Variation of and associations with the depth and evenness of sequencing coverage in a sample of archived plastid genomes

Depth and evenness of sequencing coverage are considered potential indicators of genome assembly quality. In plastid genomics, where new data generation has outpaced the development of suitable assembly quality indicators, these coverage metrics could offer insights into the quality of plastomes of different sizes, structures, or taxonomic origins. However, the typical variation of sequencing depth and evenness among archived plastid genomes, their variability between plastome partitions, and any association with methodological factors have yet to be evaluated. This study explores the variation of sequencing depth and evenness across a sample of publicly accessible plastid genomes and their potential associations with plastome structure, assembly accuracy, and the methodological provenance of the genome data using statistical tests. Our results indicate significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides, and a significant difference in sequencing evenness between several DNA sequencing platforms. These findings highlight that many publicly accessible plastid genomes are based on sequence data with highly variable sequencing depth and evenness and that this variation is influenced, at least partially, by genome structure and methodological factors.