Search Results (2,532)

Background: Cultivar identification and the reconstruction of breeding relationships require markers that reflect both parents, yet plastome sequencing is often applied to these problems on its own. Methods: We tested how far chloroplast data alone can go in Rubus crataegifolius Bunge, using one plant of each of eight cultivars from Korean breeding programs. Complete chloroplast genomes (155,664–155,770 bp) were assembled for all eight and compared with nuclear resequencing data from the same plants. Results: The 526 plastome variants were concentrated in non-coding regions, and Ka/Ks ratios well below one indicated strong purifying selection on plastid genes. The eight cultivars carried only five distinct plastome haplotypes: three shared one identical sequence and two another. Mapping to a Rubus idaeus reference recovered 4,872,213 cultivar-polymorphic nuclear SNPs, which separated every cultivar pair, including all four with identical plastomes, and the result was unchanged after stringent filtering of heterozygous calls. Cultivars sharing an identical plastome spanned 27% of the entire range of nuclear distances, and the two measures were only weakly correlated. Conclusions: Plastome sequencing therefore describes maternal lineage rather than cultivar identity among these cultivars; genome-wide nuclear SNPs discriminate them, and the five-SNP panel derived from them is a candidate tool that requires validation on independent plants. Full article

Background: Penstemon, a core genus of the tribe Cheloneae in Plantaginaceae, possesses significant ecological and horticultural value. However, its interspecific phylogenetic relationships remain unclear due to morphological convergence, hybridization events, and limited genomic resources. This study aimed to characterize the complete chloroplast (cp) genome of Penstemon digitalis and explore its genomic features and phylogenetic position within Plantaginaceae. Methods: We sequenced the cp genome of P. digitalis using high-throughput sequencing, assembled and annotated the genome, and compared it with other Plantaginaceae species. Repetitive sequences and hypervariable regions were identified. Phylogenetic analyses were performed using maximum likelihood (ML) based on complete cp genomes from 46 taxa (36 Plantaginaceae, six Scrophulariaceae, and four outgroup species). Results: The cp genome is 152,993 bp with a typical quadripartite structure, containing 132 functional genes (87 protein-coding, 37 tRNA, and eight rRNA). Comparative analyses showed high gene content and structural conservation within the tribe Cheloneae. Several hypervariable regions and repeats were detected as potential markers. ML analysis strongly supported the monophyly of Penstemon among the sampled species (100% bootstrap) and placed P. digitalis in a well-supported clade within the genus; Penstemon was recovered as the sister group of Russelia equisetiformis. Conclusions: This study provides the first complete cp genome resource for P. digitalis, confirming its phylogenetic affinity and offering valuable genomic data for future studies on population genetics, species delimitation, and adaptive evolution in Penstemon. These findings will aid taxonomic revision and conservation efforts for this diverse genus. Full article

Tylosema esculentum (Burch.) A. Schreib. (also known as marama) is a perennial legume native to the arid and semi-arid regions of southern Africa, where it thrives under extreme climatic conditions, particularly in hot and water-limited environments and nutrient-poor soils. This review outlines current knowledge on marama’s nutritional and medicinal potential, as well as genomic insights and drought adaptation mechanisms, to ensure sustainable food systems. Marama has added advantages since the entire crop, including grains/beans, stems and tubers, can be used as a source of food for animals and humans. However, the nutritional value and safe consumption of different tissues are dependent on developmental stages and appropriate processing to reduce anti-nutritional compounds and improve digestibility. Marama beans possess exceptional nutritional value, being rich in protein; unsaturated lipids; essential micronutrients; and health-promoting phytochemicals including phenolics, flavonoids, saponins and phytosterols. To date, the chloroplast and mitochondrial genomes of Tylosema esculentum (marama) have been sequenced and assembled, while its nuclear genome size has been estimated at approximately 1 gigabyte, providing valuable genomic resources for further research. Marama exhibits a predominantly drought-avoidance strategy characterized by the development of deep tubers for water and nutrient storage, reduction in transpiration through leaf senescence and stomatal regulation, and maintenance of plant water status during prolonged dry periods. Marama also exhibits osmotic adjustment, which further enhances cellular protection and stress tolerance under water-deficit conditions. Despite these promising attributes, marama remains largely underutilized due to limited agronomic data to support its cultivation and insufficient data on its metabolic and genetic architecture that drives drought adaptation and socio-economic potential. Thus, there is an urgent need for integrated research efforts that will facilitate the transition of this crop from a wild-harvested resource to a sustainable, climate-resilient crop suited to arid and semi-arid agroecosystems. Full article

