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PubMed2026

Chloroplast genome comparative analysis and phylogenetic relationships of 15 Syringa species (Oleaceae).

Syringa is a crucial shrub genus in the family Oleaceae, which has significant ornamental, economic, and medicinal value. However, research on the chloroplast genome (CPG) phylogeny and lineage diversification of this genus remains limited. In this study, all 15 Syringa CPGs exhibited a characteristic quadripartite structure, with genome lengths ranging from 154,019-158,020 bp. These CPGs were highly conserved and moderately differentiated, each containing 130-132 genes. Analysis of inverted repeat (IR) boundaries indicated structural conservation, with six genes: rps19, rpl2, ycf1, trnN, ndhF, and trnH present at the IR/single-copy (SC) junctions. The small single copy (SSC) region displayed greater sequence variability than the IR regions. ycf1, ndhH, trnL-rpl32, ndhF-ycf1, and rbcL-accD were identified as potential molecular markers and rps11, ycf2, and ycf4 may have contributed to the adaptive evolution of Syringa. Phylogenetic reconstruction based on whole CPG data supported the monophyly of the 15 species, which were divided into three distinct subclades. Molecular dating estimated that Syringa diverged from its sister genus approximately 58 million years ago, with most Syringa species diversifying further approximately 47.49 million years ago during the Eocene. Our findings will hopefully stimulate further studies on this genus that may enhance biodiversity knowledge.

Journal Article↗

PubMed2026

Insights into phylogenetic relationships of Veronica species (Plantaginaceae) based on comparative chloroplast genomics.

INTRODUCTION: Veronica L. is one of the most species-rich genera in Plantaginaceae and several species have medicinal, horticultural, or ecological value. METHODS: In this study, the complete chloroplast genomes of three Veronica species were assembled and annotated using Illumina sequencing data. RESULTS: The plastomes exhibited a typical quadripartite structures, with total lengths of 150,202 bp for Veronica biloba L., 151,159 bp for Veronica ciliata Fisch. and 151,098 bp for Veronica vandellioides Maxim. Each genome contained 130-132 unique genes, including 86-87 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analyses of 24 Veronica plastomes indicated that the IR/SC junctions were largely conserved, although slight boundary shifts occurred around rps19, ndhF, and ycf1. Forward, palindromic, complement, and reverse repeats were detected, and A/T mononucleotide repeats were the dominant SSR type. Nucleotide diversity analysis identified rpl32-trnL, trnK-rps16, rpl32, ycf1, ndhF, accD, matK, and rpoB as highly variable regions. Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species. Divergence time estimation suggested that the estimation suggested of Veronica was around 14.9 Ma, with V. biloba, V. ciliata and V. vandellioides diverging approximately 3.9 Ma, 0.6 Ma, and 6.9 Ma, respectively. DISCUSSION: Because the analyses were based on plastid genomes, the inferred topology should be interpreted as chloroplast phylogenetic evidence rather than a complete species-history reconstruction. These results provide plastome resources and molecular evidence for taxonomy, species identification, and future evolutionary studies of Veronica.

Plantaginaceae↗

PubMed2026

Comparative chloroplast genomics of six Bupleurum (Apiaceae) accessions: candidate barcodes, phylogeny based on available plastomes, and candidate RNA-editing sites.

