Difference between revisions of "IC4R008-Genome-2016-26984283"
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==Project Title== | ==Project Title== | ||
*Indica rice genome assembly, annotation and mining of blast disease resistance genes | *Indica rice genome assembly, annotation and mining of blast disease resistance genes | ||
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==The Background of This Project== | ==The Background of This Project== | ||
*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. | *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. | ||
| + | <br> | ||
==Plant Culture & Treatment== | ==Plant Culture & Treatment== | ||
| − | + | *The genome of indica rice cultivar, HR-12 was assembled using combination of short reads (PE and MP libraries) from Illumina and long reads from Pacific Biosciences. | |
| + | *HR-12 genome was sequenced using PacBio RS SMRT platform with 20x coverage. | ||
| + | *We scaffolded HR-12 contigs by utilizing stranded RNA sequencing data, which reduced scaffold numbers from 61001 to 59692. | ||
| + | *The gene prediction using MAKER-P in gap filled assembly of HR-12 genome yielded 56,284 protein-coding transcripts. We performed two-way comparison of genes from short read and gap filled assemblies, resulting into 31,933 genes with 100 % identity. | ||
| + | <br> | ||
==Research Findings== | ==Research Findings== | ||
| − | * | + | *The researchers assembled over 86 % (389 Mb) of rice genome and annotated 56,284 protein-coding genes from HR-12 genome using Illumina and PacBio sequencing. |
<br> | <br> | ||
| − | [[File:IC4R008-Genome-2016-26984283-t1.png |center |thumb |10000px | | + | [[File:IC4R008-Genome-2016-26984283-t1.png |center |thumb |10000px |]] |
<br> | <br> | ||
*Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. | *Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. | ||
| − | [[File:IC4R008-Genome-2016-26984283-f2.png |center |thumb |10000px | | + | <br> |
| + | [[File:IC4R008-Genome-2016-26984283-f2.png |center |thumb |10000px |]] | ||
<br> | <br> | ||
*To mine disease resistance genes, the researchers 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. | *To mine disease resistance genes, the researchers 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. | ||
| − | [[File:IC4R008-Genome-2016-26984283-f3.png |center |thumb |10000px | | + | <br> |
| + | [[File:IC4R008-Genome-2016-26984283-f3.png |center |thumb |10000px |]] | ||
<br> | <br> | ||
*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. | *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. | ||
| + | <br> | ||
| + | [[File:IC4R008-Genome-2016-26984283-t2.png |center |thumb |10000px |]] | ||
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*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. | *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. | ||
| + | <br> | ||
| + | [[File:IC4R008-Genome-2016-26984283-f4.png |center |thumb |10000px |]] | ||
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==Labs working on this Project== | ==Labs working on this Project== | ||
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*Manipal University, Manipal 576104, India. | *Manipal University, Manipal 576104, India. | ||
*Genomics Discovery Program, School of Conservation, Life Science and Health Sciences, TransDisciplinary University, Foundation of Revitalization of Local Health Traditions, Bengaluru 560064, India. | *Genomics Discovery Program, School of Conservation, Life Science and Health Sciences, TransDisciplinary University, Foundation of Revitalization of Local Health Traditions, Bengaluru 560064, India. | ||
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==Corresponding Author== | ==Corresponding Author== | ||
*'''malalig'''@ccamp.res.in & '''malalig'''@frlht.org | *'''malalig'''@ccamp.res.in & '''malalig'''@frlht.org | ||
Latest revision as of 16:54, 26 June 2016
Contents
Project Title
- Indica rice genome assembly, annotation and mining of blast disease resistance genes
The Background of This Project
- 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.
Plant Culture & Treatment
- The genome of indica rice cultivar, HR-12 was assembled using combination of short reads (PE and MP libraries) from Illumina and long reads from Pacific Biosciences.
- HR-12 genome was sequenced using PacBio RS SMRT platform with 20x coverage.
- We scaffolded HR-12 contigs by utilizing stranded RNA sequencing data, which reduced scaffold numbers from 61001 to 59692.
- The gene prediction using MAKER-P in gap filled assembly of HR-12 genome yielded 56,284 protein-coding transcripts. We performed two-way comparison of genes from short read and gap filled assemblies, resulting into 31,933 genes with 100 % identity.
Research Findings
- The researchers 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, the researchers 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.
Labs working on this Project
- 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.
- Pacific Biosciences, Boon Lay Way, Singapore 609964, Singapore.
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences,Ohio State University, Columbus 43210, USA.
- Manipal University, Manipal 576104, India.
- Genomics Discovery Program, School of Conservation, Life Science and Health Sciences, TransDisciplinary University, Foundation of Revitalization of Local Health Traditions, Bengaluru 560064, India.
Corresponding Author
- malalig@ccamp.res.in & malalig@frlht.org
