Search Results (164)

In this study, we sequenced, assembled, and characterized the first complete chloroplast (cp) genome of Eutrema scapiflorum, an alpine species endemic to the Qinghai–Tibet Plateau (QTP). The assembled plastome is 153,041 bp in length and exhibits a typical quadripartite structure, comprising a large single-copy (LSC) region of 83,547 bp and a small single-copy (SSC) region of 17,506 bp, which are separated by two inverted repeats (IRs) of 25,994 bp each. Structurally, the genome encodes 132 unique genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis across eight species revealed that genome size variation is primarily driven by the SSC region. Notably, the IR/SC boundaries in E. scapiflorum are highly conserved, which contrasts with the significant IR expansion observed in Capsella tenella. Furthermore, simple sequence repeat (SSR) analysis identified 78 loci, predominantly mononucleotide A/T repeats located in intergenic spacers. Nucleotide diversity analysis pinpointed accD and ycf1 as the most variable genes. Selection pressure analysis indicated that most genes are under purifying selection, while seven protein-coding genes (ycf2, nadhE, cemA, clpP, psbH, ycf4, nadhB) exhibited signatures of positive selection (Ka/Ks > 1). Subsequently, phylogenomic analyses robustly resolved E. scapiflorum within the tribe Arabideae, showing its closest relationship to Alliaria petiolata. Divergence time estimation dated the split between E. scapiflorum and its closest relative to the middle Miocene (~17.57 Ma). Collectively, these findings provide crucial genomic resources and new insights into the structural evolution, phylogenetic placement, and potential adaptive mechanisms of this alpine species within the Brassicaceae family. Full article

Background: The phylogenetic placement and chloroplast-inferred maternal relationships of commercial pluot cultivars remain unclear, largely because plastome-level evidence is limited for assessing their affinities with Prunus salicina and Prunus ussuriensis. Although chloroplast genome structure has been well characterized in angiosperms and in several Prunus species, complete plastome resources and comparative genomic evidence for commercial pluot cultivars remain scarce. Methods: Here, we assembled the complete chloroplast genomes of six commercial pluot cultivars and performed comparative genomic, phylogenomic, and divergence time analyses using representative Prunus species. Results: All genomes exhibited the typical circular quadripartite structure and ranged from 157,865 to 158,138 bp in length. Genome organization, GC content, and gene content were highly conserved, whereas the IR regions showed an elevated GC content of approximately 42.6%, owing to rRNA gene enrichment. IR boundary comparison revealed contraction at the IRb/SSC boundary in P. ussuriensis, while pluot cultivars were structurally more similar to P. salicina. In total, 370 SSR loci and four hypervariable regions, namely rpoB–trnC-GCA, petN–psbM, trnV-UAC–trnM-CAU, and trnP-UGG–psaJ, were identified as candidate molecular markers for Prunus germplasm identification and genetic analysis. Phylogenomic analysis resolved four major clades within Prunus and showed that ‘Flavor King’, ‘Flavor Supreme’, and ‘Flavor Queen’ grouped with P. ussuriensis, whereas ‘Flavorosa’, ‘Dinosaur Egg’, and ‘Flavorich’ grouped with P. salicina. Conclusion: Overall, this study provides the first comparative plastome analysis of six commercial pluot cultivars and offers chloroplast-level evidence for their maternal affinities within Prunus, together with useful marker resources for cultivar identification and germplasm evaluation. Full article