INTRODUCTION: Bupleurum L. (Apiaceae), a taxonomically intricate genus of about 190 species and a source of Radix Bupleuri (Chai Hu), is difficult to discriminate because of convergent morphology, infraspecific variation, and limited genomic sampling. This study aimed to characterize plastome variation, identify and validate candidate molecular markers, reconstruct plastid phylogenetic relationships, and assess candidate plastid RNA-editing sites in Bupleurum. METHODS: We assembled six plastomes from subgenus Bupleurum, screened 51 Bupleurum plastomes for diagnostic loci, reconstructed whole-plastome and partitioned protein-coding-sequence phylogenies, and predicted plastid C-to-U RNA-editing candidates across the six newly assembled plastomes using a PREP-Cp-compatible workflow. Candidate barcode performance was evaluated against the reference plastome phylogenies, and codon-based models were used to test for positive selection. RESULTS: The plastomes were 154,496-155,778 bp with the canonical quadripartite structure and GC contents of 37.67-37.73%. Gene content was stable (131-132 genes; 86-87 protein-coding genes); B. falcatum subsp. cernuum lacked ycf15 but contained an additional inverted-repeat-associated ycf1 annotation. A/U-ending synonymous codons were favoured. Finite pairwise Ka/Ks estimates were below 1 for most genes, and site-specific codon models detected no positive selection. Each plastome contained 55-61 pure microsatellites, dominated by A/T mononucleotide motifs. MarkerSeek ranked 265 features and identified atpF-atpH, petA-psbJ, rpl32-trnL-UAG, and ycf1 as leading candidate barcodes. ycf1 recovered 38 of 41 nodes strongly supported by both reference trees, whereas a partitioned four-locus analysis recovered 40 of 41 and distinguished all 51 accession sequences. However, only one of seven multi-accession operational binomial groups was monophyletic, and only one showed a positive local barcode gap. The whole-plastome phylogeny recovered Bupleurum as monophyletic relative to Chamaesium. The two sampled Penninervia accessions occupied early-diverging positions without forming an exclusive clade. B. falcatum subsp. cernuum was sister to B. ranunculoides, with B. ranunculoides subsp. telonense sister to that pair. A partitioned 74-CDS analysis recovered the same key relationships and 45 of 50 internal bipartitions. Across the six newly assembled plastomes, 57-63 nonsynonymous C-to-U candidates were predicted per accession (367 total) in 21-22 genes; 269 affected the second codon position and 98 the first. DISCUSSION: Bupleurum plastomes are structurally conservative but retain localised divergence useful for marker development. Concordant whole-plastome and CDS genealogies support genus monophyly, whereas sparse Penninervia sampling and maternal plastid inheritance preclude rejecting traditional subgeneric classification. The predicted RNA-editing sites represent candidates for future experimental validation rather than an established Bupleurum editome. These genomic resources support authentication, conservation, and evolutionary research in Bupleurum.

Apiaceae↗

PubMed2025

The complete chloroplast genome of Secale strictum ssp. strictum provides insights into Triticeae evolution and breeding.

The complete chloroplast genome of Secale strictum ssp. strictum (Poaceae: Triticeae) was sequenced and analyzed to support its use in rye and wheat breeding. The genome is 137,063 bp long and includes a pair of inverted repeats (IRs; 21,580 bp each) that separate the small (SSC; 12,817 bp) and large (LSC; 81,086 bp) single-copy regions. It contains 113 genes: 74 protein-coding, 30 tRNA, four rRNA genes, and five conserved open reading frames. A total of 42 repeat sequences were identified, mainly in the LSC region, with direct repeats being most common. All mononucleotide SSRs consisted of A/T motifs. Seven highly variable regions were identified, offering potential as molecular markers for species identification and phylogenetic studies. Phylogenetic analysis based on 73 protein-coding genes confirmed the systematic placement of the species and showed that S. strictum ssp. strictum is closely related to S. cereale and other S. strictum accessions. This study presents the first complete plastome of S. strictum ssp. strictum, now available as a reference genome under GenBank accession number OL979486.

Genome, Chloroplast↗

PubMed2024

Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution.

In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018 bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.

Genome, Chloroplast↗

PubMed2026

Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships in Fraxinus (Fraxinus mandshurica).

Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.

Fraxinus↗

PubMed2026

Characterisation of the chloroplast genome of Macrotyloma species: comparative analysis and phylogenomic insights.

