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A community effort towards phylogenetic-based curation
of ribosomal databases for environmental sequencing
Javierdel Campo
LauraParfrey
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Motivation
Integrate expert views on taxonomy into public database resources
Improve resources for high throughput sequence annotation
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• Catalyze experts in protist taxonomy to engage in curation and validation of a ribosomal DNA marker gene database for eukaryotic lineages across the tree of life.
• Synthesize the efforts of individual curators to produce a phylogenetically curated ribosomal DNA marker gene database for eukaryotes.
• Use the improved reference database to characterize the environmental distribution of eukaryotic microbes from large-scale HTES datasets.
Aims
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1) HTES 18S rDNA sequence retrieval
2) Reference database annotation
3) Community analysis using classification
High-throughput environmental sequence (HTES) analysis of eukaryotes
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Starting reference database 18S phylogeny
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Use the phylogeny to improve classification
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Reference database 18S phylogenyAfter curation
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Integrate environmental metadata
Where was this sequence isolated?• Fresh water or marine?• Aerobic or anoxic?• Host information? (symbiotic clades)
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0 500 1000 1500 2000 2500 3000 3500 HTS readsA manually curated reference DBThe opisthos example
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Outputs for each group
• Set of curated sequences– Files with chimeric sequences and short sequences
• Alignment of these sequences• Phylogenetic tree• Database
– Full classification (unlimited ranks)– Environmental metadata
• Open access after 1 year embargo (if desired)
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18S reference DB curation pipeline (simplified)
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18S reference DB curation pipeline
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• A refined curation pipeline, associated computational tools, and curation instructions
• Reference databases for individual lineages
• Synthesis of classification for each group
Workshop Outputs
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After the workshop…
• Continued curation.
• Recruit new curators using refined tools.
• Coordinate with other groups.
• Integrate data from different curation efforts (into a cohesive database).
• Data sharing and distribution.
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Acknowledgments
Thank you!Advisers and participants