Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule...

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Generating nuclear data for polyploid organisms presents significant challenges for phylogenetic studies.
• Previous methods were often slow, inconvenient, and struggled with the complexity of polyploid genomes.

Purpose of the Study:

• To develop and validate a high-throughput protocol and bioinformatics pipeline for generating nuclear data in polyploids.
• To demonstrate the utility of this approach for inferring phylogenetic relationships in polyploid species.

Main Methods:

• A high-throughput protocol involving amplification and PacBio sequencing of four nuclear loci (approx. 1 kb each).
• Development of the Pipeline for Untangling Reticulate Complexes (Purc) bioinformatics pipeline to process raw sequencing reads.
• Purc utilizes an iterative approach to correct errors, remove chimeras, and infer accurate sequences of all gene copies (homeologs, paralogs, alleles).

Main Results:

• Successful generation of nuclear data for multiple gene copies across numerous polyploid accessions from the fern family Cystopteridaceae.
• Purc accurately inferred underlying sequences from raw PacBio reads, demonstrating its efficacy in handling complex polyploid data.
• Inferred a multi-labeled species tree for a subset of accessions, showcasing the downstream phylogenetic utility.

Conclusions:

• The described high-throughput protocol and Purc pipeline offer an easy, economical, and accurate method for polyploid phylogenetics.
• This approach facilitates the study of broad patterns of polyploid evolution, especially when combined with advanced analytical methods.