The Pan-Plastome of Walnuts (Juglans regia L.) from Xinjiang Reveals New Insights into Their Genetic Diversity

Persian walnut (Juglans regia L.) is an economically important tree species in the Juglandaceae family. Comparative analysis of its chloroplast genome sequences is of great significance for species identification and evolutionary research. In this study, high-throughput sequencing was performed using the Illumina HiSeq platform, followed by de novo assembly of the chloroplast genome, and then analyses of its repetitive sequences, codon usage bias, nucleotide polymorphism and population structure. The results showed that the chloroplast genome size of walnut ranged from 160,311 bp to 160,367 bp with a GC content of 36.11%. It exhibited a typical quadripartite circular structure, and a total of 78 distinct protein-coding genes (PCGs), 30 tRNA genes and four rRNA genes were annotated. A total of 16 distinct SSR motifs were identified, among which A/T motifs were the most abundant; 31–40 bp long tandem repeats were the most abundant in all samples, which increased genomic variability. Codon usage bias analysis revealed that all walnut samples preferentially use the codon UUA (Leu), and most codons end with A/U. Nucleotide sequence alignment identified 129 polymorphic sites. Single nucleotide variants (SNVs) were the dominant variation type, followed by InDels. Furthermore, the phylogenetic tree, principal component analysis (PCA), haplotype network and population structure classified the 41 walnut samples into three genetic clusters (C1, C2 and C3). This study elucidated the conserved characteristics and evolutionary variations in walnut chloroplast genomes, providing theoretical support for its phylogenetic research and germplasm resource utilization.