Macrotyloma is an underutilised legume genus within the tribe Phaseoleae (Fabaceae) that includes nutritionally and agronomically important crops such as horse gram (Macrotyloma uniflorum) and Kersting's groundnut (Macrotyloma geocarpum). Despite their importance, knowledge of the chloroplast (cp.) genome of this genus remains limited. In this study, we assembled and analysed the complete chloroplast genomes of three Macrotyloma species: M. uniflorum, M. geocarpum, and M. axillare. The chloroplast genomes were assembled into two isoforms that differ in the orientation of the small single-copy (SSC) region. Genome sizes ranged from 150,811 to 151,013 bp and exhibited the canonical quadripartite structure, comprising a pair of inverted repeats (IRa and IRb; 26,416-26,436 bp each), a large single-copy region (LSC; 80,229-80,446 bp), and a small single-copy region (SSC; 17,710-17,711 bp). Each genome encoded 110 unique genes, including 4 rRNA genes, 30 tRNA genes, and 76 protein-coding genes. All three species also possessed the ~ 50 kb inversion in the LSC region, a synapomorphy shared among a large clade within the Papilionoideae subfamily of Fabaceae. Although overall chloroplast genome structure and organisation were highly conserved among Macrotyloma species, gene-wise nucleotide diversity analysis identified seven relatively variable genes: rps18, rps15, ccsA, ndhA, ycf1, ycf4, and psaI. Phylogenomic analysis based on complete chloroplast genomes robustly resolved Macrotyloma as a monophyletic group within the Phaseolinae clade of the Papilionoideae subfamily. Within the genus, M. uniflorum and M. axillare formed a strongly supported sister pair, with M. geocarpum sister to this clade. Overall, this study provides valuable insights into chloroplast genome evolution in Macrotyloma and enhances understanding of its phylogenetic placement within Phaseoleae, offering genomic resources for future evolutionary, taxonomic, and conservation studies of this underutilised legume genus.

Genome, Chloroplast↗

PubMed2026

Characterization and comparative analysis of the complete chloroplast genomes of twelve Allium species from Kazakhstan.

The genus Allium L. represents one of the largest and taxonomically complex groups of monocots, with Central Asia recognized as a major center of its diversity. Despite the high species richness of Allium in Kazakhstan, genomic data for many native taxa remain limited. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of 12 Allium species from Kazakhstan. All chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes ranging from 152,029 to 153,521 bp and a uniform gene content of 137 genes, including 88 protein-coding genes, 38 tRNAs, 8 rRNAs, and 3 pseudogenes. Comparative analyses revealed high structural conservation, with most sequence divergence concentrated in intergenic regions. Several highly variable regions, including ycf1, matK, rpoC2, and ycf2, were identified as potential molecular markers. Phylogenetic analyses based on chloroplast genome sequences using Maximum Likelihood and Bayesian approaches recovered three major chloroplast genome-based lineages within Allium, largely consistent with previous phylogenomic studies. Divergence-time analyses suggested that major chloroplast lineage diversification events within the genus occurred during the early Eocene (ca. 47.97 Mya). Overall, this study expands the currently available chloroplast genomic resources for Allium from Kazakhstan, provides insights into chloroplast genome evolution and chloroplast genome-based relationships, and establishes a valuable foundation for future phylogenetic, taxonomic, and evolutionary studies of this diverse genus.

Genome, Chloroplast↗

PubMed2026

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships among Syndiclis species.

