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PubMed2026

Evaluating three alternative scenarios for the origin of a disjunct Arctium tomentosum population in the Pyrenees.

BACKGROUND: Disjunctions in species distributions offer natural experiments for investigating the mechanisms underlying distributional breaks, such as range contraction, long-distance pollen transport, or long-distance seed dispersal. Here, we document and characterise a floristic novelty in the Pyrenean and Iberian regions, and use it as a case study to investigate the processes underlying disjunct species distributions. Our analysis focuses on Arctium L. (burdocks), a genus native to Eurasia comprising several cosmopolitan weedy species. It is characterised by hooked capitula that facilitate epizoochorous dispersal. METHODS: To clarify the taxonomic identity of a previously undocumented Pyrenean population resembling A. tomentosum, we adopted an integrative approach, combining distribution information, morphology, genome size, repetitive DNA analysis and chloroplast data across the four known European species. Additionally, we conducted a comparative study of functional capitulum traits, predispersal fruit predation, and associated entomofauna for the newly discovered population and nearby A. minus populations. RESULTS: The discovered population constitutes a floristic novelty for the region and is identified as A. tomentosum, exhibiting signatures of past introgression from A. minus, as indicated by cytonuclear discordance. We evaluated three alternative scenarios to explain its origin: (i) persistence as a relict from a previously wider distribution, (ii) long-distance pollination by migrating insects, and (iii) long-distance seed dispersal from an A. tomentosum population with a history of past introgression. Of these, only the third is consistent with the available evidence. These results highlight the complexity of interpreting disjunct species distributions and underscore the value of integrative approaches for resolving population identity, origin, dispersal, and persistence across environments.

Arctium↗

PubMed2026

Mitogenome assembly and phylogenetic relationships of Phalaris arundinacea.

INTRODUCTION: As a perennial herb of Poaceae, Phalaris arundinacea plays key roles in grazing, production, and soil and water conservation because of its well-developed rhizomes and seed dispersal. We assembled and annotated the first mitogenome of P. arundinacea to support evolutionary and taxonomic research. METHODS: We assembled and annotated the first complete mitochondrial genome of P. arundinacea by integrating Illumina short reads with Nanopore long reads via a hybrid assembly strategy. The genome architecture was comprehensively characterized, encompassing codon usage bias, repetitive sequence organization, and inter-organellar genetic exchange with the chloroplast genome. RESULTS AND DISCUSSION: Assembly of the P. arundinacea mitogenome revealed two circular structures with a combined length of 526,717 bp. The genome comprised a set of 37 protein-coding genes (PCGs), 27 tRNAs, and 8 rRNAs, with the rRNA genes exhibiting full assembly (100% coverage). The mitochondrial genome contained 154 forward and 164 palindromic repeats, along with 25 tandem repeats and 124 simple sequence repeats (SSRs). Notably, 102 SSRs were distributed on contig1, predominantly in tetrameric form. Furthermore, 376 RNA editing sites were predicted. A total of 104 fragments were integrated into the mitochondrial genome from the chloroplast, amounting to 55,866 bp of transferred sequence. Finally, phylogenetic analysis of 28 plant mitogenomes placed P. arundinacea closest to species within the genus Poa (P. chaixii and P. pratensis). Comparative analysis of non-synonymous-to-synonymous substitution rate (Ka/Ks) ratios across divergent species revealed that the mitochondrial genome of P. arundinacea underwent stabilizing evolutionary dynamics, characterized by predominant purifying selection with several lineage-specific variations in selective pressure. Our findings support the close phylogenetic relationship between P. arundinacea and species of the genus Poa and provide a reference mitochondrial genome resource for future comparative studies within Phalaris that incorporate broader taxon sampling. These results support deeper phylogenetic investigations of P. arundinacea and facilitate future work on its germplasm characterization and applied use.

Phalaris arundinacea↗

PubMed2026

The complete chloroplast genome sequence and phylogenetic position of Mallotus apelta.

Mallotus apelta is a perennial species of Euphorbiaceae widely distributed in subtropical East and Southeast Asia. In this study, we sequenced and analyzed its complete chloroplast genome. The genome was 164,055 bp in length and exhibited a typical quadripartite structure, comprising an LSC region of 88,899 bp, an SSC region of 18,494 bp, and two IR regions of 28,331 bp each. A total of 124 genes were annotated. Comparative analyses revealed conserved genome organization and IR boundaries among Mallotus species. Phylogenetic analysis showed that M. apelta was closely related to M. paniculatus, providing valuable resources for Mallotus phylogenetic studies.

