。总体而言，此详细比较分析包括两个单倍型P。条锈病f.sp 。Tritici是了解全基因组水平上双核锈菌进化的第一步。