Search Results (267)

Liverwort organellar genomes are generally highly conserved, but the subclass Pellidae (simple thalloids) shows unusual variation. This ancient yet unexplored lineage of simple thalloid liverworts provides an excellent model for investigating organellar genome evolution. In this study, we assembled four new plastid and four new mitochondrial Pellidae genomes using Oxford Nanopore sequencing, supplementing 86 plastomes and 82 mitogenomes from databases. We assessed nucleotide diversity and codon usage, and inferred phylogenies using IQ-TREE with fossil-calibrated dating. Plastomes ranged 120.6–126.5 kb, and mitogenomes 109–180 kb, with Apopellia endiviifolia featuring an exceptionally reduced mitogenome (~109 kb). Native RNA sequencing enabled a revised annotation of the mitochondrial atp1 gene in Apopellia, revealing two introns (previously thought absent) and reducing the intergenic region share to 36.26%, the lowest known among liverworts. Comparative analyses revealed contrasting evolutionary dynamics between organelles: Plastomes displayed higher nucleotide diversity and phylogenetically inconsistent codon usage patterns, likely influenced by compositional bias, whereas mitogenomes were more conserved and largely consistent with established phylogenetic relationships among the orders. Phylogenomic analyses yielded discordant topologies: Chloroplast data recovered Pellidae as a monophyletic clade, whereas mitochondrial data placed Pelliales (Pellia/Apopellia) as basal Jungermanniopsida, rendering Pellidae paraphyletic. Within Pellidae-relevant clades, several major divergences were dated to the Carboniferous–Permian, but with systematic chloroplast–mitochondrial offsets. These results highlight recurrent organellar incongruence and the dynamic evolutionary history of Pellidae organellar genomes. Full article

Juncus (Juncaceae) comprises over 300 species with high morphological plasticity, and its systematics remain incompletely resolved due to limited genomic resources. Here, we generated complete plastid genomes for two Korean Juncus species (J. decipiens and J. gracillimus) and incorporated plastid coding genes from an additional species to reconstruct phylogenetic relationships and examine plastome evolution within Juncaceae. Comparative analyses revealed substantial plastome size variation across Juncus and Luzula, largely driven by changes in inverted repeat (IR) length, with Luzula plastomes showing pronounced IR expansion. Within Juncus, extensive structural rearrangements were detected, including multiple inversion events, and closely related taxa shared conserved inversion patterns. Phylogenomic analyses recovered well-supported clades that were associated with structural traits such as extreme small single-copy (SSC) contraction and consistent loss of the plastid ndh, some rps and rpl gene families, indicating clade-specific plastome evolution in Juncaceae. To support applied molecular identification, we identified J. decipiens-specific plastid diagnostic SNPs (matK, rpl2) and validated allele-specific PCR markers using individuals from different species within the Juncus genus. In parallel, transcriptome sequencing of J. decipiens generated 133,559 transcripts and 66,324 unigenes, enabling discovery of high-confidence nuclear exonic SNP loci by mapping reads to a J. effusus nuclear genome. Collectively, our results provide new insights into plastome structural evolution and gene loss in Juncus and deliver validated plastid and nuclear markers for authentication and future conservation or utilisation studies on J. decipiens. Full article

Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome features and evolutionary position are still unclear. This study aims to assemble and characterize its complete chloroplast genome and clarify its phylogenetic placement within Delphinium. Methods: Using Illumina NovaSeq data, we de novo assembled the D. densiflorum plastome, annotated it with CPGAVAS2, and compared it with 12 published Ranunculaceae plastomes. We analyzed IR-boundary dynamics, genome-wide sequence variation, and codon-usage bias and constructed a maximum-likelihood phylogeny based on 69 shared protein-coding genes. Results: The plastome is 154,161 bp (GC 38.24%) with a canonical quadripartite structure, encoding 131 genes (87 CDS, 8 rRNA, 37 tRNA). An IR expansion into the SSC region yields the shortest SSC reported among the compared Delphinium species and produces unique structural variants. Photosynthetic genes are extremely conserved (nucleotide diversity Pi ≤ 0.01), whereas several loci (e.g., ycf1 and psaC) are highly divergent (Pi ≥ 0.05). Codon usage shows a strong bias toward AU-ending triplets. Phylogenetically, D. densiflorum forms a 100%-bootstrap clade with other high-altitude congeners, supporting the non-monophyly of Delphinium. Conclusions: This study delineates the plastome architecture and putative adaptive signatures of D. densiflorum, identifies robust candidate loci for DNA barcoding, and provides molecular evidence for taxonomic revision and conservation strategies in Delphinium. Full article

