Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing

Area of Science:

• Evolutionary biology
• Genomics
• Phylogenetics

Background:

• Hybridization and polyploidization are common in eukaryotes but challenging to study, especially in phylogenetic analysis.
• The genus Fragaria exhibits diverse ploidy levels, yet its species' phylogenetic origins remain unclear.
• Understanding polyploid origins is crucial for plant evolution and taxonomy.

Purpose of the Study:

• To infer the evolutionary origins of polyploid strawberries within the genus Fragaria.
• To investigate hybridization events and coalescence processes in Fragaria evolution.
• To apply novel sequencing and phylogenetic approaches to resolve complex plant evolutionary histories.

Main Methods:

• Utilized next-generation sequencing (NGS) data from 20 diploid and polyploid Fragaria species.
• Generated haplotype sequences for 257 low-copy nuclear markers using Illumina target capture sequencing.
• Employed phylogenetic analysis and coalescence framework to identify hybridization events and infer ancestry.

Main Results:

• Confirmed allopolyploid ancestry for Fragaria chiloensis and Fragaria virginiana.
• Proposed new hypotheses for the allopolyploid origins of F. iturupensis, F. moschata, and F. orientalis.
• Detected evidence of gene flow between diploid species F. bucharica and F. vesca.

Conclusions:

• This study pioneers the use of target capture sequencing and haplotype deconvolution for tracing polyploid origins.
• Provides novel perspectives on the evolutionary history and reticulate evolution within the Fragaria genus.
• Highlights the importance of considering population-level processes in phylogenetic studies of polyploids.