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Related Experiment Video

Updated: Jun 29, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
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LocoGSE, a sequence-based genome size estimator for plants.

Pierre Guenzi-Tiberi1, Benjamin Istace1, Inger Greve Alsos2

  • 1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.

Frontiers in Plant Science
|March 29, 2024
PubMed
Summary

LocoGSE accurately estimates plant genome size from low-coverage data without a reference genome. This new tool aids evolutionary and ecological studies by providing reliable genome size analysis for diverse plant species.

Keywords:
1C1Cxenvironmental DNAgenome sizegenome size estimationgenome-skimmingplant genomicsploidy

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Genome size variation is extensive in eukaryotes, especially land plants.
  • Accurate genome size estimation is crucial for biological research.
  • Existing sequence-based methods struggle with low-coverage datasets.

Purpose of the Study:

  • Introduce LocoGSE, a novel genome size estimator for low-coverage genome skimming data.
  • Address limitations of current methods for plant genome size estimation.
  • Provide a user-friendly and reliable tool for genomic analysis.

Main Methods:

  • LocoGSE maps reads to single copy consensus proteins, bypassing the need for a reference genome assembly.
  • Calibration involved 430 low-coverage Angiosperm genome skimming datasets.
  • Performance was compared against existing genome size estimators.

Main Results:

  • LocoGSE accurately predicts monoploid genome size even with coverage below 1X.
  • The tool performs reliably on highly heterozygous samples.
  • Estimates remain stable across individuals with different ploidy levels.

Conclusions:

  • LocoGSE effectively estimates genome size from low-coverage, unassembled sequencing data.
  • The method is applicable to diverse plant lineages after initial calibration.
  • This tool will advance plant genome analysis, supporting evolutionary and ecological research.