Background: The subtribe Pleurothallidinae is a diverse group within Orchidaceae with a complex taxonomic history. Comparative plastome analysis can provide insights into genome evolution and facilitate phylogenetic reconstruction. Methods: Here we analyzed 25 complete chloroplast genomes representing 15 genera, including 14 newly assembled genomes, to investigate plastome evolution in this subtribe. Results: All genomes exhibited the typical quadripartite structure (148, 246–158, 138 bp) with conserved gene content (128–134 genes). While most protein-coding genes were under purifying selection, we detected signatures of positive selection in specific lineages. Notably, ndhF in Lepanthes tachirensis showed a markedly elevated Ka/Ks ratio (3.65), which may be associated with adaptation to an extensive distributional range. ENC-plot analysis indicated that natural selection, rather than mutation pressure alone, shapes codon usage bias, with patterns varying among species from different geographic regions. Nucleotide diversity analysis identified eight hypervariable intergenic regions (psbK-psbI, atpI-rps2, petN-psbM, psbB-psbT, petD-rpoA, rpoA-rps11, rps3-rpl22, ccsA-ndhD) suitable as candidate molecular markers. Phylogenetic analysis confirmed that Lepanthes and Pleurothallis are non-monophyletic as traditionally defined. Conclusions: These findings expand plastome resources for Pleurothallidinae, reveal lineage-specific patterns of selection, and provide molecular markers for future taxonomic and evolutionary studies. Full article

Background: Viburnum (Adoxaceae) is a species-rich woody genus whose taxonomy is complicated by morphological convergence and hybridization. Methods: We assembled complete plastomes of eight species representing five sections and analyzed their structural variation, sequence divergence, and molecular evolution. Results: All plastomes displayed the conserved quadripartite structure typical of angiosperms, with limited size variation attributable primarily to intergenic spacer-length polymorphisms. Sequence divergence was unevenly distributed, with single-copy regions exhibiting substantially higher nucleotide diversity than inverted repeat regions. We identified multiple hypervariable intergenic spacers such as the region trnK-UUU–rps16, suitable as molecular markers for population genetics and species identification. Selection pressure analysis revealed that while most protein-coding genes evolved under strong purifying selection, three genes involved in fatty acid biosynthesis and protein import—accD, ycf1, and ycf2—showed significantly relaxed constraints, suggesting ongoing functional divergence. Phylogenetic analysis recovered well-supported relationships consistent with previous classifications, while clarifying the positions of Viburnum amplificatum and Viburnum tinus. Conclusions: These findings provide molecular resources for Viburnum systematics and offer insights into the evolutionary dynamics of plastome genes with non-photosynthetic functions. Full article

