Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes

Area of Science:

• Microbial genomics
• Bioinformatics
• Evolutionary biology

Background:

• Conventional metabarcoding lacks the intraspecific resolution needed to study microbial strain evolution.
• Resolving selection and competition among microbial strains requires laborious isolation and genotyping.

Purpose of the Study:

• Introduce Bamboozle, a novel bioinformatics tool for identifying hypervariable genetic loci.
• Enable direct identification and tracking of microbial genetic strains from population samples.

Main Methods:

• Bamboozle scans entire genomes to find allele-rich barcodes for amplicon sequencing.
• Identified and validated hypervariable loci in microalgal species Skeletonema marinoi and Chlamydomonas reinhardtii.
• Utilized single nucleotide polymorphisms (SNPs) as reliable genetic markers.

Main Results:

• Identified 4 and 22 hypervariable loci in S. marinoi and C. reinhardtii, respectively, capable of resolving genotypes.
• Discovered loci within protein-coding genes, with SNPs offering high strain-specific resolution.
• Demonstrated 100% heterozygosity in S. marinoi loci, aiding strain quantification and denoising.

Conclusions:

• Bamboozle provides a powerful method for strain-level microbial population analysis.
• The tool facilitates tracking microbial strain dynamics in experimental evolution.
• Bamboozle's flexibility supports adaptation to new species and evolving sequencing technologies.