Beyond its function as a carrier of hereditary information, recent research has uncovered novel properties of extracellular DNA, including its role in the adaptation to the environment when released from plants. The secreted DNA has been shown to exert insecticidal effects against insect pests, which play an adaptive role in plant-insect interactions, particularly in regulating populations of economically important sap-feeding insects. The molecular mechanisms underlying this insecticidal effect are underinvestigated and remain largely unknown. Therefore, there is a need for more efforts to uncover these mechanisms to better understand plant–pest interactions, which would provide new insights into natural pest control strategies and inspire biotechnological applications. In the current study, we show that Pittosporum tobira (P. tobira) secretes single-stranded DNA (ssDNA) that exerts an insecticidal effect on Coccus hesperidum (C. hesperidum). We collected extracellular DNA from P. tobira leaves and tested its potential insecticidal effect by applying it to C. hesperidum, which is a well-known pest that causes damage to P. tobira. Our results revealed that the outermost layer of the leaf cuticle of P. tobira predominantly contains ssDNA of approximately 100 nt in length, originating from both chloroplast and nuclear genomes. This DNA exhibited pronounced insecticidal activity against C. hesperidum, with chloroplast-derived sequences significantly enriched compared to the total DNA in intact plant cells. These findings suggest that the microevolution of the P. tobira nucleome and plastome contributed to the formation of extracellular DNA with insecticidal properties (eci-DNA), which is part of its defense strategy against insect pests. Moreover, in this article, for the first time, we show that antisense DNA (illustrated with oligonucleotide insecticide Coccus-11) is capable of activating insect retrotransposons and upregulating their RT-RNase H, a crucial enzyme for the DNA containment mechanism and successful action of oligonucleotide insecticides. Notably, the laboratory-developed ssDNA-based ‘genetic zipper’ technology, designed for sustainable pest management, possesses characteristics similar to eci-DNA found in nature, highlighting a potential natural parallel to this biotechnological approach for sustainable pest management. Full article

Background/Objectives: Grimmia tergestina is a lithophytic moss of Grimmiaceae, but its complete plastome has not previously been reported. This Brief Report presents the complete chloroplast genome of G. tergestina as a genomic resource for future work on species identification, phylogeny, and plastome evolution in Grimmiaceae. Methods: Illumina NovaSeq PE150 reads were quality filtered and assembled into a circular plastome. Genome annotation was verified using current organellar annotation tools and manual curation, and a preliminary phylogenetic analysis was performed using shared chloroplast protein-coding genes from representative moss plastomes. Results: The complete plastome of G. tergestina was 124,153 bp in length and exhibited the typical quadripartite structure of moss plastomes. It encoded 126 genes, including 82 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, with an overall GC content of 28.49%. Fourteen genes contained introns, and nine genes were duplicated in the inverted repeat regions. Codon-usage analyses showed a preference for A/U-ending codons, consistent with the AT-rich composition of the plastome, and supplementary ENC and PR2 analyses supported a conservative interpretation of codon-usage bias. A total of 569 chloroplast simple sequence repeats and 222 dispersed repeats were identified. The preliminary maximum-likelihood phylogeny placed G. tergestina within Grimmiaceae and resolved it close to Niphotrichum japonicum in the sampled plastome dataset. Conclusions: The newly characterized plastome of G. tergestina enriches genomic resources for Grimmia and provides a foundation for future comparative and phylogenetic studies of Grimmiaceae. Full article

The genus Desmidorchis Ehrenb. (Apocynaceae) is a characteristic component of the succulent flora of the Arabian Peninsula, where high levels of endemism and increasing environmental pressures highlight the need for integrated genomic and conservation research. This study assessed the conservation status of three ethnomedicinally important endemics—D. adenensis, D. arabica, and D. awdeliana—and characterizes their complete plastomes to resolve their evolutionary and temporal history. Conservation assessments were conducted following IUCN Red List criteria, and complete plastomes were sequenced and compared within a dataset of 15 subtribe Stapeliinae taxa. Comparative analyses examined the genome structure, divergence hotspots, repetitive sequences, codon usage bias, and selection pressure, while divergence times were estimated using fossil-calibrated molecular clock analyses. All three species were classified as Near Threatened (NT), primarily due to anthropogenic and environmental pressures. Plastome analyses revealed a highly conserved genome structure; however, hypervariable regions, particularly ycf1 and clpP1, exhibited elevated sequence divergence and phylogenetic informativeness. Simple sequence repeats (SSRs) were also identified as potentially informative features at the genus level. Codon usage and Ka/Ks analyses further indicated that most plastid protein-coding genes are under strong purifying selection, whereas only a few loci, particularly clpP1, showed comparatively elevated evolutionary rates. Phylogenomic analyses supported the monophyly of Desmidorchis, with molecular dating indicating recent Pleistocene diversification (~0.34–1.51 Ma), potentially associated with Quaternary climatic oscillations. Overall, this study provides an important genomic foundation for future taxonomic, evolutionary, and conservation studies of rare Arabian taxa. Full article

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

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

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