Rice Galaxy: an open resource for plant science

Juanillas, Venice Margarette; Dereeper, Alexis; Beaume, Nicolas; Droc, Gaëtan; Dizon, Joshua Gregor A.; Mendoza, J.; Perdon, Jon Peter; Mansueto, Locedie; Triplett, Lindsay R.; Lang, Jillian M.; Zhou, Gabriel; Ratharanjan, Kunalan; Plale, Beth; Haga, Jason; Leach, Jan E.; Ruiz, Manuel; Thomson, Michael J.; Alexandrov, Nickolai; Larmande, Pierre; Kretzschmar, Tobias; Mauleon, Ramil

doi:10.1101/358754

Cited by 6 publications

(7 citation statements)

References 41 publications

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“…3000 Rice Genomes Project data are available from the Gigascience GigaDB repository [70]. Snapshots of the code and Docker images are also available from GigaDB [71].…”

Section: Availability Of Supporting Data and Materialsmentioning

confidence: 99%

Rice Galaxy: an open resource for plant science

et al. 2019

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Background Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non−computer savvy rice researchers. Findings The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented. Conclusions Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.

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“…3000 Rice Genomes Project data are available from the Gigascience GigaDB repository [70]. Snapshots of the code and Docker images are also available from GigaDB [71].…”

Section: Availability Of Supporting Data and Materialsmentioning

confidence: 99%

Rice Galaxy: an open resource for plant science

et al. 2019

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“…To avoid misidentification of Xol as a Xoc or Xoo in future studies, genomes were compared to identify regions of specificity to base diagnostic primer design with UniqPrimer (Juanillas et al, 2018). Two primer sets were validated for specificity against over 30 closely and distantly related bacteria (Supplementary Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…Previously described universal US Xo primers were also tested to differentiate Xol from this novel US clade within the species (Triplett et al, 2011). UniqPrimer was employed to compare draft Xol genomes (BAI23 and NCPPB4346) and generate primers specific to Xol as previously described (Ash et al, 2014; Lang et al, 2014, 2017; Juanillas et al, 2018). Specificity was validated by screening Xol primers against diverse pools of bacterial genomic DNA (Table 1).…”

Section: Methodsmentioning

confidence: 99%

A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems

Lang

Pérez‐Quintero

Koebnik³

et al. 2019

Front. Plant Sci.

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Xanthomonas oryzae ( Xo ) are globally important rice pathogens. Virulent lineages from Africa and Asia and less virulent strains from the United States have been well characterized. Xanthomonas campestris pv. leersiae ( Xcl ), first described in 1957, causes bacterial streak on the perennial grass, Leersia hexandra , and is a close relative of Xo . L. hexandra , a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo . We used long read, single molecule real time (SMRT) genome sequences of five strains of Xcl from Burkina Faso, China, Mali, and Uganda to determine the genetic relatedness of this organism with Xo . Novel transcription activator-like effectors (TALEs) were discovered in all five strains of Xcl . Predicted TALE target sequences were identified in the Leersia perrieri genome and compared to rice susceptibility gene homologs. Pathogenicity screening on L. hexandra and diverse rice cultivars confirmed that Xcl are able to colonize rice and produce weak but not progressive symptoms. Overall, based on average nucleotide identity (ANI), type III (T3) effector repertoires, and disease phenotype, we propose to rename Xcl to X. oryzae pv. leersiae ( Xol ) and use this parallel system to improve understanding of the evolution of bacterial pathogenicity in rice agroecosystems.

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“…Burkholderia glumae-specific primers F-CGAAGGGTGTGGTTTGAACT and R-AACCTGCCA ACCTGTAATGC were designed based on comparisons of genomic sequences from pathogenic strains from Colombia, Panama, Venezuela, and Costa Rica using the same strategy described for other bacterial pathogens [17,18]. Primer specificity was tested using 10 ng of total bacterial DNA from strains of Pseudomonas fuscovaginae and Acidovorax avenae, 23 different Burkholderia species, Xanthomonas oryzae pv.…”

Section: Molecular Detection Of B Glumaementioning

confidence: 99%

Understanding the complexity of disease-climate interactions for rice bacterial panicle blight under tropical conditions

Echeverri-Rico¹,

Petro

Fory

et al. 2021

PLoS ONE

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Bacterial panicle blight (BPB) caused by Burkholderia glumae is one of the main concerns for rice production in the Americas since bacterial infection can interfere with the grain-filling process and under severe conditions can result in high sterility. B. glumae has been detected in several rice-growing areas of Colombia and other countries of Central and Andean regions in Latin America, although evidence of its involvement in decreasing yield under these conditions is lacking. Analysis of different parameters in trials established in three rice-growing areas showed that, despite BPB presence, severity did not explain the sterility observed in fields. PCR tests for B. glumae confirmed low infection in all sites and genotypes, only 21.4% of the analyzed samples were positive for B. glumae. Climate parameters showed that Montería and Saldaña registered maximum temperature above 34°C, minimum temperature above 23°C, and Relative Humidity above 80%, conditions that favor the invasion model described for this pathogen in Asia. Our study found that in Colombia, minimum temperature above 23°C during 10 days after flowering is the condition that correlates with disease incidence. Therefore, this correlation, and the fact that Montería and Saldaña had a higher level of infected samples according to PCR tests, high minimum temperature, but not maximum temperature, seems to be determinant for B. glumae colonization under studied field conditions. This knowledge is a solid base line to design strategies for disease control, and is also a key element for breeders to develop strategies aimed to decrease the effect of B. glumae and high night-temperature on rice yield under tropical conditions.

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Rice Galaxy: an open resource for plant science

Abstract: 24Background 25

Cited by 6 publications

References 41 publications

Rice Galaxy: an open resource for plant science

Rice Galaxy: an open resource for plant science

A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems

Understanding the complexity of disease-climate interactions for rice bacterial panicle blight under tropical conditions

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