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely impairs photosynthesis and chloroplast function in citrus. However, Persian lime (Citrus latifolia) exhibits remarkable tolerance, maintaining productivity despite infection. Pentatricopeptide repeat (PPR) proteins regulate organellar RNA metabolism and are essential for chloroplast function. Here, we investigated whether plastid-targeted PPR regulatory networks are transcriptionally altered during CLas infection. We combined transcriptome-wide identification of PPR proteins, prediction of chloroplast RNA targets, gene expression analyses, and chlorophyll a fluorescence measurements. A total of 515 PPR proteins were identified, with 30.5% predicted to localize to plastids. Predicted RNA targets included chloroplast genes involved in transcription and photosynthesis, such as ycf2, rpoC1, psbB, and psbC. Despite this extensive predicted regulatory network, neither plastid-targeted PPR genes nor their chloroplast targets showed differential expression between HLB-positive and HLB-negative leaves. In contrast, infected leaves exhibited reduced Fv/Fm, PIabs, and electron transport efficiency, although the characteristic OJIP transient remained largely preserved, indicating maintenance of PSII structural organization. These findings suggest that constitutive plastid PPR regulatory mechanisms remain stable during CLas infection and may contribute to the chloroplast resilience underlying HLB tolerance in Persian lime. Full article

The Thai-Malay Peninsula is an important marine biodiversity hotspot at the boundary between the Indian and Pacific Oceans. Yet, phylogeographic understanding of macroalgae along the Andaman Sea coast of Thailand remains limited relative to other benthic species. Here, by sequencing mitochondrial cox1 and chloroplast rbcL sequences from 333 specimens of the red seaweed Halymenia durvillei across 20 sites, we found low genetic diversity (11 and 4 haplotypes, respectively) and a lack of pronounced population structure. A single dominant haplotype per marker was restricted to Phuket Island and Phang Nga. Analysis of variance (AMOVA) revealed no significant genetic differentiation between the Myanmar Shelf and the Malacca Strait Shelf, with most of the variation (90.28–98.63%) partitioned within populations. Gene-flow estimates revealed significantly asymmetric migration among populations, with most sites (i.e., Ranong, Phangnga, and Phuket) functioning as both sources and sinks of migrants, broadly consistent with the dispersal mediated by ocean currents during the northeast monsoon season. Bayesian Skyline Plot analysis revealed a sharp demographic contraction during the early middle Miocene, followed by a progressive expansion since the early Pleistocene. The presence of endemic haplotypes in the northern Malacca Strait suggests this area likely served as a marine refugium during glacial maximal low stands. In brief, phylogeographic homogeneity of H. durvillei along the Andaman Sea reflects the combined effects of glacial bottlenecks during glacial sea-level fluctuations and postglacial recolonization driven by ocean circulations. These results highlight populations with unique genetic diversity (e.g., Tankhen Bay, Phuket, and Lam Kaen Beach, Phangnga) as candidates for in situ protection and integration into protected area networks under climate warming. Full article

