rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects

Area of Science:

• Genomics
• Parasitology
• Bioinformatics

Background:

• Population-scale genome projects have advanced parasitic protozoa research.
• Mitochondrial genome complexity in Kinetoplastida hinders analysis.
• Existing tools like KOMICS automate assembly but lack efficient diversity visualization.

Purpose of the Study:

• To introduce rKOMICS, a user-friendly R package for analyzing minicircle sequence diversity.
• To streamline the examination and visualization of mitochondrial genome variation in parasitic protozoa.
• To facilitate population-scale analyses of Kinetoplastid parasites.

Main Methods:

• Developed rKOMICS as an R package for minicircle sequence diversity analysis.
• Implemented functionalities for examining, summarizing, and visualizing minicircle sequence clusters.
• Applied the tool suite to a whole-genome sequencing dataset of Leishmania braziliensis.

Main Results:

• rKOMICS efficiently analyzes minicircle sequence diversity within and between samples.
• Demonstrated differences in minicircle sequence richness and composition across Leishmania subspecies and subpopulations.
• Showcased the applicability of rKOMICS across all 27 trypanosomatid genera.

Conclusions:

• rKOMICS provides a framework for efficient manipulation and exploration of mitochondrial minicircle data.
• Facilitates the development of molecular markers for species identification.
• Supports evolutionary studies by providing insights into parasite ancestry and population structure.