Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research

Area of Science:

• * Evolutionary Biology
• * Bioinformatics
• * Genomics

Background:

• * The Angiosperms353 gene set (AGS) comprises 353 universal low-copy nuclear genes critical for phylogenetic and population genetics studies across diverse angiosperm species.
• * Existing bioinformatics pipelines struggle to efficiently and accurately retrieve AGS from high-throughput sequencing (HTS) data, limiting their utility.

Purpose of the Study:

• * To develop an efficient and accurate reference-guided assembly tool for recovering the AGS from various HTS data types.
• * To provide a user-friendly assembler with both graphical and command-line interfaces for broad accessibility.

Main Methods:

• * Development of Easy353, an open-source, reference-guided assembly tool.
• * Compatibility with diverse HTS data, including genome skimming, RNA-seq, and target enrichment.
• * Evaluation using simulated and empirical datasets to assess assembly accuracy and error rates.

Main Results:

• * Easy353 demonstrates high efficiency and accuracy in recovering the AGS from HTS data.
• * The tool provides low rates of assembly errors, validated through rigorous testing.
• * User-friendly interfaces (GUI and CLI) enhance accessibility for researchers.

Conclusions:

• * Easy353 significantly improves the recovery of the Angiosperms353 gene set from HTS data.
• * The tool enhances the reliability and efficiency of phylogenetic and population genetics analyses in angiosperms.
• * Easy353 represents a valuable advancement for genomic research in plant science.