Chloroplast Genome Assembly and Genetic Structure Analysis of Coffea arabica L. Based on Maternal Inheritance Markers

Background: Codon usage bias has been analyzed in the Coffea arabica L. nuclear genome, yet comprehensive genomic resources for this species remain limited. The chloroplast genome, characterized by its maternal inheritance and high conservation, represents a valuable resource for investigating plant phylogeny, crop domestication, and maternal lineage evolution. Results: We assembled complete chloroplast genomes for 52 C. arabica accessions, encompassing four cultivars (Geisha, Catimor, Bourbon, and Caturra), four improved breeding lines within the Geisha group (Yunka No. 3, Yunka No. 4, G02, and G13), two Catimor breeding lines (CCCA25 and T5175), and four accessions of unknown cultivar origin. Comparative genomics, unrooted phylogenetic reconstruction (neighbor-joining and maximum likelihood), haplotype inference, and exploratory principal component analysis (PCA) were integrated to characterize the genetic architecture of these chloroplast genomes. These genomes ranged from 155,133 bp to 155,192 bp in length, displayed the typical quadripartite architecture, and exhibited GC contents of 37.43–37.44%. Gene annotation identified 131 genes, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. Codon usage analysis revealed a pronounced bias toward A or U at the third codon position. We detected 194 SSR loci per plastome, among which mononucleotide A/T repeats predominated. Neighbor-joining and maximum-likelihood phylogenies, PCA, and haplotype network reconstruction consistently resolved the 52 accessions into three genetic clusters (C1–C3; C1 represented by a single divergent accession) and five distinct haplotypes. SNP and InDel profiling further showed that intergenic spacer (IGS) regions harbored the highest density of genetic variation. Conclusions: These genomes provide resources for germplasm characterization, phylogenetic studies, and marker-assisted breeding in coffee. They also establish a chloroplast-genome framework that, when integrated with nuclear genomics and expanded sampling, will help fully resolve the maternal history, domestication, and allopolyploid origin of Coffea arabica.