LocoGSE

LocoGSE estimates monoploid genome size from low-coverage genome skimming sequencing data in plants by mapping reads to single-copy consensus proteins.

Key Features:

• Low-Coverage Capability: Operates on very low-depth genome skimming sequencing data and provides reliable estimates at coverage levels below 1X.
• No Reference Genome Required: Does not require a reference genome assembly, using single-copy consensus proteins for read mapping instead.
• Accurate and Stable Estimates: Calibrated on 430 low-coverage Angiosperm genome skimming datasets and yields accurate monoploid genome size estimates across samples with varying heterozygosity and ploidy.
• Mapping Strategy: Maps sequencing reads to single-copy consensus proteins to derive monoploid genome size estimates.

Scientific Applications:

• Genome Size Variation: Assessing genome size variability among eukaryotes, particularly land plants such as Angiosperms, from low-coverage data.
• Evolutionary Biology: Supporting evolutionary studies that require monoploid genome size estimates without high sequencing coverage or reference genomes.
• Ecology and Comparative Genomics: Enabling ecological and comparative analyses that incorporate genome size across species with differing ploidy and heterozygosity.

Methodology:

Sequencing reads from genome skimming are mapped to single-copy consensus proteins, and estimates are calibrated using 430 low-coverage Angiosperm genome skimming datasets to produce monoploid genome size values.