Complete chloroplast genome of Atriplex taltalensis (Amaranthaceae), an endangered endemic species from the Chilean Atacama Desert

Background Atriplex taltalensis is an endangered halophytic species endemic to the Chilean Atacama Desert, for which genomic resources are currently lacking. Complete chloroplast genomes provide valuable resources for comparative genomics, phylogenetics, and conservation genetics because of their conserved structure and informative evolutionary patterns. This study aimed to assemble and characterize the first complete chloroplast genome of A. taltalensis and compare it with representative Atriplex plastomes. Results The complete chloroplast genome of A. taltalensis was a circular molecule of 150, 919 bp with the typical quadripartite structure, comprising a large single-copy region, a small single-copy region, and two inverted repeats. The plastome encoded 130 genes, including 85 protein-coding genes, 37 tRNAs, and 8 rRNAs, with an overall GC content of 37.29%. Comparative analyses of 15 Atriplex plastomes revealed high conservation of genome organization and gene content, together with high sequence similarity, whereas nucleotide variation was concentrated in a limited number of intergenic regions and a few coding genes. Hypervariable loci, simple sequence repeats, and long repeats were identified as potential candidates for informative molecular markers. Most protein-coding genes showed Ka/Ks ratios consistent with strong functional constraint, while a limited number of genes exhibited elevated pairwise Ka/Ks ratios in specific comparisons. Phylogenomic reconstruction based on complete plastomes recovered well-supported plastome relationships within Atriplex , supporting their utility for resolving relationships among closely related taxa. Conclusions This study provides the first complete chloroplast genome sequence of A. taltalensis and establishes a valuable genomic resource for comparative genomics, phylogenomics, and conservation genetics.