The complete mitochondrial genome (mitogenome) of Syndiclis anlungensis, a critically endangered tropical tree, was determined in this study. The mitogenome spans 2,368,454 bp across four contigs and harbors 41 protein-coding genes, 22 tRNA genes, and three rRNA genes. Potential mutation regions, including 1317 repeat sequences and 698 simple sequence repeats (SSRs), were accurately located in the S. anlungensis mitogenome. Sixty-five transferred fragments of the repeats were found between its mitochondrial and chloroplast genomes. When compared to three other Laurales mitogenomes, extensive gene order shuffling is evident, leaving only five conserved gene clusters intact. Codon usage analysis reveals a pronounced A/T bias in both mitochondrial and chloroplast genes, and three mitochondrial genes (atp9, rps19, and sdh3) stand out for their high divergence across eleven Syndiclis taxa. Selection analyses indicate strong purifying pressure on rpl2, rpl16, and sdh3 (Ka/Ks < 1), with no positive selection detected. Using 41 mitochondrial protein-coding gene sequences from sixteen and three individuals of Syndiclis and Beilschmiedia species, respectively, our phylogenetic tree recovers Syndiclis as monophyletic, with two well-supported clades: one includes S. anlungensis, S. chinensis, S. lotungensis, S. marlipoensis, and a putative new Syndiclis species from Yunnan; the other contains S. furfuracea, S. hongkongensis, S. kwangsiensis, and three putative new Syndiclis species from Guangdong and Vietnam.

Genome, Mitochondrial↗

PubMed2026

Plastome evolution and phylogenomic relationships in Ajuga (Lamiaceae, Ajugoideae).

BACKGROUND: Ajuga is currently known to include approximately 69 species, with a combined distribution extending throughout Eurasia, Africa, and Australia. Its popularity and significance are largely based on an extensive history of medicinal and horticultural use. It is divided into two sections based on morphological characters, and this sectional classification is also reflected in pronounced geographic patterns. Although previous studies have largely focused on Ajuga sect. Ajuga in East Asia, A. sect. Chamaepithys, which ranges from the Mediterranean to Central Asia, remains insufficiently sampled, thereby limiting a comprehensive understanding of infrageneric sectional relationships within the genus. Here, we generated complete plastid genomes for 12 species representing both sections of the genus and used these data to characterize plastome structure and infer evolutionary relationships. RESULTS: In this study, 21 Ajuga plastomes were analyzed, including 12 newly sequenced plastomes and 9 previously published plastomes representing 19 species. Comparative analyses showed that all plastomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 149,963 to 150,740 bp and GC contents varying from 38.2% to 38.3%. Each plastome contained 133 genes, including 88 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The boundaries between the inverted repeat (IR) and single-copy (SC) regions were also highly conserved across species. In addition, 796 simple sequence repeats (SSRs), 874 long repeat sequences (LRSs), and 12 highly variable regions (ccsA-ndhD, ndhF-rpl32, petA-psbJ, rpl32-trnL-UAG, rps2-rpoC2, trnH-GUG-psbA, trnK-UUU-rps16, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, ycf15-trnL-CAA, ndhF, and ycf1) were identified among the 21 plastomes. Phylogenetic analyses based on four datasets and conducted using Maximum Likelihood and Bayesian Inference recovered two major clades corresponding to the traditionally recognized sectional classification, with one distributed from the Mediterranean to Central Asia and the other in East Asia. CONCLUSION: This study represents the most comprehensive plastome-based sampling of Ajuga to date, including representative species from the Mediterranean, Central Asia, and East Asia. Our results have significantly enhanced our understanding of its infrageneric relationships. The plastome resources generated in this study provide a valuable foundation for future research on species delimitation, phylogeny, and the evolutionary history of Ajuga.

Phylogeny↗

PubMed2026

Comparative genomics and phylogenetic analysis of three Malvaceae species on the basis of chloroplast genomes.

