Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata
Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata
复制标题
DOI：
10.1534/g3.119.400047
复制
发表时间：
2019-08-01
影响因子：
2.6
通讯作者：
Lemaire, Christophe
中科院分区：
文献类型：
--
作者：
Le Cam, Bruno;Sargent, Dan;Lemaire, Christophe
Venturia 属包括作为蔷薇科宿主植物上的病原体的真菌物种，包括苹果上的 V. inaequalis 和 V. asperata、山梨上的 V. aucupariae 和梨上的 V. pirina。尽管已经对不平等弧菌种群的遗传结构进行了详细研究，但这些细分的基因组特征仍然知之甚少。在这里，我们报告了代表 V. inaequalis 内每个物种和每个种群的 87 个 Venturia 菌株的全基因组测序。 We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate.所选基因组的大小通过流式细胞术确定，范围为 45 至 93 Mb。 V. inaequalis 和 V. aucupariae 的基因组组件含有高含量的转座元件 (TE)，其中大部分属于 Gypsy 或 Copia LTR 超家族，并已因重复诱导点突变而失活。 V. inaequalis 的参考组装呈现出主要包含预测基因的 GC 平衡区域和主要由 TE 组成的 AT 富集区域的镶嵌结构。六对菌株被鉴定为克隆。这些克隆之间的单核苷酸多态性 (SNP) 分析显示，由于错位，大量 SNP 大多位于富含 AT 的区域，并允许确定错误发现率。这些基因组序列的可用性预计将刺激文丘里病原体的遗传学和群体基因组学研究。特别是，它将有助于了解对不同宿主致病的文丘里菌物种的进化历史，这一历史可能受到 TE 的重大影响。
The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis. We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.