Depth and evenness of sequence coverage are associated with assembly quality, genome structure, and choice of sequencing platform in archived plastid genomes

Abstract

In plastid genomes, the depth and evenness of sequence coverage are considered important indicators for assembly quality. However, the precise manifestations that sequencing depth and evenness can have in the assembly of these genomes, as well as any differences across individual genome sections, have yet to be evaluated. This investigation aims to identify the impact that sequencing depth and evenness can have on the assembly of plastid genomes and how both metrics are related to plastid genome structure. Specifically, we assess if sequencing evenness and reduced sequencing depth have significant correlations with, or significant differences among, individual genome sections, assembly quality metrics, the sequencing platforms employed, and the software tools used for genome assembly. To that end, we retrieve published plastid genomes as well as their sequence reads and genome metadata from public databases, measure sequencing depth and evenness across their sequences, and test several hypotheses on genome assembly and structure through non-parametric statistical tests. The results of our analyses show significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the plastid genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides per genome, and significant differences in sequencing evenness between various sequencing platforms. Based on these results, we conclude that the observed differences and correlations are not a product of chance alone but possibly genuine manifestations of sequencing depth and evenness during the assembly of these genomes.