INTRODUCTION: The Malvaceae family shows rich species diversity and has substantial economic and medicinal value. However, the frequent interspecific hybridization among members of this family has resulted in confused phylogenetic relationships among the groups, limiting the usefulness of traditional classification methods. METHODS: This study aimed to investigate the phylogenetic relationships among selected taxa of Malvaceae by evaluating 23 chloroplast (CP) genomes, including three newly assembled CP genomes. Among these three genomes, the CP genome of Hibiscus schizopetalus L. was reported for the first time, while the CP genomes of Alcea rosea L. and Hibiscus grewiifolius L., which have been deposited in NCBI, were re-analyzed here alongside newly generated data for comparative purposes. In addition, 20 downloaded CP genomes encompassing 13 genera were analyzed using SNPs in whole CP genomes data. RESULTS: The results showed that the genomes ranged from 160,403 to 161,978 base pairs in length and consisted of small single copies (SSCs) and large single copies (LSCs) separated by two inverted repeat sequences (IRs), forming a typical quadripartite circular structure. The entire genome sequence showed relative conservation across species in terms of structure, GC content, codon usage, and gene composition. The mutation sites were mainly located in the LSC and SSC regions, and the variability in the non-coding regions was higher than that in the coding regions. The nucleotide polymorphism (Pi) analysis identified the non-coding regions such as ndhF-rpl32 and psbZ-trnG as high variable hotspots. A maximum likelihood phylogenetic tree was constructed based on SNPs in whole CP genomes data. The phylogenetic analysis divided these 23 species into five highly supported clades. It also revealed a close sister-group relationship between Abelmoschus and Hibiscus species, suggesting that Hibiscus may have a separate lineage from okra species. DISCUSSION: In conclusion, the increasing availability of CP genome resources will enhance our understanding of the classification and evolutionary patterns of the Malvaceae family. The development of molecular markers will provide important molecular evidence for precise identification and classification revision of plants in this family.

Malvaceae↗

PubMed2026

Genome-scale insights into metabolic streamlining and photosynthetic energy balance in the extremophile green alga Picocystis salinarum (Picocystophyceae, Chlorophyta).

Picocystis salinarum is an early-diverging chlorophyte and the sole described member of the Picocystophyceae, frequently dominating hypersaline and alkaline lakes despite extreme physicochemical constraints. To elucidate the genomic foundations of its ecological success, we generated a fully annotated, chromosome-scale nuclear genome assembly of the type strain originally isolated from a saline pond in San Francisco Bay. The 18.5-Mb genome comprises 30 chromosomal assemblies, exhibits clear diploidy, and contains multiple copies of intact Ty3/Gypsy and Ty1/Copia long terminal repeat retrotransposons encoding polyproteins with atypical accessory domains. Phylogenomic analyses reveal strong affinity with the Nephroselmidophyceae. Comparative analyses reveal extensive metabolic streamlining, including the absence of a queuosine salvage pathway, the 2-methylcitrate cycle, β-oxidation of propionate, and branched-chain amino acid catabolism, traits retained in several marine prasinophyte lineages. In contrast, the genome preserves multiple ancestral bacterial derived systems. Notably, P. salinarum features a complete chloroplast NADH dehydrogenase-like complex, including all membrane, electron binding, and assembly components, a configuration not previously reported in sequenced chlorophyte algae. This retention implies substantial capacity for cyclic electron flow and chlororespiration, processes expected to be critical in chronically low-light and chemically extreme environments. The genome further reveals a distinctive biochemical CO2-concentrating mechanism centered on plastid-targeted phosphoenolpyruvate carboxykinase, complete plastid peptidoglycan biosynthetic and remodeling pathways, and partial retention of lipid-A-related machinery. Conversely, P. salinarum lacks canonical non-photochemical quenching proteins while retaining xanthophyll-cycle enzymes that support slower photoprotective responses. Together, these features define a coordinated genomic architecture that underpins the specialization of P. salinarum to hypersaline, alkaline, and persistently low-light ecosystems.

3‐deoxy‐D‐manno‐octulo↗

PubMed2025

Reverse genetics in the Arabidopsis chloroplast genome identifies rps16 as a transcribed pseudogene.