Background/Objectives: Heat-shock protein 70 is a key plant molecular chaperone whose family response to combined high temperature and humidity stress in melon remains uncharacterized. This study aimed to characterize the CmHSP70 family genome-wide and compare its expression dynamics between cultivars with contrasting responses to HTH stress. Methods: The CmHSP70 genes in melon were identified via bioinformatic analysis, with characterization covering phylogeny, gene structure, cis-elements, synteny, and selection pressure. Expression profiles under HTH stress were compared between the tolerant cultivar JD versus the sensitive cultivar JTL across 0 to 3 days using transcriptome with qRT-PCR validation, supplemented by three-dimensional (3D) structure prediction plus protein interaction network analysis. Results: The 16 CmHSP70 proteins were predicted to show diverse subcellular localizations, predominantly in the cytoplasm, endoplasmic reticulum (ER), and chloroplasts, and were grouped into five subfamilies with closest homology to cucurbit crops. Cis-acting element analysis showed that the promoters of CmHSP70 genes contain various stress-responsive and hormone-responsive elements, implying their broad roles in stress adaptation. Gene duplication analysis revealed only one segmental duplication event and no tandem duplications in the CmHSP70 family, indicating limited expansion during melon evolution. Ka/Ks ratios below 1 for all paralogous pairs further suggest strong purifying selection and highly conserved protein functions. Furthermore, expression profiling under high temperature and humidity (HTH) stress identified CmHSP70-4, -7, -8, and -13 as key candidates, showing sustained upregulation through day 3 in the tolerant cultivar but transient induction followed by decline in the sensitive cultivar. Predicted 3D structures and a STRING-based protein–protein interaction network further highlighted these four genes within the predicted chaperone interaction framework. Conclusions: This study provides candidate gene resources for future functional validation and breeding of HTH-tolerant melon and other cucurbit crops. The association between sustained CmHSP70 induction and the tolerant cultivar response offers a working hypothesis for molecular breeding under climate change. Full article

Climate change-driven high-temperature stress has become a major threat to global wheat production, and developing effective strategies to ensure heat-resilient, stable-yield cultivation is an urgent scientific priority. Mn₃O₄ nanozymes, a newly developed type of nanozyme, have not yet been tested for improving wheat heat tolerance. This study investigated the physiological mechanisms by which Mn₃O₄ nanozymes alleviate high-temperature stress during wheat grain filling. A polyethylene film greenhouse simulated a high-temperature environment, increasing the average canopy temperature of wheat by 2–3 °C. Under stress, plants were sprayed with distilled water (M0) or with Mn₃O₄ nanozymes at 100 (M1), 150 (M2), or 200 mg·L⁻¹ (M3), while an additional control (CK) was sprayed with distilled water under natural conditions. Compared with the CK, high-temperature stress significantly disrupted chloroplast structure, altered stomatal morphology, and reduced SPAD values, flag leaf area, and photosynthetic parameters in flag leaves, ultimately leading to a decrease in thousand-kernel weight (down 4.86%) and wheat yield (down 21.24%); in contrast, under high-temperature stress, Mn₃O₄ nanozyme treatment resulted in milder damage to chloroplast membrane structure; the thylakoid membrane system exhibited a slightly relaxed state overall, and stomatal aperture remained favorable. This treatment slowed the decline in photosynthetic capacity and significantly enhanced antioxidant enzyme activity, thereby mitigating the impact on yield. Among these, the M1 treatment yielded the best results, with thousand-kernel weight and yield increasing by an average of 2.62% and 18.26%, respectively, compared to M0; however, this mitigating effect diminished as the concentration rose. Compared with the M0 treatment, M2 and M3 treatments produced average yield increases of 9.04% and 5.34%, respectively. Therefore, Mn₃O₄ nanozymes at an appropriate concentration can mitigate the adverse effects of high-temperature stress on wheat at multiple levels, thereby effectively alleviating yield losses during the grain-filling stage. Full article

