Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

Comparative Genomic and Phylogenetic Analysis of Chloroplasts in Citrus paradisi Mac.cv. Cocktail

Background:Citrus paradisi Mac. cv. Cocktail is globally valued for its abundant nutrients and bioactive compounds, particularly in tropical and subtropical regions. A novel albino phenotype mutant of C. paradisi Mac. cv. Cocktail (designated WT) was identified in Quzhou and subsequently named C. paradisi Mac. cv. Cocktail mosaic mutant (MT). To distinguish C. paradisi Mac. cv. Cocktail from conventional grapefruit cultivars and to elucidate genomic differences between WT and MT, this study conducted a comprehensive comparison of their chloroplast genomes with those of previously reported Citrus species. Methods: The complete chloroplast genomes of WT and MT were assembled through Illumina PE150 sequencing, enabling detailed comparative genomic and evolutionary studies. Results: The results revealed that both WT and MT chloroplast genomes exhibit a conserved quadripartite structure. Each genome measures 160,186 base pairs in length, with a uniform GC content of 38.5%. Annotation revealed 138 genes (91 protein-coding, 10 rRNA, 37 tRNA), 82 repeats, and A/U-biased codons. Genome boundaries and genome comparison showed WT and MT were identical but divergent from other Citrus. The 52 conserved protein-coding genes showed comparable selection pressures in both WT and MT. Phylogenetically, WT and MT are closely related and are distinguished from all of the traditional grapefruits. Conclusions: The albino phenotype of MT is unrelated to chloroplast variations. Chloroplast genomics supports C. paradisi cv. Cocktail's differentiation from conventional grapefruits. This study expands the chloroplast genomic resources for Citrus and establishes a theoretical framework for future research on C. paradisi cv. Cocktail and related varieties.

Decoding the Chloroplast Genome of Korean endemic plant Acer okamotoanum: Comparative Genomics, Phylogenetic Insights, and Potential for Marker Development

Acer okamotoanum, a medicinally significant endemic plant of Korea, has seen limited genomic research. To address this gap, we conducted a comprehensive sequencing and analysis of its chloroplast genome. The assembled genome is 156,242 bp in length, with typical quadripartite structure, consisting of a large single-copy region, a small single-copy region, and two inverted repeat regions. It contains 130 genes, including 85 protein-coding, 37 tRNA, and 8 rRNA genes. Sixteen genes have a single intron, while clpP and ycf3 possess two introns each. Additionally, 17 genes are duplicated within the inverted repeat regions. The genome analysis revealed 92 Simple Sequence Repeats (SSRs), predominantly located in intergenic regions, with a bias toward A/T-rich codons. Comparative analysis with five closely related Acer species highlighted a highly conserved genomic structure, but also revealed differences in SSRs and repeat sequences. Hypervariable regions, such as rpl32-trnL and ycf1, were identified as potential molecular markers for phylogenetic and population studies. Phylogenetic analysis involving 37 chloroplast genomes confirmed the monophyly of the Acer genus and placed A. okamotoanum within the Platanoidea section, closely related to A. truncatum. This study improves the understanding of A. okamotoanum's genomic structure, offering insights for phylogenetic analysis, marker development, and conservation efforts.