PACVr: plastome assembly coverage visualization in R

摘要

The sequencing and comparison of complete plastid genomes has become a popular method in plant evolutionary research, rendering the precise genome assembly and its quality assessment of high importance. The plastid genomes of most photosynthetically active land plants display a circular, quadripartite structure and comprise two single copy (SC) regions separated by two identical inverted repeats (IR) [ ]. A total of four partitions with markedly different lengths can, thus, be defined in typical land plant plastomes: the large single copy (LSC) region of ca. 70-90 kilobases (kb), the small single copy (SSC) region of ca. 15-25 kb, and the two IR regions (IRa and IRb) of ca. 20-25 kb each [ ]. The IR regions represent reverse complements of each other and are primarily homogenized through a recombination-mediated replication process [ , ]. The plastid genomes of most photosynthetically active land plants encode a total of ca. 100-120 proteins, which play a central role in organelle metabolism and photosynthesis [ ]. Due to their strong structural conservation, uniparental inheritance, a near absence of recombination, and a high copy number per plant cell, plastid genomes are highly suitable for comparative genomic studies [ ]. Numerous investigations have sequenced and compared complete plastid genome sequences over the past decade [ , ], and the number of publicly available plastid genomes continues to increase dramatically [ ]. Recent studies on plastid genome structure and evolution have evaluated polymorphisms across hundreds [ – ] or even thousands [ , ] of plastid genome sequences, rendering the precise assembly process of plastid genomes and their quality assessment ever more important.