Environmental contamination with heavy metals severely impairs crop productivity, primarily by inhibiting growth and triggering oxidative damage. To counteract these adverse effects, plants undergo complex metabolic reprogramming. Among these adaptations, the accumulation of purine-derived ureides—particularly allantoin—has been proposed as a protective mechanism, though its role under copper (Cu) stress remains unexplored. Here, we demonstrate that wild-type (Arabidopsis thaliana, WT) plants accumulate allantoate—the product of allantoin hydrolysis catalyzed by allantoinase (ALN, EC 3.5.2.5)—rather than allantoin when exposed to Cu toxicity. However, blocking this downstream catabolic step via loss of ALN function results in allantoin accumulation and is associated with enhanced Cu tolerance. Under Cu stress, aln-1 and aln-4 loss-of-function mutants maintained higher biomass and accumulated lower levels of malondialdehyde, superoxide anions, and hydrogen peroxide compared to WT. Furthermore, aln lines exhibited a stronger Cu-induced activation of key antioxidant enzymes (SOD, CAT, POD, APX) alongside higher expression of genes encoding specific isoforms targeted to multiple cellular compartments: cytosolic (CSD1), chloroplastic (CSD2, tAPX), peroxisomal (APX3, CAT3), and apoplastic (Prx51, Prx47). These results reveal that the loss of ALN function promotes a multi-compartmental antioxidant response under Cu toxicity, highlighting the pivotal role of purine catabolism in plant redox homeostasis and pointing to ureide metabolism as a potential avenue for enhancing crop stress tolerance. Full article

Dendrobium officinale is an important medicinal Orchidaceae species with considerable ecological and economic value. While its chloroplast genome has been well characterized, the structure features of its mitochondrial genome remain largely unexplored, which further hinders our understanding of its evolutionary dynamics and adaptive mechanisms. This study presents a comprehensive characterization of the mitochondrial genome of D. officinale, revealing a complex multibranched structure of 22 chromosomes totaling 639,931 bp, encoding 35 PCGs, 3 rRNA genes, and 24 tRNA genes. Codon usage analysis revealed a distinct codon bias, while the genome harbors abundant repetitive elements and 522 RNA editing sites. Comparative genomic analysis identified 125 MTPT fragments totaling 108,012 bp (16.88% of the mitogenome), indicating frequent inter-organellar DNA transfer. Dendrobium nobile exhibited the highest genomic homology with D. officinale. Ka/Ks analysis indicated that most mitochondrial genes are under strong purifying selection. In addition, we conducted a comparative analysis between the newly assembled mitochondrial genome of D. officinale and seven Orchidaceae species. Phylogenetic analysis based on the maximum likelihood, maximum parsimony and bayesian inference approaches resolved the phylogenetic position of D. officinale within Orchidaceae. Collectively, these findings provide a valuable reference for future studies on Orchidaceae phylogenomics and mitochondrial evolution. Full article

A new species, Smilax sinovietnamensis P. Li & X.J. Jin, sp. nov. (Smilacaceae), from the Sino-Vietnamese Border, is described and illustrated. Using nuclear ribosomal DNA (nrDNA), chloroplast DNA (cpDNA), and orthologous nuclear genes (ONGs), we examined the phylogenetic position of this species within the family Smilacaceae. Furthermore, phylogenetic analyses of concatenated sequences of nrITS, five cpDNA (ndhA, ndhF, rpl16, matK, and rbcL), and two ONGs (At103 and Agt1) from 37 Smilacaceae species all strongly supported that S. sinovietnamensis is sister to S. cocculoides. Further comparative morphological analysis showed that S. sinovietnamensis can be clearly distinguished morphologically from its closely related species S. cocculoides. It has quadrangular stems and an abscission zone at one-third of the petioles’ length. Combining detailed morphological comparisons and molecular evidence, we confirm the novelty of S. sinovietnamensis. Additionally, we report the plastome characteristics of S. sinovietnamensis, enriching our understanding of the evolutionary relationships within Smilacaceae. Collectively, integrating diagnostic morphological traits with nrITS, cpDNA, ONGs, and the newly assembled plastome not only confirms S. sinovietnamensis as a new species but also offers practical tools for resolving taxonomic challenges in Smilacaceae. Additionally, the species’ unique quadrangular stem—an evolutionary morphology—provides significant reference value for understanding angiosperm evolution. Full article

