Dvorak Etienne, Mazet Isabelle D, Couture Carole, Delmotte François, Foulongne-Oriol Marie
SAVE, INRAE, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon F-33140, France.
MYCSA, INRAE, Villenave d'Ornon F-33140, France.
G3 (Bethesda). 2025 Jan 8;15(1). doi: 10.1093/g3journal/jkae259.
Plasmopara viticola, the causal agent of grapevine downy mildew, is a biotrophic oomycete engaged in a tight coevolutionary relationship with its host. Rapid adaptation of the pathogen is favored by annual sexual reproduction that generates genotypic diversity. With the aim of studying the recombination landscape across the P. viticola genome, we generated 2 half-sibling F1 progenies (N = 189 and 162). Using targeted SNP sequencing, between 1,405 and 1,894 markers were included in parental linkage maps, and a consensus map was obtained by integrating 4,509 markers. The reference genome could be assembled into 17 pseudochromosomes, anchoring 88% of its physical length. We observed a strong collinearity between parental genomes and extensive synteny with the downy mildew Peronospora effusa. In the consensus map, the median recombination rate was 13.8 cM/Mb. The local recombination rate was highly variable along chromosomes, and recombination was suppressed in putative centromeric regions. Recombination rate was found negatively correlated with repeats' coverage and positively correlated with gene coverage. However, genes encoding secreted proteins and putative effectors were underrepresented in highly recombining regions. In both progenies, about 5% of the individuals presented karyotypic anomalies. Aneuploidies and triploidies almost exclusively originated from the male-transmitted chromosomes. Triploids resulted from fertilization by diploid gametes, but also from dispermy. Obligatory sexual reproduction each year may explain the lower level of karyotypic variation in P. viticola compared to other oomycetes. The linkage maps will be useful to guide future de novo chromosome-scale assemblies of P. viticola genomes and to perform forward genetics.
葡萄霜霉病菌（Plasmopara viticola）是葡萄霜霉病的致病因子，是一种活体营养型卵菌，与其寄主处于紧密的协同进化关系中。病原体的快速适应得益于每年产生基因型多样性的有性繁殖。为了研究葡萄霜霉病菌基因组的重组图谱，我们构建了2个半同胞F1子代群体（分别为N = 189和162）。通过靶向SNP测序，在亲本连锁图谱中纳入了1405至1894个标记，并通过整合4509个标记获得了一个共识图谱。参考基因组可以组装成17条假染色体，锚定了其88%的物理长度。我们观察到亲本基因组之间具有很强的共线性，并且与霜霉病菌霜霉（Peronospora effusa）具有广泛的同线性。在共识图谱中，重组率中位数为13.8 cM/Mb。局部重组率在染色体上高度可变，并且在假定的着丝粒区域重组受到抑制。发现重组率与重复序列覆盖率呈负相关，与基因覆盖率呈正相关。然而，编码分泌蛋白和假定效应子的基因在高重组区域中代表性不足。在两个子代群体中，约5%的个体出现了核型异常。非整倍体和三倍体几乎完全源自雄性传递的染色体。三倍体是由二倍体配子受精产生的，但也有双精受精的情况。每年必需的有性繁殖可能解释了与其他卵菌相比，葡萄霜霉病菌核型变异水平较低的原因。这些连锁图谱将有助于指导未来葡萄霜霉病菌基因组的从头染色体规模组装，并用于正向遗传学研究。
