A5055951269- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Rice Cultivation and Yield Improvement
- Cannabis and Cannabinoid Research
- GABA and Rice Research
- Genetics and Plant Breeding
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- Transgenic Plants and Applications
- Algorithms and Data Compression
- Plant Taxonomy and Phylogenetics
- Plant nutrient uptake and metabolism
- Plant Virus Research Studies
- RNA and protein synthesis mechanisms
- Autophagy in Disease and Therapy
- Metabolomics and Mass Spectrometry Studies
- Wheat and Barley Genetics and Pathology
- Photosynthetic Processes and Mechanisms
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
Southern Cross University
2024
International Rice Research Institute
2005-2019
Max Planck Institute of Biochemistry
2010
University of the Philippines Diliman
2005
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with five major groups previously recognized, but also suggest several unreported subpopulations that correlate geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 small indels over 90,000 structural variations contribute to within- between-population variation....
We have identified about 20 million rice SNPs by aligning reads from the 3000 genomes project with Nipponbare genome.The and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/),which consists of Oracle database having total number rows SNP genotypes close to 60 billion (20 M × 3 K lines) web interface for convenient querying.The allows quick retrieving alleles all varieties in given genome region, finding different predefined querying basic passport...
We describe updates to the Rice SNP-Seek Database since its first release. ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides Nipponbare reference genome, was run on genome assemblies of IR 64, 93-11, DJ 123 Kasalath. New genotype query display features are added for assemblies, datasets indels. JBrowse now displays BAM, VCF other annotation tracks, additional an embedded VISTA comparison viewer. Middleware is...
The 3000 Rice Genomes Project generated a large dataset of genomic variation to the world's most important crop, Oryza sativa L. Using Burrows-Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK) variant calling on this dataset, we identified ∼40 M single-nucleotide polymorphisms (SNPs). Five reference genomes rice representing major variety groups were used: Nipponbare (temperate japonica), IR 64 (indica), 93–11 DJ 123 (aus), Kasalath (aus). results are accessible through SNP-Seek...
Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial medicinal applications have spurred recent genetic genomics research. An international research community emerged identified the need a web portal to host cannabis-specific datasets that seamlessly integrates multiple data sources serves omics-type analyses, fostering information sharing. The Tripal platform was used public genome assemblies, gene annotations, quantitative...
The data provided by the International Cannabis Genomics Research Consortium (ICGRC, https://icgrc.info) web portal consists of published results from past analyses, and generated using steps described in this protocol. We used public datasets, open software commonly for specific tasks, suggested best practices, or other Tripal sites. sections protocol can be grouped into Data Generation (steps 1-8), Setup Modules 9-15), Multi-omics API Integration (step 16,17), non-Tripal pages 18).
A growing interest in
Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for study extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction microorganism. The itself represents knowledge base haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, experimentally determined several parameters relevant growth,...
Cannabis sativa is seeing a global resurgence as food, fiber and medicinal crop for industrial hemp industries respectively. However, widespread moratorium on the use research of C. throughout most 20th century has seen development improved cultivars specific end uses lag behind that conventional crops. While significant investments in recent past, resulting suite publicly available genomic resources tools, versatile cost-effective mid-density genotyping platform applied purposes breeding...
Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies high-density genotyping platforms for genome variation analysis gene discovery. Germplasm collections representing rice improved varieties, elite breeding materials are accessible through banks use in with many having sequences genotype data available. Combining phenotypic genotypic information on these accessions enables genome-wide association...
Global changes in Cannabis legislation after decades of stringent regulation, and heightened demand for its industrial medicinal applications have spurred recent genetic genomics research. An international research community emerged identified the need a web portal to host Cannabis-specific datasets that seamlessly integrates multiple data sources serves omics-type analyses, fostering information sharing. The Tripal platform was used public genome assemblies, gene annotations, QTL maps,...
The International Cannabis Genome Research Consortium (ICGRC) has taken up the task of providing an authoritative source rigorous and peer-reviewed scientific information relating to genetics, genomics phenotyping. Just out in GigaByte are papers presenting two these outputs, CannSeek database bringing together many datasets, a community-driven bioinformatics platform facilitate multi-omics research. promoting resources, details on how use them, most importantly insight into they were put...
Abstract Background Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies high density genotyping platforms for genome variation analysis gene discovery. Germplasm collections representing rice improved varieties elite breeding materials are accessible through banks use in with many having sequences genotype data available. Combining phenotypic genotypic information on these accessions enables...