Pseudolysimachion pyrethrinum var. gasanensis (Gasan spike speedwell) is a valuable Korean endemic variety with significant horticultural potential. Despite its morphological distinctiveness, its taxonomic status and evolutionary position have remained a subject of debate. In this study, we assembled and characterized the first complete chloroplast (cp) genome of P. pyrethrinum var. gasanensis using high-throughput sequencing. The complete plastome is 152,251 bp in length, exhibiting a typical quadripartite structure with a large single-copy (LSC) region (83,191 bp), a small single-copy (SSC) region (17,690 bp), and two inverted repeats (IRs) (25,685 bp each). The genome contains 133 genes, including 88 protein-coding, 37 tRNA, and 8 rRNA genes. Genomic analysis identified 42 simple sequence repeat (SSR) units across 38 distinct loci, predominantly mononucleotide A/T motifs, which serve as potential molecular markers for variety-level identification. Selective pressure analysis revealed that the majority of protein-coding genes are under strong purifying selection (Ka/Ks < 1.0), emphasizing the evolutionary stability of the plastome. Comparative analysis of IR boundaries using IRscope revealed a high degree of structural conservation among Pseudolysimachion species, with minor variations at the junction sites. Phylogenetic analysis based on 18 complete plastomes strongly supported the monophyly of the genus Pseudolysimachion (Bootstrap = 100%) and placed P. pyrethrinum var. gasanensis as a sister to the European P. spicatum. These genomic resources provide a foundational tool for the molecular breeding, systematic conservation, and sustainable utilization of this endemic variety, while offering clarity to its taxonomic classification within the tribe Veroniceae. Full article

Background/Objectives: The Fagopyrum dibotrys complex is a specialized high-altitude lineage in southwestern China with medicinal and breeding potential, but species delimitation remains unresolved. Methods: We sequenced 26 complete chloroplast genomes from the Hengduan Mountains to the Yunnan–Guizhou Plateau, analyzing genomic structures, variation patterns, and phylogenetic relationships. Results: All genomes exhibited typical quadripartite structures (152,213–160,302 bp), containing 133 genes (88 protein-coding, 8 rRNA, and 37 tRNA) with GC content of 37.9%. Collinearity analysis revealed highly conserved structures without structural rearrangements. Variations were concentrated in the large single-copy(LSC)/small single-copy(SSC) non-coding regions, with hotspots at ycf4–cemA and ndhF–rpl32. Codon usage showed an A/U bias, with leucine being most abundant and cysteine the least. Simple sequence repeats (SSRs) were predominantly mononucleotide repeats enriched in the LSC, while long repeats were mainly palindromic/forward. Maximum likelihood and Bayesian phylogenies consistently resolved three clades: Tibetan high-altitude specialists, limestone specialists, and a widespread Hengduan–Yunnan–Guizhou clade, with geographic clustering indicating isolation as the primary differentiation driver. Conclusions: This study refines the phylogenetic resolution of the F. dibotrys complex and identifies informative chloroplast markers, providing a genomic foundation for reliable species delimitation, evolutionary inference, and conservation management of this medicinal lineage. Full article

Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG–ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM–trnD, and rpl32–trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus. Full article

Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional approaches. To address the challenge of discriminating Toona sinensis varieties, we sequenced and compared 15 complete chloroplast genomes from five varieties in northern China. Although these genomes exhibited a highly conserved structure, we identified eight variety-specific simple sequence repeats (SSRs), two unique tandem repeats, and several hypervariable regions with elevated nucleotide diversity. Phylogenetic analysis demonstrated that whole chloroplast genomes provided the highest resolution for variety identification, outperforming conventional barcodes. Furthermore, we developed 13 specific primer pairs targeting variable regions, and PCR validation confirmed their reliable amplification across varieties. In addition, sequence-level validation by Sanger sequencing of representative SSR and tandem repeat markers revealed stable, variety-specific repeat copy number differences. These results demonstrate that the identified chloroplast markers can effectively discriminate closely related T. sinensis varieties. This study confirms that despite overall conservation, the T. sinensis plastome contains sufficient variation for reliable identification, providing a robust framework for future germplasm conservation and molecular breeding. Full article

