PACVr: plastome assembly coverage visualization in R

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Plastid genomes possess a complex circular, quadripartite structure with inverted repeats, complicating automated assembly.
• Accurate plastid genome assembly is crucial for downstream analyses of genome structure and evolution.
• Assessing genome assembly quality often relies on coverage depth, but existing tools lack specialized visualization for plastid genomes.

Purpose of the Study:

• To develop a user-friendly software tool for visualizing plastid genome assembly coverage depth.
• To account for the unique quadripartite structure of plastid genomes in visualization.
• To facilitate the identification of regions with suboptimal assembly confidence.

Main Methods:

• Introduction of 'PACVr', an R package designed for plastid genome visualization.
• Utilizes a variable window approach for flexible visualization scales.
• Confirms sequence identity and visualizes gene synteny within inverted repeat regions.

Main Results:

• PACVr effectively visualizes coverage depth in relation to the circular, quadripartite plastome structure and individual genes.
• The tool identifies regions with coverage depth deviating from user-defined thresholds.
• PACVr confirms sequence equality and visualizes gene synteny between inverted repeat regions.

Conclusions:

• PACVr offers a user-friendly solution for visualizing plastid genome assembly coverage and gene synteny.
• The tool enhances the optimization of plastid genome assemblies.
• PACVr improves the reliability of publicly available plastome sequences.