The plastid (chloroplast) genomes of seed plants contain a conserved set of ribosomal protein genes. The rps16 gene represents an exception: It has been lost from the plastid genomes of gymnosperms and several lineages of angiosperms, and may have undergone pseudogenization in a few other lineages, including members of the Brassicaceae family. Here we report a reverse genetic approach to test the annotated rps16 gene in the Arabidopsis plastid genome for functionality. Employing the recently developed plastid transformation technology for the model plant Arabidopsis, we have deleted the putative rps16 gene from the Arabidopsis plastid genome. We report that the resulting transplastomic plants display wild-type-like growth and photosynthetic performance under a wide range of conditions. Moreover, genome-wide analyses of chloroplast transcript levels and ribosome footprints revealed unaltered plastid translational activity in Δrps16 mutants compared with wild-type plants. We conclude that the annotated rps16 gene in the plastid genome of Arabidopsis is a transcribed pseudogene that has been replaced in evolution by a nuclear gene copy that supplies functional S16 protein to chloroplasts.

Arabidopsis↗

PubMed2026

The complete chloroplast genomes of Rhamnus arguta Maxim. and R. parvifolia Bunge (Rhamnaceae).

The genus Rhamnus L. (Rhamnaceae) has high medicinal, ecological, and ornamental value, but its infrageneric classification remains unclear. Here, we sequenced, assembled, and annotated the complete chloroplast genomes of Rhamnus arguta and R. parvifolia using Illumina sequencing. Both plastomes exhibit the typical quadripartite structure, with lengths of 160,566 bp and 161,243 bp, containing 128 and 129 genes, respectively. Phylogenetic analyses support the monophyly of Rhamnus and its close relationship with Frangula. This study provides genomic resources for further phylogenetic and comparative studies within Rhamnaceae.

Chloroplast genome↗

PubMed1978

The kinetic complexity of Acetabularia chloroplast DNA.

The kinetic complexity of Acetabularia cliftonii chloroplast DNA is 1.52 +/- 0.26 . 10(9) daltons, compared to 0.2 .10(9) daltons for Chlamydomonas chloroplast DNA. There is an average of three genomes per chloroplast. The unusually large size of the Acetabularia genome may reflect the ancient evolutionary history of this organism.

Acetabularia↗

PubMed2026

Integrated phytochemical and bioactivity profiling of Xanthium strumarium fruits from Korea and China: Implications for origin-specific quality specification.

BACKGROUND: Geographic origin influences the phytochemical composition and biological activities of medicinal plant resources. Xanthium strumarium L. (XS) fruit is widely used in East Asian traditional medicine. However, current pharmacopeial standards primarily recognize Chinese-derived material, despite the availability and traditional use of XS in Korea. To address this gap and support origin-informed quality specification, we compared fruits from Korea (XS-K) and China (XS-C) using chloroplast genome sequencing, targeted phytochemical profiling (high-performance liquid chromatography (HPLC) for selected phenolics and gas chromatography-flame ionization detection (GC-FID) for fatty acids and phytosterols, and multivariate chemometric analysis. RESULTS: Chloroplast genome analysis revealed high overall similarity but localized divergence around the rpoC2 locus and a greater mutation burden in XS-C, supporting origin-associated genomic differentiation. Phytochemical profiling revealed distinct origin-dependent metabolic signatures. XS-K showed higher levels of phytosterols, chlorogenic acid, 4,5-dicaffeoylquinic acid (4,5-DCQ), and xanthatin was detected only in XS-K, whereas XS-C exhibited greater abundance of total fatty acids, particularly oleic acid. Unsupervised clustering and log2 fold-change ranking confirmed clear compositional separation, and variable importance in projection (VIP) analysis identified chlorogenic acid, β-sitosterol, oleic acid, 4,5-DCQ, and xanthatin as major discriminators between origins. Bioactivity assays demonstrated that XS-K exerted stronger antioxidant effects in ABTS, DPPH and FRAP assays, stronger skin-related enzyme inhibition, and greater antibacterial activity against Staphylococcus aureus, consistent with its enriched phenolic and sterol profile. CONCLUSION: Together, chloroplast sequence variation, targeted metabolite quantification, and screening bioassays consistently distinguished XS-K from XS-C. These findings support the use of candidate markers for the origin-based authentication and quality control of XS fruit-derived ingredients. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Fruit↗

PubMed2026

Comprehensive analysis of synonymous codon usage bias and evolutionary dynamics in the chloroplast genomes of eight Coptis species.

