SLANG

SLANG performs locus assembly, orthology estimation, and single-nucleotide polymorphism (SNP) extraction from Nanopore long-read multi-locus data for phylogenomic and population-genetic analyses.

Key Features:

• Locus assembly: Assembles loci from long-read Nanopore multi-locus sequencing data.
• Orthology estimation: Infers orthologous loci across samples for comparative analyses.
• SNP extraction: Identifies single-nucleotide polymorphisms from assembled loci.
• Sequencing platform: Operates on data generated with Nanopore sequencing technology.
• AFLP-based library preparation: Uses an amplified fragment length polymorphism (AFLP)-based approach to reduce genome complexity prior to Nanopore sequencing.
• Empirical results: Identified 704 orthologous loci with 12,368 SNPs in Leucanthemum spp. and 448 loci with 10,048 SNPs in Senecio spp. (Compositae).
• Phylogenetic consistency: Produced phylogenetic networks identical to Illumina GBS results for Leucanthemum and consistent with morphological species circumscriptions for Senecio.

Scientific Applications:

• Phylogenomic inference: Reconstruction of phylogenetic networks from multi-locus Nanopore data using assembled loci and SNPs.
• Population genetics: Analysis of genetic variation and SNP-based population structure from long-read data.
• Phylogeography: Investigation of geographic patterns of genetic diversity using loci and SNPs derived from Nanopore sequencing.
• RADseq/GBS alternative: Enables analyses analogous to restriction site-associated DNA sequencing (RADseq)/genotyping-by-sequencing (GBS) workflows using Nanopore long reads.

Methodology:

Implemented as a Python-based pipeline that performs locus assembly, orthology estimation, SNP extraction, and construction of phylogenetic networks from Nanopore long-read multi-locus data.