Seance

Seance performs reference-based phylogenetic placement of short 18S ribosomal RNA (rRNA) amplicon sequences to infer species relationships within environmental and community-level studies.

Key Features:

• Phylogenetic placement approach: Leverages a reference phylogeny constructed from complete marker genes and iteratively extends that reference with short amplicon sequences to increase phylogenetic signal.
• Integration with Pagan: Uses Pagan for alignment extension and phylogenetic placement to ensure precise alignment of short sequences within the reference framework.
• Comprehensive data processing suite: Provides preprocessing, clustering, and dataset visualization capabilities for multi-sample analyses.
• Application to microscopic eukaryotes: Targets cases where limited horizontal gene flow makes 18S rRNA a reliable indicator of species phylogeny.
• Performance and accuracy: Demonstrates improved operational taxonomic unit (OTU) picking at higher sequence similarity and phylogenetic placement accuracy comparable to maximum likelihood methods, as shown on 454 sequencing data from a longitudinal intestinal parasite study in Microcebus rufus.
• Adaptation to alternative markers: Concepts enable application to other marker genes by creating corresponding reference data.

Scientific Applications:

• 18S rRNA amplicon community profiling: Infers species relationships from short 18S amplicons in environmental and metagenomic samples.
• Microscopic eukaryote phylogeny: Resolves species-level relationships in eukaryotic microbial communities where rRNA reflects organismal phylogeny.
• Nematode community studies: Applies reference-based placement to nematode surveys using the 18S marker gene.
• Longitudinal parasite community analysis: Enables analysis of intestinal parasite communities from 454 sequencing data, exemplified by studies in Microcebus rufus.

Methodology:

Construct a reference phylogeny from complete marker genes; iteratively extend the reference with short metagenomic amplicon sequences via phylogenetic placement; perform alignment extension and placement using Pagan; execute preprocessing and clustering of datasets.