Comprehensive whole genome hybrid assembly unravels genes and secretome of Albugo candida (Indian isolate), causing white rust disease in Brassica juncea

Abstract

White rust disease elicited by the biotrophic pathogen Albugo candida is a leading cause of yield losses in oilseed Brassica crops, especially in the widely cultivated Brassica juncea. In the present investigation, the high-quality draft genome of a virulent Ac2V race of A. candida infecting B. juncea was sequenced using Illumina and Nanopore technologies. The raw data were assembled into a genome of 36.88 Mb with 415 scaffolds and N50 = 301.91 kb. The variant analysis showed 124,974 single nucleotide polymorphisms (SNPs) with an average density of 3.3 SNP per kb genome against the Ac2VPB reference assembly. Approximately 24.29% of the genome was constituted of repetitive elements, including 1,039 SSRs. A total number of 13,715 coding genes were revealed in the genome with an average distribution of 359.03 genes per Mb. Out of these predicted genes, 11,556 were annotated based on sequence homology and 355 were predicted as effectors with no transmembrane domain and N-terminal signal peptide. The annotation of 355 effectors revealed that 141 of them had homologs, while the remaining 214 were novel. Depending on the conserved motifs, these effectors were characterized, and their role in pathogenesis was established through qPCR in B. juncea. Additionally, phylogenetic analysis through average nucleotide identity revealed a similarity of 99.6% between the Canadian and Indian Ac2V isolate. Furthermore, 62 new contigs were identified in the Indian isolate that showed no sequence similarity to the Canadian isolate, suggesting variation within the race. Altogether, the present work provides genomic resources and framework for the dissection of this pathogen, which will refine our understanding of the Albugo–Brassica interaction.