A comparative analysis of plastome evolution in autotrophic Piperales

Area of Science:

• Plant genomics
• Molecular evolution
• Bioinformatics

Background:

• Plastome diversity in autotrophic Piperales is extensive but understudied due to limited comparative analyses.
• Previous studies often focused on single species or genera, hindering a comprehensive understanding of Piperales plastome evolution.

Approach:

• Performed de novo assembly of newly generated plastome data and reanalyzed existing public data for >100 autotrophic Piperales.
• Utilized Sanger sequencing and read mapping for assembly verification and gap filling.
• Reconstructed phylogenetic relationships to support comparative plastome genomics.

Key Points:

• Identified numerous assembly and annotation errors in published plastome data, primarily at inverted repeat (IR) boundaries, artificially inflating diversity.
• Discovered stable IR-SSC junctions but significant variation at IR-LSC boundaries as a major source of plastome differences.
• Found evidence suggesting a pseudogene-like status for cemA and ycf15 in several Piperales species.

Conclusions:

• IR-LSC junctions serve as valuable markers for taxonomic discrimination within Piperales.
• Incorrect IR-SSC boundary identification is a critical issue leading to erroneous plastome assembly.
• Proposed a gold standard for high-quality plastome assembly and annotation using de novo methods and robust gene references.