Life on Earth originated in the Precambrian, around 4 billion years ago. This review focuses on microbes (viruses, bacteria, archaea) which developed in these prehistoric times and their roles during the later evolution of protists (eukaryotes). Among the different theories of life evolution, the author favors the theory of the RNA world as having been first. Over the past few decades, new molecular biological technologies and findings have changed the paradigm of mutation and selection as being the main driving force of biological evolution. Instead, microbes and microbe-derived genetic elements (e.g., plasmids, transposons) have been found to be capable of changing whole genomes and creating new species. Versatile RNA molecules have played important roles, such as regulating gene expression and affecting epigenetic changes, from primordial times up to the present. Microbes have been reported to show parasitic as well as mutualistic symbiotic relationships with their infected hosts. Examples of endosymbiogenesis are chloroplasts and mitochondria acting as new organelles, which facilitate photosynthesis and respiration within eukaryotic host cells. Considering the importance of these events, molecular mechanisms of photosynthesis and respiration are described in some detail in this review. Full article

Photosynthesis is the ultimate source of energy for crop productivity, and leaf morphology as well as chlorophyll content are traditional, indirectly related traits of photosynthesis. However, the genetic basis of these traits remains unexplored in sugarcane. In this study, we conducted genome-wide association studies (GWAS) to identify loci controlling nine photosynthesis-related traits, including four leaf morphological traits (leaf length, leaf width, leaf ratio, and leaf area) and five chlorophyll-related traits (chlorophyll a, chlorophyll b, chlorophyll a/b ratio, total chlorophyll, and SPAD value). The analysis was performed using whole-genome resequencing data from 219 elite, globally diverse sugarcane materials evaluated at two locations across two years (four environments). Based on 5,964,084 high-quality single nucleotide polymorphisms (SNPs), we identified 308 GWAS-significant SNPs (p ≤ 1.5 × 10⁻⁶) that were consistently detected in two or more environments, defining 97 GWAS-associated intervals across 30 chromosomes. Within these intervals, 98 putative genes were predicted, of which 20 genes in 16 intervals were potentially associated with leaf photosynthesis based on functional annotation and literature mining. These candidates are primarily involved in pathways related to ADP-ribosylation factors, ATP-dependent Clp protease proteolytic subunits, protein kinases, F-box proteins, MYB and WRKY transcription factors, UVR8, pentatricopeptide repeat-containing (PPR) proteins, Aux/IAA proteins, monogalactosyldiacylglycerol (MGDG) synthase, Orange (OR) proteins, PsbP domain-containing (PPD) proteins, and chloroplast stem-loop binding proteins of 41 kDa b (CSP41b). Ten genes were prioritized for future functional validation. Notably, these photosynthesis-related structural and pigment traits represent a different regulatory layer from direct gas exchange parameters (e.g., net photosynthetic rate), and their associations with actual photosynthetic efficiency require further validation. Nevertheless, this study provides novel candidate genes and molecular markers to assist marker-assisted breeding aimed at improving the photosynthetic structure and light-harvesting capacity of sugarcane. Full article

