Abstract
Chloroplast genomes of land plants typically possess a conserved quadripartite structure consisting of large and small single-copy regions (LSC and SSC) separated by two large inverted repeats (IRs). Here, we present chloromapper, a lightweight Rust program designed to automate the arrangement of pre-assembled chloroplast contigs into a complete circular genome. Given three or more plastome contigs in arbitrary order, orientation, and fragmentation, chloromapper identifies IR sequences using inverted-duplicate or read-depth evidence, chains fragmented single-copy contigs based on exact end overlaps, assigns sequences to the LSC and SSC regions, and resolves their relative orientations using IR–single-copy junctions. The program subsequently reconstructs the canonical circular LSC–IRb–SSC–IRa arrangement, merging overlapping contigs and representing unresolved junctions or pre-existing assembly gaps with ambiguous nucleotides.We evaluated chloromapper using synthetic assemblies derived from the complete chloroplast genome of Arabidopsis halleri (GenBank KX886356.1), including resolved-IR, collapsed-IR, and fragmented short-read-style scenarios.