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ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.

Yuhao Tong1,2, Vanessa Rossetto Marcelino3,4, Robert Turnbull5

  • 1School of Computing and Information Systems, The University of Melbourne, Carlton, Victoria, Australia.

Molecular Ecology Resources
|April 20, 2026
PubMed
Summary

ChloroScan, a new bioinformatics pipeline, efficiently extracts eukaryotic plastid genomes from metagenomic data. This tool aids in discovering novel protist lineages by overcoming challenges associated with nuclear genome analysis.

Keywords:
algaebioinformaticsgenome‐resolved metagenomicsmicrobiomeplastid

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Area of Science:

  • Metagenomics
  • Eukaryotic genomics
  • Bioinformatics

Background:

  • Genome-resolved metagenomics aids prokaryotic genome discovery.
  • Mining eukaryotic genomes, especially protists, is challenging due to introns and repeats.
  • Organellar genomes offer valuable phylogenetic data but are underutilized in metagenomic discovery.

Purpose of the Study:

  • Introduce ChloroScan, a novel bioinformatics pipeline for extracting eukaryotic plastid genomes from metagenomes.
  • To improve the discovery of novel protistan lineages using organellar genomes.
  • To provide a user-friendly tool for analyzing metagenomic data.

Main Methods:

  • Developed ChloroScan, a bioinformatics pipeline utilizing a deep learning contig classifier.
  • Incorporated an automated binning module guided by a curated marker gene database.
  • Implemented user-friendly output formats including annotated coding sequences and proteins.

Main Results:

  • ChloroScan outperforms MetaBAT2 in recovering high-quality plastid bins from simulated metagenomes.
  • Successfully recovered 16 medium to high-quality metagenome-assembled genomes (MAGs) from protist-size-fraction metagenomes.
  • Identified several novel protistan lineages among the recovered MAGs, demonstrating high taxonomic novelty.

Conclusions:

  • ChloroScan is an effective tool for extracting eukaryotic plastid genomes from metagenomic data.
  • The pipeline facilitates the discovery of novel protist lineages, expanding our understanding of eukaryotic diversity.
  • ChloroScan provides valuable insights into microbial eukaryotes through organellar genome analysis.