Euphorbiaceae↗

PubMed2026

Assembly and characterization of the first complete mitochondrial genome of Epimedium sagittatum (Sieb. et Zucc.) Maxim (Berberidaceae):an invaluable traditional Chinese medicine.

BACKGROUND: Epimedium sagittatum (Sieb. et Zucc.) Maxim is an invaluable traditional Chinese medicine plant known for its properties of tonifying kidney yang, strengthening bones and muscles, and dispelling rheumatism. The chloroplast (cp) genome of E. sagittatum have been sequenced, offering critical insights for breeding and phylogenetic research. However, the mitochondrial (mt) genome of E. sagittatum remains uncharacterized, limiting comprehensive insights into its genomic evolution. RESULTS: In this study, we assembled the first complete mt genome of E. sagittatum employing Illumina and Nanopore sequencing technology and subsequently investigated comparative analysis with its closely related species. The mt genome of E. sagittatum was assembled as a multi-branched structure with a length of 339,191 bp, within a GC content of 46.91%. Our annotation results have shown 39 protein-coding genes (PCGs), 22 tRNA genes, three rRNA genes and four pseudogenes in the E. sagittatum mt genome. The analysis of sequence repeats has detected 79 simple sequence repeats (SSRs), 10 tandem repeats and 255 dispersed repeats in the E. sagittatum mt genome. A total of 720 C to U RNA editing sites of the 34 PCGs was predicted in E. sagittatum. The codons exhibited a strong preference for A or U bases in the E. sagittatum mt genome. The analysis of nucleotide diversity (Pi) highlighted differences in genetic variability across the tested genes, with atp9 gene exhibiting the highest genetic variation. Selection pressure analysis showed that most genes were affected by negative selection during evolution, whereas ccmB, rps10, and rps12 underwent positive selection in different plants. Additionally, a Bayesian phylogenetic tree showed that E. sagittatum was closely related to E. wushanense and E. pubescens. In total of 14 homologous fragments totaling 8,954 bp were identified between the cp and mt genomes of E. sagittatum. CONCLUSIONS: This study presents the first assembled and annotated mt genome of E. sagittatum, which provides a valuable genetic resource for the Epimedium genus and lays the foundation for investigating the phylogenetic relationship and genetic variation of this invaluable medicinal plant.

Epimedium↗

PubMed2026

Characterization and comparative analysis of the complete mitochondrial genome sequence of Aucklandia lappa Decne.

BACKGROUND: Aucklandia lappa Decne, a precious medicinal herb in China, utilises the dried rhizome as its medicinal part, which riches in volatile oils, sesquiterpene compounds and other active constituents. Although the mitogenome of A. lappa has been assembled, related research remains in its preliminary stages, far from achieving comprehensive and in-depth understanding. RESULTS: In this paper, the complete mitogenome of A. lappa was assembled by employing a hybrid strategy that combined Illumina short-read and Nanopore long-read sequencing. The assembled mitogenome is 436,648 bp in size with a GC content of 45.06%. The mitogenome has only one chromosomal structure, It contains 54 genes, including 31 protein-coding genes(PCG), 19 tRNA genes, and 4 rRNA genes. A total of 32 high-frequency codons exhibiting significant AT-bias, 431 RNA editing sites, and 26 homologous fragments were transferred from the chloroplast to mitochondria genes (7,337 bp, 1.68%). Furthermore, we conducted a phylogenetic analysis involving in A. lappa and 27 other taxa to clarify its evolutionary and taxonomic status. These findings provide a foundation for further understanding the evolutionary relationships within Asteraceae plant. CONCLUSION: Through the assembly and comprehensive analysis of A. lappa mitogenome, This study has for the first time fully elucidated its mitogenomic structural characteristics.These results not only provide high-quality genetic resources for research on the Asteraceae mitogenome but also lay a solid foundation for in-depth exploration of the evolution and functional genomics of medicinal plants in the Asteraceae family.

Genome, Mitochondrial↗

PubMed2025

The Complete Chloroplast Genome and the Phylogenetic Analysis of Panicum bisulcatum (Thumb.) (Poaceae).