Background/Objectives: Soroseris hookeriana, a Tibetan medicinal plant endemic to the high-altitude Qinghai–Tibet Plateau, possesses significant pharmacological value but lacks fundamental genomic characterization. This study aims to generate and comparatively analyse its complete chloroplast genome. Methods: Total DNA was sequenced, assembled with GetOrganelle, annotated with CPGAVAS2, and compared with eight Asteraceae species; phylogenetic placement was inferred with IQ-TREE from 21 complete plastomes. Results: The circular chloroplast genome is 152,514 bp with a typical quadripartite structure (LSC 84,168 bp, SSC 18,528 bp, two IRs 24,909 bp each). It contains 132 unique genes (87 protein-coding, 37 tRNA, 8 rRNA; 18 duplicated in IRs yield 150 total copies). Twenty-three genes harbour introns; clpP and ycf3 have two. Overall GC content is 37.73%, elevated in IRs (43.12%). Codon usage shows strong A/U bias at the third position; 172 SSRs and 39 long repeats are detected. IR-SC boundaries exhibit the greatest inter-specific variation, notably in ycf1 and ndhF. Conclusions: The complete plastome robustly supports S. hookeriana and Stebbinsia umbrella as sister species (100% bootstrap) and provides essential genomic resources for species identification, population genetics, and studies of high-altitude adaptation. Full article

Zingiber salarkhanii (Zingiberaceae family) is an endemic species of Bangladesh. It possesses biological effects, including analgesic, anxiolytic, cytotoxic, and antioxidant properties. Although genomic data on Zingiber is scarce, the entire chloroplast (cp) genome has been extensively used as a molecular marker to resolve phylogenetic issues. The genome size is 163,980 bp, and it has a standard quadripartite structure, with an average GC content of 36.91%. The genome contains 138 genes (113 unique), comprising 90 protein-coding genes, 79 unique genes, 48 noncoding genes (34 unique), 40 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). Codon usage analysis of the cp revealed 14 high-frequency codons besides 18 optimal codons in this species. A repetitive study revealed 211 simple sequence repeats (SSRs), predominantly A/T mononucleotide repeats. Sequence alignment indicated that variable regions were primarily located in the single-copy regions. Sequence comparison showed that most variable regions were located within the single-copy regions, and nucleotide diversity (π = 0–0.11289) indicated overall low divergence with 11 mutation hotspots. Phylogenetic investigations using both coding sequences and complete cp genomes indicated that Z. salarkhanii is most closely related to the Zingiber genus. Phylogenetic investigations using both coding genes and complete cp genomes placed Z. salarkhanii within the core Zingiber lineage, revealing its closest relationship to Z. recurvatum rather than to the genus. It conducted an extensive analysis of many cp genomic characteristics for phylogenetic significance, including overall genome architecture, codon usage bias, repetitive sequences, inverted repeat borders, and phylogenetic reconstruction. These findings provide a basis for further research to elucidate the molecular evolutionary dynamics of individual population variability within the species and genus. The plastome reported here also provides an essential genomic reference for future work on population variation and species differentiation within Zingiber. Full article

Camellia sinensis ‘hainanensis’ (Hainan Sheng tea) is an endemic tea germplasm resource native to Hainan Island, China. Using complete chloroplast genome sequencing combined with comprehensive comparative analyses, we elucidated the genetic architecture of six C. sinensis accessions. The chloroplast genomes exhibited a typical quadripartite circular structure (~157 Kb) comprising 80 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Expansion and contraction of the inverted repeat (IR) regions led to boundary shifts affecting genes, while nucleotide diversity within the large single-copy (LSC) and small single-copy (SSC) regions (Pi > 0.0035) markedly exceeded that of the conserved IR regions. Phylogenetic reconstruction revealed that C. sinensis ‘hainanensis’ shared the closest evolutionary relationship with Yunnan large-leaf tea (Camellia grandibracteata), supporting its independent lineage within the genus. A polymorphic molecular marker derived from the hypervariable non-coding region (trnT–psbD) may serve as a useful preliminary marker for distinguishing C. sinensis ‘hainanensis’ from related taxa and hybrids. This study provides the first comprehensive comparison of complete chloroplast genomes of six C. sinensis ‘hainanensis’, identifies three distinct plastome types, and develops a molecular marker that can reliably distinguish these types, offering valuable genomic resources for future studies on tea evolution and germplasm identification. Full article

