iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes

Area of Science:

• Genomics
• Microbial Ecology
• Bioinformatics

Background:

• Ciliates are crucial, diverse single-celled eukaryotes in microbial food webs.
• Most ciliate research relies on wild organisms with unavoidable contaminants, hindering genomic diversity studies.
• Cultivation methods are lacking for many ciliate species, exacerbating contamination issues.

Purpose of the Study:

• To establish an automated pipeline for filtering contaminants from ciliate genome assemblies.
• To improve the quality of genomic data from wild ciliate specimens.
• To provide a valuable resource for ciliate biodiversity, phylogeny, ecology, and evolution research.

Main Methods:

• Developed the integrated Genome Decontamination Pipeline (iGDP).
• iGDP combines homology search, telomere reads-assisted, and clustering approaches.
• Benchmarked iGDP using contaminated ciliate cultures, synthetic datasets, and real-world wild specimens.

Main Results:

• iGDP achieved 91.9% recall and 96.9% precision in filtering contaminated ciliate genomes.
• Demonstrated superior performance compared to popular metagenome binning tools.
• Successfully decontaminated and generated high-quality genomes from three wild ciliate specimens.

Conclusions:

• The iGDP method effectively removes contaminants from ciliate genome assemblies.
• Generated high-quality ciliate genomes will advance research in biodiversity, phylogeny, ecology, and evolution.
• The pipeline is automatable and adaptable for other microeukaryotes.