Accepted_test

An approach to assembling MAGs of intracellular parasites with a reduced genomes from MDA data

by Nassonova Elena | Mikhail Rayko | Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS | Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS

Abstract ID: 426

Event: BGRS-abstracts

Sections: [Sym 5] Section “Molecular phylogenetics and phylogenomics of Plants, Fungi, Protists, Prokaryotes and Viruses”

Representatives of the group Opisthophagea are of interest from the evolutionary point of view. These organisms are intracellular parasites, and their genome reduction due to parasitic lifestyle poses challenges for sequencing and analysis. Our study aims to develop a pipeline for analyzing MDA-based metagenomic data to assembly genomes of interest (MAGs), construct phylogenomic trees and track gene loss patterns during parasitic genome reduction.

Our approach involve assembling the metagenome using SPAdes and binning with MaxBin2, followed by completeness and contamination checks using BUSCO and BlobTools. A phylogenomic tree is constructed using supermatrix and supertree-based approaches. The resulting tree helps determine the taxonomic position, identify gene loss patterns, and distinguish parasitic genome reduction from assembly issues.

We applied our pipeline to several dozen samples. Through target bin selection, decontamination, and quality assessment, we achieved consistent completeness assessment values (20-45% by BUSCO) across multiple samples and clades. Phylogenomic analysis revealed shared gene loss patterns, facilitating the creation of accurate phylogenetic trees for Opisthophagea branches. This work contributes to the elucidation of gene loss mechanisms in parasitic genome reduction and evolutionary patterns across diverse microbial taxa.