REVIEW ARTICLE Biology of B. sorokiniana (syn. Cochliobolus sativus) in genomics era Pushpendra K. Gupta 1 • Neeraj K. Vasistha 1 • Rashmi Aggarwal 2 • Arun K. Joshi 3 Received: 17 June 2017 / Accepted: 7 September 2017 Ó Society for Plant Biochemistry and Biotechnology 2017 Abstract Bipolaris sorokiniana (Sacc.) Shoemaker is a hemi-biotrophic fungal pathogen, which is an anamorph (teleomorph Cochlibolus sativus). It causes spot blotch, root rot and leaf spot diseases in a number of cereals including wheat, barley and other small grain cereals. In the genomics era, the fungus has been subjected to a variety of studies using molecular approaches. Correct chromosome number was determined and molecular karyotypes were prepared using contour-clamped homo- geneous electric field. Molecular maps were prepared using markers like RFLPs, SSRs, RAPDs and SNPs. For this purpose, segregating progenies derived from crosses between diverse isolates of the pathogen were used. Whole genome sequencing (WGS) data was collected not only for B. sorokiniana isolates, but also for several species of Cochliobolus. Genes involved in secondary metabolism and virulence were identified from genome sequences. The WGS data has also been utilized for comparative genomics giving useful information about evolutionary trends. A brief account of this information is presented in this review. Keywords Spot blotch Á Bipolaris sorokiniana Á Karyotypes Á NRPSs Á VHv1 Á Genomics Abbreviations SB Spot blotch CRR Common root rot ITS Internal transcribed spacer PTI PAMP-triggered immunity ETI Effector-triggered immunity ETS Effector triggered susceptibility NRPS Non-ribosomal peptide synthetases PKS Polyketide synthases NGS Next generation sequencing NBS LRR Nucleotide-binding site leucine-rich repeat S/TPK Serine/threonine protein kinase NE Necrotrophic effector CHEF Contour-clamped homogeneous electric field GTBM Germ tube burst method AFLP Amplified fragment length polymorphism HST Host-selective toxin Avr Avirulence NLS Nuclear localization signals SSP Small secreted protein EST Expressed sequence tag SSR Simple sequence repeat qRT-PCR Quantitative real-time polymerase chain reaction Introduction Bipolaris sorokiniana (Sacc.) Shoemaker is an important fungal pathogen causing several diseases in wheat, barley, and other small grain cereals. These diseases include spot blotch (SB), common root rot (CRR) and leaf spot. In 1990, the fungus was declared to be the most important foliar pathogen of wheat in warm regions of the world (‘‘Wheat & Pushpendra K. Gupta pkgupta36@gmail.com 1 Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India 2 Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India 3 The International Maize and Wheat Improvement Center (CIMMYT), G-2, B-Block, NASC Complex, DPS Marg, New Delhi, India 123 J. Plant Biochem. Biotechnol. DOI 10.1007/s13562-017-0426-6