IC4R008-Genome-2016-26984283 - Revision history

Guangyi: /* Research Findings */

2016-06-26T16:54:56Z

‎Research Findings

Guangyi at 09:15, 26 June 2016

2016-06-26T09:15:15Z

Guangyi: /* Plant Culture & Treatment */

2016-06-26T09:13:12Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-06-26T09:11:56Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-06-26T09:10:35Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-06-26T09:08:19Z

‎Plant Culture & Treatment

Guangyi: /* Research Findings */

2016-06-26T08:41:05Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-26T08:40:44Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-26T08:39:45Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-26T08:36:14Z

‎Research Findings

@@ Line 12: / Line 12: @@
 <br>
 ==Research Findings==
-*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.
+*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>
 [[File:IC4R008-Genome-2016-26984283-t1.png |center |thumb |10000px |]]
@@ Line 32: / Line 32: @@
 [[File:IC4R008-Genome-2016-26984283-f4.png |center |thumb |10000px |]]
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 ==Labs working on this Project==
 *Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP),National Centre for Biological Sciences (NCBS), Bengaluru 560065, India.

@@ Line 1: / Line 1: @@
 ==Project Title==
 *Indica rice genome assembly, annotation and mining of blast disease resistance genes
+<br>
 ==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.
@@ Line 9: / Line 10: @@
 *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==
 *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.
@@ Line 31: / Line 32: @@
 [[File:IC4R008-Genome-2016-26984283-f4.png |center |thumb |10000px |]]
 <br>
 ==Labs working on this Project==
 *Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP),National Centre for Biological Sciences (NCBS), Bengaluru 560065, India.
@@ Line 39: / Line 39: @@
 *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.
+<br>
 ==Corresponding Author==
 *'''malalig'''@ccamp.res.in & '''malalig'''@frlht.org

@@ Line 8: / Line 8: @@
 *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.
 ==Research Findings==

@@ Line 7: / Line 7: @@
 *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.
 ==Research Findings==

@@ Line 5: / Line 5: @@
 *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 (Additional file 2) from Pacific Biosciences (Additional file 3).
+*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.
 ==Research Findings==

@@ Line 13: / Line 13: @@
 *Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels.
 <br>
-[[File:IC4R008-Genome-2016-26984283-f2.png |center |thumb |10000px |'''''']]
+[[File:IC4R008-Genome-2016-26984283-f2.png |center |thumb |10000px |]]
 <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.
 <br>
-[[File:IC4R008-Genome-2016-26984283-f3.png |center |thumb |10000px |'''''']]
+[[File:IC4R008-Genome-2016-26984283-f3.png |center |thumb |10000px |]]
 <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.
 <br>
-[[File:IC4R008-Genome-2016-26984283-t2.png |center |thumb |10000px |'''''']]
+[[File:IC4R008-Genome-2016-26984283-t2.png |center |thumb |10000px |]]
 <br>
 *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 |'''''']]
+[[File:IC4R008-Genome-2016-26984283-f4.png |center |thumb |10000px |]]
 <br>