Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Low-coverage whole-genome sequencing (genome skimming) is an affordable method for large-scale phylogenetic analyses.
• Genome skimming is primarily used for organellar genomes, with limited application for single-copy nuclear markers due to a lack of specialized tools for fragmented assemblies.

Purpose of the Study:

• Introduce Patchwork, a novel software tool designed for mining phylogenetic markers from highly fragmented short-read assemblies and raw sequence reads.
• Address the challenge of recovering single-copy nuclear markers from genome skimming data.

Main Methods:

• Patchwork utilizes DIAMOND for sequence similarity searches to identify homologous regions.
• A 'hit stitching' phase merges adjacent or overlapping homologous regions.
• A novel sliding window algorithm is employed to trim noncoding regions from the assembled sequences.

Main Results:

• Patchwork accurately retrieves near-universal single-copy orthologs from genome skimming datasets.
• The software demonstrates high computational speed and outperforms existing tools in performance benchmarks.
• Effective recovery of genes across various sequencing depths was confirmed.

Conclusions:

• Patchwork is a valuable and efficient tool for extracting single-copy nuclear markers from fragmented genome skimming data.
• The software enhances the utility of genome skimming for large-scale phylogenomic analyses.
• Patchwork offers an accurate and fast solution for recovering phylogenetic markers, surpassing current available software.