Plants coordinate their growth and developmental programs through dynamic communication in the core of the nucleus, enabling them to adapt to persistently high-temperature environments. Upon heat stress, plants primarily perceive and transduce thermal signals between the nucleus and other organelles, a process defined as nuclear-organellar communication. The published research on plants in response to heat environments mainly focuses on sensing heat physical signals from the plasma membrane (PM)/cytosol to the nucleus, eliciting nuclear transcriptional reprogramming and decoding organelle-derived retrograde signals to the nucleus. Consequently, plants have evolved sophisticated systems to decode adverse temperature signals relying on efficient nuclear-organellar coordination. This review summarizes how plants maintain cellular homeostasis via nuclear crosstalk. Heat signals are initially perceived, which triggers the production of secondary messengers including phosphatidic acid (PA), calcium ions (Ca²⁺) and reactive oxygen species (ROS). In addition, proteins also deliver thermal signals to the nucleus. As the central signaling hub, the nucleus orchestrates global transcriptional reprogramming predominantly through the Heat Shock Transcriptional Factors (HSFs)–heat shock proteins (HSPs) regulatory module, and sends instructions to the endoplasmic reticulum (ER), chloroplasts and mitochondria. Conversely, organelle-derived retrograde signals coordinate stress adaptation: the unfolded protein response relieves ER stress, and heat stress activates ROS-mediated chloroplast-to-nucleus and mitochondria-to-nucleus feedback pathways. We further outline candidate thermosensing proteins residing in different organelles, and highlight major unsolved issues. Critical knowledge gaps include the intrinsic thermosensing capacity of chloroplasts and mitochondria, inter-organellar coordination of second-messenger dynamics, specific organelle functions, and the biological roles of membrane contact sites. Further mechanistic insights will facilitate the application of genome editing, synthetic biology and artificial-intelligence-aided design to breed heat-tolerant crops without yield penalties. Full article

Populus × canescens (Aiton) Sm. is a natural hybrid between Populus alba L. and Populus tremula L., but its genetic diversity and population structure in Western Kazakhstan remain poorly characterized. Here, we investigated 12 individuals representing five geographically separated populations in the West Kazakhstan Region using chloroplast matK and rbcL sequences. The concatenated 1318 bp dataset was analyzed to assess genetic diversity, haplotype relationships, population differentiation, demographic history, and phylogenetic relationships. Seven haplotypes were identified, with relatively high haplotype diversity but low nucleotide diversity. The predominant haplotype was shared among four populations, whereas several population-specific haplotypes were detected. Pairwise nucleotide divergence ranged from 0.000635 to 0.002096, with the highest value observed between Pop4 and Pop5. Significant negative Tajima’s D and Fu and Li’s statistics were detected; however, the predominantly unimodal mismatch distribution was interpreted cautiously because the low nucleotide diversity and limited sample size reduced its sensitivity for demographic inference. Therefore, the observed pattern should not be considered conclusive evidence of demographic expansion. Bayesian phylogenetic analysis revealed heterogeneous placement of P. × canescens individuals relative to P. alba and P. tremula. These findings provide the first molecular baseline for P. × canescens in Western Kazakhstan and contribute to understanding its chloroplast genetic diversity, population structure, and evolutionary relationships. Full article

Background/Objectives: Acorus verus (A. verus), an important medicinal plant with increasing interest in genomic characterization, relies on genomic research to improve its germplasm and industrial applications. Methods: To fill the gap in chloroplast genome data for this species in Guangxi, China, this study sequenced and annotated its chloroplast genome. Results: The research analyzed structural features, codon usage, simple sequence repeats, Inverted Repeat Region boundaries, and phylogenetic relationships. The results indicated that the chloroplast genome of A. verus from Guangxi has a total length of 152,784 bp, exhibiting a typical cyclic tetrad structure. The GC content was 38.74%, with 129 annotated genes: 83 protein-coding, 38 tRNA, and 8 rRNA genes. Codon preference analysis identified 30 high-frequency codons, mostly ending in A/T (72.3%). There were 89 SSR sites, with 73% being single-nucleotide repeats favoring AT bases. Several variable regions were identified, including psbM–trnD-GUC in the Large Single-Copy Region (LSC) and ndhF–rpl32 in the Small Single-Copy Region (SSC) suggesting their potential as candidate loci for future molecular identification and provenance studies. Phylogenetic analysis placed the Guangxi accession within the A. verus lineage, closely related to the Yunnan and Fujian accessions. Conclusions: This study provides the first chloroplast genome resource for A. verus from Guangxi and establishes a reference for accession authentication, comparative plastome analysis, germplasm evaluation, and sustainable utilization of this regional medicinal resource (PZ698195). Full article