AbstractPremiseMany plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed.MethodsWe performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics.ResultsWe identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single‐copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single‐copy (LSC) region.ConclusionsThis study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR‐LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene‐like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR‐SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high‐quality plastomes based on de novo assembly methods and appropriate references for gene annotation.