The Genome Center, University of California, Davis, CA 95616, USA.
U.S. Department of Agriculture-Agriculture Research Service, Salinas, CA, 93905, USA.
G3 (Bethesda). 2023 Mar 9;13(3). doi: 10.1093/g3journal/jkac340.
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.
几种卵菌属的种引起玉米霜霉病，在亚洲可导致重大产量损失。对这些病原体进行生物监测是预防美国玉米流行病和随后对美国经济造成损害的当务之急。卵菌属的未解决的分类学和分子资源的缺乏阻碍了这些努力。P. sorghi 是一种具有全球分布的高粱和玉米病原体，在美国南部检测到的多样性有限。我们对代表美国 6 型致病型的分离物进行了基因组、转录组和线粒体基因组特征分析。高度纯合的基因组使用 10× Genomics 连接读取进行组装，并使用 Hi-C 支架构建成 13 条染色体。总组装长度为 303.2Mb，大于以前组装的任何其他卵菌。线粒体基因组为 38kb，与其他卵菌相似，尽管它具有独特的基因顺序。在核基因组中注释了近 20000 个基因，超过了其他引起霜霉病的卵菌。P. sorghi 的 13 条染色体与 Peronospora effusa 的 17 条染色体高度同线性，具有保守的着丝粒区域和独特的染色体融合。P. sorghi 增加的组装大小和基因数是由于广泛的反转录转座，导致可能的假基因化。祖先基因的转录丰度更高，并且差异表达丰富。这项研究为分析 Peronosclerospora 以及与其他卵菌属的比较提供了基础资源。对全球 Peronosclerospora spp.的进一步基因组研究将确定线粒体基因组、祖先基因和假定的假基因在标记开发和分类关系中的适用性。
