Comparative Analysis of Chloroplast Genome Sequences and Phylogeny in Three Macadamia integrifolia Cultivars

<b>Background/Objectives</b>: <i>Macadamia integrifolia</i> is a valuable subtropical fruit tree, yet genomic studies on its cultivars are limited. This study aims to elucidate the chloroplast genome features, variations, and phylogenetic relationships of three main cultivars ('Guilin No. 1', 'Nanya No. 1', 'Qian'ao No. 1') to support germplasm identification and breeding. <b>Methods</b>: chloroplast genomes of three <i>M. integrifolia</i> cultivars from Guangxi, Guangdong, and Guizhou were sequenced using Illumina technology, followed by assembly, annotation, and comparative analyses of structure, repeats, and codon usage. Phylogenetic relationships were reconstructed using complete genome sequences. <b>Results</b>: The three chloroplast genomes displayed typical quadripartite structures, with lengths of 159,714 bp, 159,195 bp, and 159,508 bp, and GC contents of 38.12%, 38.16%, and 38.14%, respectively. Each encoded 135 genes. Codon usage was biased towards A/U-ending codons. We identified 81, 87, and 80 SSRs and 26, 21, and 20 long repeats, respectively. IR boundary regions were highly conserved. Phylogenetically, the cultivars showed close relationships with <i>M. integrifolia</i>, <i>Macadamia tetraphylla</i>, and <i>Macadamia</i><i>ternifolia</i>, forming a sister clade to Platanus occidentalis. <b>Conclusions</b>: This study provides essential chloroplast genomic resources for three <i>M. integrifolia</i> cultivars, revealing conserved structures and specific variations. The findings offer crucial insights for the genus's genetic diversity, supporting future germplasm evaluation and phylogenetic research.