FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

Naithani, Sushma; Partipilo, Christina M.; Raja, Rajani; Elser, Justin; Jaiswal, Pankaj

doi:10.3389/fpls.2016.00242

Cited by 14 publications

(10 citation statements)

References 84 publications

(134 reference statements)

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“…The species with the highest number of manual curated pathways are tomato (87 pathways), tobacco (72 pathways), potato (56 pathways), petunia (25 pathways), pepper (14 pathways) and the wild tomato species Solanum habrochaites (12 pathways). Metabolic databases with a high degree of manual curation and continuous updating are rare and mostly limited to model organisms, for instance, Arabidopsis thaliana in AraCyc ( 23 ) or species with high impacts on human nutrition ( 26 ) and health ( Supplementary Table S1 ). The latter involves two databases that focus on parasitic protozoans known to cause sleeping sickness ( Trypanosoma brucei ) and the skin affecting Leishmaniasis disease ( Leishmania major ).…”

Section: Resultsmentioning

confidence: 99%

“…To date, about 9400 such derivative PGDBs have been generated and made available in the BioCyc database collection ( http://biocyc.org/ ), but very few have been curated in a way that would corroborate the predicted metabolic network and integrate experimental information from the published scientific literature ( 16 , 18 ). MetaCyc has become the de-facto standard in species-specific database curation, and Pathway Tools generated and manually curated PGDBs have been created across the domains of life, including bacteria [ Escherichia coli in EcoCyc ( 21 )], fungi ( Saccharomyces cerevisiae in YeastCyc http://yeast.biocyc.org/ ), mammals [ Bos taurus in CattleCyc ( 22 )] and plants such as Arabidopsis thaliana in AraCyc ( 23 , 24 ), Medicago truncatula in MedicCyc ( 25 ), Fragaria vesca in FragariaCyc ( 26 ), Oryza sativa in RiceCyc ( 27 ) and Zea mays in MaizeCyc ( 28 ). While most PGDBs are created at the species level, this is not required and they can be generated at arbitrary levels in the taxonomic hierarchy.…”

Section: Introductionmentioning

confidence: 99%

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SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

et al. 2018

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SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species.Database URL https://solgenomics.net/tools/solcyc/

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

et al. 2018

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“…Gene expression data can be further combined with other genomics data, typically metabolome, to assign putative functions to the genes. Data could be examined using visualization tools such as Pathway-Tools platform (Naithani et al, 2016) and further analysed using various statistical means such as correlation network analysis (Pillet et al, 2015). However, correlative information is by itself not sufficient to assign a function to a gene.…”

Section: What Tools Do We Have To Study the Relationships Between Genmentioning

confidence: 99%

Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

Denoyés-Rothan¹,

Amaya²,

Liston³

et al. 2017

Acta Hortic.

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In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.

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“…These systems-level platforms such as Ensembl–Gramene (1), Phytozome (2), Kyoto Encyclopedia of Genes and Genomes (KEGG) (3), Reactome (4), Plant Reactome (5), BioCyc (6) and species-specific metabolic networks [i.e. Plant Metabolic Network (7), RiceCyc (8), MaizeCyc (9), VitisCyc (10), FragariaCyc (11), etc.] allow integration of various automated, semiautomated and/or manual biocuration pipelines, and provide researchers a user-friendly framework based on data mining, back-end data processing and biocuration.…”

Section: Introductionmentioning

confidence: 99%

Involving community in genes and pathway curation

et al. 2019

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Biocuration plays a crucial role in building databases and complex systems-level platforms required for processing, annotating and analyzing ‘Big Data’ in biology. However, biocuration efforts cannot keep pace with a dramatic increase in the production of omics data; this presents one of the bottlenecks in genomics. In two pathway curation jamborees, Plant Reactome curators tested strategies for introducing researchers to pathway curation tools, harnessing biologists’ expertise in curating plant pathways and developing a network of community biocurators. We summarize the strategy, workflow and outcomes of these exercises, and discuss the role of community biocuration in advancing databases and genomic resources.

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FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

Cited by 14 publications

References 84 publications

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks inSolanumandNicotianaspecific databases

Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

Involving community in genes and pathway curation

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