Characterization and Phylogenetic Analysis of the Chloroplast Genome of Elaeagnus oxycarpa Schltdl

Background: Elaeagnus oxycarpa Schltdl. (Elaeagnaceae) is a vital sand-fixing tree species in the arid, semi-arid, and desert regions of China, holding significant ecological and economic value. However, its chloroplast (cp) genome has not been previously characterized. Results: In this study, we sequenced the complete cp genome of Elaeagnus oxycarpa using Illumina high-throughput sequencing technology. We performed de novo assembly, annotation, and comparative genomic and phylogenetic analyses with six other Elaeagnaceae species. The results revealed a typical quadripartite structure for the E. oxycarpa cp genome, with a total length of 150,567 bp and a GC content of 36.90%. Annotation identified 132 genes, comprising 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Codon usage bias analysis indicated a preference for A/U endings, with leucine codons being the most frequent (9.5%). Additionally, 77 simple sequence repeat (SSR) loci were detected, predominantly mononucleotide repeats (71.4%). Comparative genomic analysis demonstrated high sequence conservation among the seven Elaeagnus species, with nucleotide variations primarily concentrated in non-coding regions and intergenic spacers of genes such as rps16, ycf1, and trnC-GCA. These variable regions and SSR loci represent valuable molecular markers for future population genetics and species identification studies on Elaeagnus. Phylogenetic analysis strongly supported the notion that E. oxycarpa and Elaeagnus angustifolia form a sister clade, indicating their close genetic relationship. Conclusions: Our findings provide crucial genomic resources and a theoretical foundation for the species identification and elucidation of the evolutionary history of Elaeagnaceae.