Draft genome of Albugo candida Indian variant causing white rust in Brassica juncea unravel variations based on geographic distribution

Background White rust disease elicited by biotrophic pathogen, Albugo candida is a leading cause of yield losses in oilseed Brassica crops, especially widely cultivated B. juncea . The highly diverse nature of the A. candida pathogen and its ability to adapt to various agro-climatic conditions across the globe has posed significant challenges in effectively managing this disease. Therefore, development of a successful control strategy leveraging genomic data of the white rust pathogen is important because it can reveal profound insights into the identification of different forma specialis, phylogenetics, evolution patterns, population biology, secretome and pathogenesis thus, contributing to the oilseed cultivation in India and across the globe. In the present investigation, high quality draft genome of virulent Ac2v race of A. candida infecting B. juncea was generated by Nanopore and Illumina technologies. Results The raw sequencing data was assembled into a genome of 36.88 Mb with 415 scaffolds and N50 = 301.91kb. The variant analysis showed 1,24,974 SNPs with an average density of 3.3 per kb genome against Ac2vPB assembly. Approximately 24.29% of the genome consists of repetitive elements, including 1039 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 rest 214 were novel. Additionally, phylogenetic analysis through average nucleotide identity revealed a similarity of 99.64% between the Canadian and Indian Ac2v isolate. Furthermore, 10 new contigs were identified in the Indian isolate that showed no sequence similarity to the Canadian isolate, suggesting variation within the race based on the geography. Conclusion Altogether, the present work provides genomic resources and framework for the dissection of this complex pathogen which will help refining our understanding of the Albugo - Brassica interaction.