Comparative genome analysis of Tilletia indica inciting Karnal bunt of wheat reveals high genomic variation

Karnal bunt of wheat is an internationally quarantined disease caused by Tilletia indica . The disease is important in North-western plain zone of India. Till date no reference or complete genome of Tilletia indica is available and reported genomes are variable in size ranging from 26.7 to 43.7 Mb. Recently whole genome of Tilletia indica RAKB_UP_1 (GCA_002220835.1, IARI, New Delhi) has been sequenced. In present study, the genomes of seven isolates of T. indica viz. . DAOM_236416 (GCA_001645015.1), PSWKBGD_1_3 (GCA_001689965.1), PSWKBGH_1 (GCA_001689995.1), PSWKBGH_2 (GCA_001689945.1), RAKB_UP_1 (GCA_002220835.1), TiK_1 (GCA_002997305.1) and Tik (GCA_003054935.1) were compared. For genome mapping, all the genome assemblies were aligned against RAKB_UP_1 genome using minimap2 wherein 86–100% similarity was observed with the reference genome. Tik_1 mapped 100%. Further, comparative genome analysis was done by identification of SNPs, In-Dels, segmental duplicates, LTR and CNV. It revealed that variable number of SNPs were ranging from 1380 (Tik_1) to 160966 (Tik) and 82 (PSWKBGH_1) to 3309 (PSWKBGD_1_3) In-Dels. The maximum number of segmental duplications (SDs) were identified in TiK_1 isolate (60632 regions) while least in DAOM_236416 isolate (2082 regions). LTR retrotransposon regions were found as 307 (DAOM_236416)–833 (PSWKBGH_2). The copy number variations including duplications and deletions have also been identified and Tik had shown highest number of duplications count (100) while no duplication was found in Tik_1 which was expected also because of 100% mapping with the reference genome. In case of deletion counts, highest (37) deletion were detected in DAOM_236416. This first study revealed that T . indica genome showed high genomic variation and can be used to devise the novel management strategies against Karnal bunt of wheat.