Complete chloroplast genome assembly of the native walnut Juglans australis

Abstract

Juglans australis is a South American walnut species of ecological, economic, and pharmacological importance. However, its phylogenetic position has remained unresolved due to the lack of comprehensive molecular data. In this study, we report the first complete chloroplast genome of J. australis, assembled de novo using NOVOPlasty 3.3 from Illumina paired-end reads. The plastome is 160,388 bp in length and exhibits the typical quadripartite structure, consisting of a large single-copy (LSC) region of 89,918 bp, a small single-copy (SSC) region of 18,425 bp, and a pair of inverted repeats (IRs) of 35,918 bp each. Genome annotation identified 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs, with an overall GC content of 36.1%. Phylogenomic analysis based on complete chloroplast genomes confirmed the placement of J. australis within section Rhysocaryon, closely related to J. hindsii. Ka/Ks analysis across 75 shared coding genes indicated strong purifying selection overall, although nine genes (matK, atpF, accD, ycf1, and ndhD among them) showed signals of positive selection. The complete chloroplast genome of J. australis provides a valuable genomic resource for phylogenetic, evolutionary, and conservation studies within the genus Juglans, and fills an important gap in the plastid phylogenomic framework of South American walnuts