The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical quadripartite structure comprising a large single-copy (LSC, 82,260 bp), a small single-copy (SSC, 12,569 bp), and a pair of inverted repeats (IR, 21,830 bp each) regions. It encodes 135 genes, including 89 protein-coding genes, 49 tRNAs, and 8 rRNAs. Functional annotation revealed that most genes are involved in photosynthesis and genetic system. A total of 51 simple sequence repeats (SSRs) and 62 long repeats (LRs) were identified, providing potential molecular markers. Comparative analysis of IR boundaries highlighted both conserved features and species-specific expansion/contraction events among Panicum species. Phylogenomic analysis robustly placed P. bisulcatum within the genus Panicum, showing a closest relationship with P. incomtum and confirming the monophyly of the genus. Furthermore, single nucleotide polymorphism (SNP) analysis with its closest relative, P. incomtum, revealed 4659 SNPs, with a dominance of synonymous substitutions, indicating the action of purifying selection. This study provides the first comprehensive cp genomic resource for P. bisulcatum, which will facilitate future studies in species identification, phylogenetic reconstruction, population genetics, and the development of sustainable management strategies for this weed.

Phylogeny↗

PubMed2026

Impact of the Simultaneous Loss of the Plastid Envelope-Localized Homologous Pair Ycf10 and DLDG1 in Plant Growth and Photosynthetic Performance.

Ycf10 and DLDG1 are homologous proteins embedded in the chloroplast envelope membranes (EM) and encoded in the plastidial and nuclear genomes, respectively. We previously characterized Arabidopsis dldg1 and tobacco ycf10 mutants, and showed that these proteins mediate proton transport across the EM, thereby influencing ATP synthesis and the non-photochemical quenching (NPQ) induction. However, the consequences of the simultaneous loss of Ycf10/DLDG1 homologs have remained unclear. Here, we generated and analyzed Arabidopsis ycf10 and ycf10-dldg1 double mutants. These mutants exhibited a pale-green phenotype under continuous light conditions, which was complemented by the exogenous addition of NaCl, as previously observed in mutants lacking the plastid EM-localized K+/H+ antiporters KEA1 and KEA2. Both single mutants (ycf10 and dldg1), as well as the ycf10-dldg1 double mutant, showed enhanced NPQ induction compared with wild-type. Furthermore, the ycf10-dldg1 double mutant showed stronger NPQ induction than either single mutant upon transition from dark to light, suggesting that Ycf10 and DLDG1 function independently while playing redundant roles. These mutants also showed reduced stomatal conductance and sugar accumulation compared with the wild-type. Together, these findings indicate that EM-localized DLDG1 and Ycf10 act in concert to maintain chloroplast proton/ion homeostasis, contributing to chloroplast pH homeostasis for sustaining plant growth and efficient photosynthesis.

Photosynthesis↗

PubMed2026

The transgenic Vip3A poplar plant confers high resistance against Hyphantria cunea Drury.

Poplar is severely damaged by Hyphantria cunea (fall webworm), which significantly reduces tree productivity. However, conventional pest management methods are largely ineffective against fall webworm infestation. In this study, we demonstrated that the Vip3A protein possesses high insecticidal activity against H. cunea by overexpressing a synthetic THI1-Vip3A gene in poplar plants. A dicot codon-optimized Vip3A gene, fused with the THI1 chloroplast signal peptide sequence, was chemically synthesized and introduced into the poplar cv. '741' genome via Agrobacterium-mediated transformation. PCR, RT-PCR, and ELISA analyses confirmed the integration and successful expression of the transgene at both the mRNA and protein levels. The Vip3A protein concentration in chloroplasts was approximately 4.8-fold higher than in the whole leaf extract, indicating that the Vip3A protein was successfully targeted to and accumulated within the chloroplasts by the THI1 signal peptide. Subsequently, four transgenic lines with high Vip3A expression were subjected to H. cunea infestation. Compared to wild-type plants, these four transgenic lines exhibited significantly higher resistance, resulting in pest mortality rates exceeding 95% and significantly reduced leaf damage. Together, these results indicate that Vip3A possesses high insecticidal activity against H. cunea. Therefore, transgenic THI1-Vip3A poplar plants can serve as valuable germplasm for breeding poplar cultivars with high resistance to H. cunea infestation.

Plants, Genetically Modified↗

PubMed1977

Cellular content of chloroplast DNA and chloroplast ribosomal RNA genes in Euglena gracilis during chloroplast development.