Coptis is a medically important genus renowned for producing valuable isoquinoline alkaloids. Although its chloroplast genomes encode key components for photosynthesis and plastid gene expression, the evolutionary constraints acting on their coding sequences and synonymous codon usage remain poorly resolved. Here, we combined a transparent taxon-level sampling strategy with comparative analyses of chloroplast CDSs from eight Coptis taxa. We quantified nucleotide composition, relative synonymous codon usage, effective number of codons, neutrality and PR2 patterns, and correspondence analysis, and then integrated these results with a core-CDS distance analysis and gene-wise pairwise dN/dS estimates. The chloroplast genomes showed a conserved AT-rich composition, especially at the third codon position (GC3 approximately 30.3-30.8%), with a consistent GC1 > GC2 > GC3 trend. Thirty preferred codons were detected, 28 ending in A/T, and eleven optimal codons were shared across the genus. The core-CDS distance analysis recovered a close relationship between C. chinensis and C. chinensis var. brevisepala, whereas most coding genes showed dN/dS values below one, consistent with pervasive purifying constraint. Across 48 consistently filtered CDSs, GC3s was negatively associated with mean dN (Spearman rho = -0.404, P = 0.00439) and CAI was positively associated with mean dN (rho = 0.303, P = 0.0361), whereas the remaining associations were not significant (all P > = 0.0972). These results extend codon-usage analysis by linking synonymous-site composition to coding-sequence evolution within Coptis, while providing a hypothesis-generating resource for future plastid engineering studies.

Genome, Chloroplast↗

PubMed2026

Assembly and comparative analysis of the mitochondrial genome of Pleione yunnanensis: genome structure and evolutionary insights.

BACKGROUND: Pleione yunnanensis a terrestrial or semi-epiphytic herbaceous plant belonging to the Orchidaceae family, is valued for both its medicinal uses and ornamental appeal. Although its chloroplast genomes have been sequenced, its complete mt genome had not previously been resolved, limiting genetic and evolutionary studies of the species. RESULTS: In this work, we assembled and characterized the first complete mt genome of P. yunnanensis, revealing a structurally complex, multibranched system composed of 14 circular-mapping molecules totaling 468,176 bp with a GC content of 44.32%. The genome encodes 44 annotated genes, including 28 protein-coding genes (PCGs), 15 tRNAs, and one rRNA. The multibranched architecture provides new evidence supporting the dynamic and recombinational nature of plant mt genomes. Repeat analysis uncovered 29 simple sequence repeats (SSRs), 19 tandem repeats, and 118 dispersed repeats, indicating a comparatively lower repeat abundance than that found in closely related orchids with similar mt genome sizes. Codon-usage profiling of PCGs showed a marked bias toward A/T-ending codons. Prediction of RNA editing sites identified 4,708 putative edits across mitochondrial PCGs. Most mitochondrial genes displayed Ka/Ks ratios close to 1.0, suggesting relaxed selective constraints or lineage-specific evolutionary patterns rather than strong positive selection. Moreover, we detected 69 chloroplast-derived homologous fragments, including 15 intact genes, suggesting ongoing plastid-mitochondrial DNA transfer. Phylogenetic reconstruction and collinearity comparisons demonstrated that P. yunnanensis clustered closely with Dendrobium species, including D. amplum and D. hancockii, within the Orchidaceae clade. CONCLUSIONS: This study provides the first complete mt genome of P. yunnanensis, providing a foundational genomic resource for the genus Pleione. The results not only improve our understanding of mt genome structure and evolution in Orchidaceae, but also offer valuable molecular evidence for phylogenetic inference, germplasm identification, and conservation of this endangered medicinal species.

Orchidaceae↗