Next-generation sequencing technology was employed to read and assemble the complete plastid genome of the ‘Mejhoul’ date palm cultivar (Phoenix dactylifera L.). The genome consisted of 158,436 base pairs (bp) with a GC content of 37.24%, and it included 95 protein-coding genes, 44 tRNA genes, and eight rRNA genes. The plastome of five ‘Mejhoul’ genotypes from Jordan was compared with three genotypes from the USA, Morocco, and the UAE. It revealed 91 single-nucleotide polymorphisms (SNPs) and 23 insertions–deletions (InDels); the majority of them (62%) were located in intergenic regions, while the remaining variants were located in intragenic regions, including tRNA and rRNA genes. When the plastomes of all eight ‘Mejhoul’ genotypes were aligned, along with major cultivars ‘Barhee’ and ‘Khalas’, 24 SNPs and 23 InDels could be found. This would enable the development of a cultivar-specific fingerprint test for authentication. The phylogenetic tree was constructed using seventeen date palm cultivars. The phylogenetic analysis places ‘Mejhoul’ as a lineage derived within Clade I rather than as an early-diverging cultivar, suggesting it shares a more recent common ancestor with ‘Deglet Noor’ and ‘Barhee’. Full article

Background: The epiphytic orchids of the tribe Epidendreae represent a remarkably evolutionary radiation, yet their phylogenetic relationships and plastome evolutionary dynamics are still not fully resolved. Methods: This study has sequenced, assembled, and annotated the complete chloroplast genome of Encyclia tampensis. Through comparative analyses of a curated dataset of 40 Epidendreae plastomes, we investigated codon usage bias, evolutionary selection pressures (Ka/Ks), and phylogenetic relationships. Results: The plastome of E. tampensis (160,650 bp) has a typical quadripartite structure, with a significant AT bias (62.09%), and contains 124 annotated genes. Comparative genomic analysis across 40 Epidendreae species revealed substantial plastome size variation (123,455 to 160,650 bp), pronounced small single copy (SSC) contraction in E. tampensis (608 bp), and atypical long simple sequence repeats (SSRs) accumulation. Natural selection dominated codon usage, with strongest purifying selection in rbcL (average Ka/Ks = 0.205). Phylogenetic analyses confirmed subtribal monophyly and detected evolutionary rate heterogeneity correlated with life history strategies. Conclusions: These results establish that plastome evolution in Epidendreae has been principally driven by structural reorganization through SSC contraction and long SSR accumulation, selective constraints maintaining functional genes under purifying selection, and life history-strategy-mediated evolutionary rate diversification. These processes collectively account for the tribe’s extensive genomic diversity and phylogenetic complexity, thereby providing a theoretical framework for understanding orchid plastome evolution and a molecular basis for the systematic classification and conservation of this economically significant plant group. Full article

Background/Objectives: Chloroplast genomes (plastomes) are valuable for fern systematics, yet the epiphytic lineages have remained underexplored. Methods: The Davallia trichomanoides plastome was de novo assembled from Illumina data and annotated. Results: The plastome measures 154,217 bp with a GC content of 40.82% and contains 115 genes. Comparative analysis reveals two inverted repeat (IR) size classes (~24.0–24.6 kb vs. ~27.4–27.5 kb) and lineage-specific shifts at the IR junctions. For instance, the ndhF gene remains in the small single copy (SSC) region in D. trichomanoides and Drynaria acuminata, but it crosses into the IRb region in other species. We observed nucleotide diversity hotspots in the large single copy (LSC) and SSC regions. The IR regions are highly conserved. The ratios of nonsynonymous to synonymous substitutions (Ka/Ks) are mostly less than 1, indicating purifying selection. Phylogenetic analysis places D. trichomanoides as the sister to D. acuminata. Conclusions: This study highlights the stable plastome structure of D. trichomanoides and identifies candidate loci for barcoding. It also supports the stable placement of Davallia within the epiphytic Polypodiineae. Full article