The cellular content of chloroplast DNA in Euglena gracilis has been quantitatively determined. DNA was extracted from Euglena cells at various stages of chloroplast development and renatured in the presence of trace amounts of 3H-labeled chloroplast DNA. From the kinetics of renaturation of the 3H-labeled chloroplast DNA, compared with the kinetics of renaturation of excess nonradioactive chloroplast DNA, the fraction of cellular DNA represented by chloroplast DNA was calculated. The content of chloroplast DNA was found to increase from 4.9 to 14.6% of cellular DNA during light-induced chloroplast development. Correcting for the change in DNA mass per cell, the number of copies of chloroplast DNA is found to vary from 1400 to 2900 per cell. During this developmental transition, the cellular content of the chloroplast ribosomal RNA genes varies from 1900 to 5200 copies per cell. The ratio of the number of copies of rRNA genes to chloroplast genomes per cell remains in the range of 1-2 throughout chloroplast development, ruling out selective amplification of chloroplast rRNA genes as a means of regulation of rRNA gene expression. Direct measurement of the number of rRNA cistrons per 9.2 X 10(7) dalton genome yields a value of 1 or 2.

Animals↗

PubMed2025

Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms: implications for pathogenesis in avocado sunblotch disease.

Avocado sunblotch viroid (ASBVd) is a structured RNA molecule responsible for sunblotch disease of avocado, characterised by distinct chloroses of fruit, leaves, and stems. Despite its impact on avocado, the mechanism by which ASBVd elicits sunblotch symptoms remains unknown. Previous studies on other avsunviroids have shown that viroid-derived small RNAs (vd-sRNAs) with specific sequence mutations can trigger leaf chlorosis via RNA silencing of host genes. Building on this knowledge, we aimed to shed light on the molecular basis of ASBVd pathogenesis by analysing ASBVd sequence variants and ASBVd-sRNAs from bleached and asymptomatic leaf tissues of sunblotch-affected avocado trees. Sequencing of ASBVd clones revealed that variants carrying the pathogenic determinant for bleaching were present in both green and yellow leaf tissues. Next-generation sequencing (NGS) identified ASBVd-sRNAs that varied in abundance between symptomatic and asymptomatic leaf tissues, correlating with viroid titre. We discovered 64 vd-sRNAs spanning the pathogenic region of the ASBVd genome, which were almost exclusively found in yellow tissues. The ASBVd-sRNAs containing the bleaching-associated mutation were predicted to target numerous avocado transcripts for degradation, with 25 of these transcripts significantly downregulated in bleached tissues. Notably, one of these genes, encoding a chloroplastic protein, demonstrated strong evidence of ASBVd-sRNA-guided RNA silencing, presenting a promising candidate for future research into the molecular trigger for ASBVd-induced bleaching symptoms. This study is the first to investigate ASBVd-sRNAs in bleached leaves using NGS. Our findings support the role of RNA silencing in sunblotch symptom development and reveal a unique silencing trigger compared to other avsunviroids.

Persea↗

PubMed2025

Bundle sheath cell-specific expression of chloroplast genes encoding subunits of the NADH dehydrogenase-like complex in maize.

C4 photosynthesis alleviates the limitation caused by the oxygenase activity of Rubisco by partitioning photosynthetic functions between two distinct cell types: bundle sheath cells (BSCs) and mesophyll cells (MCs). These cell types perform different steps of photosynthesis using specialized machinery, accompanied by differential expression of chloroplast genes. To uncover the underlying molecular mechanisms for this differentiation, we isolated BSCs and MCs and compared their chloroplast transcriptomes, focusing on the chloroplast NADH dehydrogenase-like (NDH) complex, which is enriched in BSCs. To investigate whether RNA stabilization contributes to differential gene expression, we analyzed RNA footprints that reflect the binding of pentatricopeptide repeat (PPR) proteins to their RNA targets. We could not detect cell-type-specific accumulation of footprint RNAs. We then focused on transcriptional regulation, specifically on an operon that starts with the rps15 gene. The operon includes six ndh genes and the psaC gene encoding a photosystem I subunit. Transcript levels of all genes in this operon were higher in BSCs than in MCs, suggesting coordinated regulation as a transcriptional unit. Based on the genomic location of the rps15 gene within inverted repeats near the junctions on both sides of the small single copy region, we demonstrated that rps15, through two distinct promoters, is sufficient to drive preferential accumulation of downstream transcripts in BSCs.

Zea mays↗

PubMed2026

Genome-wide identification of the carotenoid cleavage dioxygenase gene family in wheat and analysis of the TaDREB-7A-TaNCED9a regulatory module conferring drought tolerance.

