Optimization of DNA extraction and size selection for NGS sequencing across plant families found in dover memorial park

Abstract

Biodiversity can be explored in a variety of ways, from species richness to phylogenetic diversity. This project aims to investigate the plant biodiversity of Montana through analyses of species diversity (floristic collections) and phylogenetic diversity (next-generation sequencing [NGS]). Plants are well known for their secondary metabolites that interfere with downstream applications, such as DNA extraction and sequencing. To investigate phylogenetic diversity, optimized protocols for DNA extraction, fragmentation, and size selection need to be developed first. By optimizing extraction protocols, unique plant family characteristics will minimally affect yields and save time spent troubleshooting downstream applications. Plant specimens collected from Dover Memorial Park over the 2022 growing season were used to optimize an NGS workflow. This study found additional fragmentation of genomic DNA was unnecessary and automated size selection was sufficient to select the optimum fragment size range.

Biodiversity can be explored in a variety of ways, from species richness to phylogenetic diversity. This project aims to investigate the plant biodiversity of Montana through analyses of species diversity (floristic collections) and phylogenetic diversity (next-generation sequencing [NGS]). Plants are well known for their secondary metabolites that interfere with downstream applications, such as DNA extraction and sequencing. To investigate phylogenetic diversity, optimized protocols for DNA extraction, fragmentation, and size selection need to be developed first. By optimizing extraction protocols, unique plant family characteristics will minimally affect yields and save time spent troubleshooting downstream applications. Plant specimens collected from Dover Memorial Park over the 2022 growing season were used to optimize an NGS workflow. This study found additional fragmentation of genomic DNA was unnecessary and automated size selection was sufficient to select the optimum fragment size range.