ORTHOSKIM

ORTHOSKIM performs in silico sequence capture from genomic and transcriptomic libraries to recover chloroplast genomes (cpDNA), mitochondrial genomes (mtDNA), nuclear ribosomal regions (rDNA), and predefined nuclear loci from low-coverage whole-genome shotgun (genome skimming) data for phylogenomic and DNA barcoding analyses.

Key Features:

• Targeted sequence capture without full organelle assembly: Captures specific cpDNA, mtDNA, and rDNA regions without requiring assembly of entire organelle genomes.
• Three-step capture workflow: Implements global sequence assembly, mapping against reference sequences, and target sequence extraction as the capture process.
• Quality control tests: Integrates quality control checks throughout the workflow to monitor accuracy and reliability of captured sequences.
• Support for coding and noncoding regions and nuclear loci: Captures coding and noncoding regions of cpDNA, mtDNA, and rDNA and predefined nuclear sequences such as ultraconserved elements and single-copy orthologue genes.
• Multiple alignment and matrix generation: Produces aligned DNA matrices via multiple sequence alignments for downstream phylogenetic reconstruction.

Scientific Applications:

• Phylogenomics: Reconstruction of evolutionary relationships among species using aligned DNA matrices from captured organelle, ribosomal, and nuclear loci.
• DNA barcoding: Recovery of organelle and rDNA barcodes from low-coverage genome skimming data for species identification.
• Genome skimming for nonmodel organisms: Extraction of abundant genomic compartments (cpDNA, mtDNA, rDNA) from low-coverage whole-genome shotgun sequencing of nonmodel taxa.
• Nuclear phylogenetics: Recovery of predefined nuclear loci such as ultraconserved elements and single-copy orthologue genes for nuclear-based evolutionary inference.

Methodology:

Global sequence assembly, mapping of assembled sequences against reference sequences, target sequence extraction, quality control tests throughout the workflow, and multiple sequence alignment to produce aligned DNA matrices.