Carotenoid cleavage dioxygenases (CCDs) play critical roles in plant growth, development, and abiotic stress responses, yet their genome-wide identification and drought response mechanisms remain unexplored in wheat. In this study, 34 TaCCD genes were identified in wheat, distributed across 15 chromosomes and phylogenetically classified into five subfamilies. Gene structure analysis indicated that members within each subfamily shared conserved motifs and similar intron-exon arrangements. Cis-regulatory element analysis suggested the potential roles of these genes in stress adaptation, developmental processes, and hormone signaling. Moreover, prediction of tertiary structures and protein-protein interactions revealed unique structural features and potential interacting partners of the TaCCD proteins. In addition, TaNCED9a, a member of the TaCCD family, showed the highest transcript level in wheat roots among all detected TaCCD genes and was significantly induced by drought stress. Subcellular localization assay indicated that TaNCED9a was located in chloroplasts. Downregulation of TaNCED9a expression led to reduced drought resistance in wheat, accompanied by an accumulation of reactive oxygen species and a decrease in endogenous abscisic acid levels. Using yeast one-hybrid, dual-luciferase, and tobacco transient co-expression assays, the upstream regulatory factor TaDREB-7A was identified, which can regulate the expression of TaNCED9a. Additionally, a KASP molecular marker was developed to identify the superior haplotype TaNCED9a-HapI, which exhibited a significantly higher germination rate compared to TaNCED9a-HapII under drought conditions, and was predominant in wheat. These results offer valuable insights into the TaCCD gene family's response mechanisms to drought stress in wheat, simultaneously identifying promising genetic resources for enhancing drought tolerance through molecular breeding.

CCD↗

PubMed2026

Molecular investigation of the progenitors, origin and domestication patterns of diploid Chinese old garden roses.

BACKGROUND AND AIMS: Chinese old garden roses are major contributors to the genetic development of modern roses. The RoKSN gene is associated with continuous flowering in roses and is proposed to have originated from Chinese wild roses. However, the wild roses that are implicated in the breeding of Chinese old garden roses and the origin of the RoKSN locus remain unidentified. We collected 25 of the most renowned and classic diploid Chinese old garden roses along with all related wild roses from East Asia. These roses were analysed with the aim of identifying the wild species that contributed to the genetic composition of Chinese old garden roses. In addition, we aimed to infer the geographical origin of the RoKSN gene and to develop a schematic overview of hybrid domestication of Chinese old garden roses. METHODS: We compared the haplotypes of internal transcribed spacers (nrITS), six nuclear single-copy genes and three chloroplast genes between Chinese old garden roses and wild roses. Additionally, we assessed genetic organization using 21 expressed sequence tag-simple sequence repeats to identify potential donor species that contributed to the emergence of these cultivars. Primers were designed for RoKSN to allow comparison of the gene across the entire distribution range of Rosa sect. Chinenses. KEY RESULTS: Our findings confirmed that the majority of rose cultivars are descendants of early hybridization events. Rosa chinensis var. spontanea, R. odorata var. gigantea and R. multiflora var. cathayensis were the primary donors for the 25 cultivar roses. Chinese old garden roses were categorized into four groups. Ten cultivars were hybrids between R. chinensis var. spontanea and R. multiflora var. cathayensis, thereby forming the 'Old Blush' group. Five cultivars were hybrids between 'Old Blush' and the R. kwangtungensis species complex, thereby forming the 'Slater's crimson' group. Six cultivars were hybrids between 'Old Blush' and R. odorata var. gigantea, thereby forming the 'Tea Rose' group, and three cultivars were hybrids that evolved from more than three donors. Moreover, we observed relatively close genetic proximity among Chinese old garden roses with an identical RoKSN-copia gene that is responsible for continuous flowering, which indicates a single origin for this retrotransposon-containing allele. Additionally, we determined that the haplotypes of the RoKSN-copia gene predominantly occurred in the Sichuan Basin region. In contrast, R. chinensis cultivated in the Ya'an region showed no markers of hybridization and displayed a genetic composition that was close to that of the wild species R. chinensis var. spontanea. This cultivar may represent the earliest mutated individual that bears the RoKSN-copia gene and may have served as a bridge from wild species to continuous-flowering old rose cultivars. CONCLUSIONS: The study provides crucial evidence that elucidates the origin of cultivated roses and lays the groundwork for further analysis of the breeding history of Chinese old garden roses using genomic data.

Domestication↗