title: Indica rice genome assembly, annotation and mining of blast disease resistance genes.
abstract: BACKGROUND
  Rice is a major staple food crop in the world. Over 80% of rice cultivation area is under indica rice. Currently, genomic resources are lacking for indica as compared to japonica rice. In this study, we generated deep-sequencing data (Illumina and Pacific Biosciences sequencing) for one of the indica rice cultivars, HR-12 from India.
  
  
  RESULTS
  We assembled over 86% (389 Mb) of rice genome and annotated 56,284 protein-coding genes from HR-12 genome using Illumina and PacBio sequencing. Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. To mine disease resistance genes, we sequenced few indica rice cultivars that are reported to be highly resistant (Tetep and Tadukan) and susceptible (HR-12 and Co-39) against blast fungal isolates in many countries including India. Whole genome sequencing of rice genotypes revealed high rate of mutations in defense related genes (NB-ARC, LRR and PK domains) in resistant cultivars as compared to susceptible. This study has identified R-genes Pi-ta and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program.
  
  
  CONCLUSIONS
  This is the first report of whole genome sequencing approach to characterize Indian rice germplasm. The genomic resources from our work will have a greater impact in understanding global rice diversity, genetics and molecular breeding.
authors.affiliation: Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065, India.|Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India.|Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, Ohio State University, Columbus, 43210, USA.
authors.forename: H B
authors.initials: HB
authors.lastname: Mahesh
authors.affiliation: Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065, India.|Manipal University, Manipal, 576104, India.
authors.forename: Meghana Deepak
authors.initials: MD
authors.lastname: Shirke
authors.affiliation: Pacific Biosciences, Boon Lay Way, Singapore, 609964, Singapore.
authors.forename: Siddarth
authors.initials: S
authors.lastname: Singh
authors.affiliation: Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065, India.
authors.forename: Anantharamanan
authors.initials: A
authors.lastname: Rajamani
authors.affiliation: Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India.
authors.forename: Shailaja
authors.initials: S
authors.lastname: Hittalmani
authors.affiliation: Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, Ohio State University, Columbus, 43210, USA.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
authors.affiliation: Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru, 560065, India. malalig@ccamp.res.in.|Genomics Discovery Program, School of Conservation, Life Science and Health Sciences, TransDisciplinary University, Foundation of Revitalization of Local Health Traditions, Bengaluru, 560064, India. malalig@ccamp.res.in.
authors.forename: Malali
authors.initials: M
authors.lastname: Gowda
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics*; D010935:Plant Diseases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: Blast resistance; Genome sequencing; Illumina; Indica; O. sativa; Pacific Biosciences; SNPs; SSRs