Search Results (20)

Indocalamus Nakai, a genus within the tribe Arundinarieae, has significant horticultural and economic value. However, its classification has long been challenging, and due to limited sampling, both intra- and intergeneric phylogenetic relationships, as well as its evolutionary history, remain unclear. In this study, extensive field surveys and comprehensive sample collection were conducted to address these challenges. A total of 31 complete plastomes of Indocalamus species were assembled. All plastomes exhibit a typical quadripartite structure, ranging in length from 139,555 bp to 139,791 bp, and contain 137 genes, including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analyses indicate that Indocalamus is polyphyletic and divided into three distinct clades (IV, V, and X). Based on integrated phylogenomic and morphological evidence, we propose a revised classification of Indocalamus into three major sections. Fossil-calibrated divergence estimates reveal that the major clades of Indocalamus are not monophyletic, highlighting a complex reticulate evolutionary history exemplifying the widespread rapid radiation observed in temperate woody bamboos. The intensification of the East Asian monsoon is likely to have played a key role in driving the rapid radiation of these lineages. Additionally, several clade-specific DNA barcodes (trnT-trnE, petN-trnC, petA-psbJ, and petD-rpoA) were identified, which will enhance the identification of Indocalamus and its closely related genera. This study, through extensive sampling and integration of morphological and molecular phylogenetic evidence, provides a preliminary delimitation of the genus Indocalamus, elucidates its complex evolutionary history, and lays a solid foundation for future systematic research and horticultural applications. Full article

The mechanisms underlying leaf variegation in the ornamental Ilex × ‘Solar Flare’ remain poorly understood. To investigate this phenomenon, we conducted a comprehensive characterization of its variegated leaves. Compared to green sectors, yellow sectors exhibited severe chloroplast structural abnormalities, including swollen chloroplasts, damaged thylakoid membranes, and reduced chloroplast numbers. These yellow sectors also showed significantly lower chlorophyll and carotenoid levels, along with a depletion of key chlorophyll precursors—protoporphyrin IX (Proto IX), magnesium protoporphyrin IX (Mg-Proto IX), and protochlorophyllide (Pchlide). Photosynthetic efficiency was significantly impaired. Comparative transcriptome analysis identified 3510 differentially expressed genes (DEGs) between yellow and green sectors. Key disruptions in chlorophyll biosynthesis included upregulated CHLD expression and downregulated CHLH and CHLG expression, leading to impaired chlorophyll synthesis. Additionally, chlorophyll degradation was accelerated by PAO upregulation. Defective chloroplast development in yellow sectors was associated with the downregulation of GLK1, GLK2, and thylakoid membrane-related genes (PsbC, PsbO, PsbR, PsaD, and PsaH). These molecular alterations likely drive the variegated phenotype of I. × ‘Solar Flare’. These observations advance our understanding of the genetic and physiological mechanisms regulating leaf variegation in this cultivar. Full article

Camphora Fabr. is a genus in the family Lauraceae, comprising over 20 tropical and subtropical tree species. Since the genera Camphora and Cinnamomum Schaeff. were described, there has been a long-lasting controversy regarding the phylogenetic relationships among taxa in both genera. In particular, phylogenetic inferences derived from plastid data remain debated, with varying hypotheses proposed and occasional disputes concerning the monophyly of Camphora taxa. To further investigate the relationships, We analyzed plastomes and nuclear ribosomal cistron sequences (nrDNA) of 22 Camphora taxa, 15 Cinnamomum taxa, and 13 representative taxa of related genera. The Camphora plastomes range from 152,745 to 154,190 bp, with a GC content of 39.1% to 39.2%. A total of 128 genes were identified in the Camphora plastomes, including 84 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. A total of 1130 SSR loci were detected from plastomes of Camphora, and A/T base repeats looked like the most common. Comparative analyses revealed that the plastomes of Camphora exhibit high similarity in overall structure. The loci ycf1, ycf2, trnK (UUU), psbJ-psbL, and ccsA-ndhD were identified as candidate DNA barcodes for these taxa. Plastome phylogenetic analysis revealed that Camphora is not monophyletic, whereas the nrDNA dataset supported the monophyly of Camphora. We propose that intergeneric hybridization may underlie the observed discordance between plastid and nuclear data in Camphora, and we recommend enhanced taxonomic sampling and precise species identification to improve phylogenetic resolution and accuracy. Full article

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources. Full article

Cross-linked polymers synthesized through inverse vulcanization of unsaturated vegetable oils (biopolymers) were used as matrices for incorporating gentamicin (GEN) to form a biocomposite that can amplify GEN antimicrobial activity against Pseudomonas aeruginosa. Two different biopolymers were synthesized using soybean (PSB) and sunflower (PSF) oils by inverse vulcanization cross-linked with sulfur in a 1:1 weight ratio. The study involves the synthesis and characterization of these biopolymers using FTIR and SEM as well as measurements of density and hydrophobicity. The results reveal the formation of biopolymers, wherein triglyceride molecules undergo cross-linking with sulfur chains through a reaction with the unsaturated groups present in the oil. Additionally, both polymers exhibit a porous structure and display hydrophobic behavior (contact angle higher than 120°). The biopolymers swell more in GEN solution (PSB 127.7% and PSF 174.4%) than in pure water (PSB 88.7% and PSF 109.1%), likely due to hydrophobic interactions. The kinetics of GEN sorption and release within the biopolymer matrices were investigated. The antibacterial efficacy of the resulting biocomposite was observed through the analysis of inhibition growth halos and the assessment of P. aeruginosa viability. A notable enhancement of the growth inhibition halo of GEN (13.1 ± 1.1 mm) compared to encapsulated GEN (PSF-GEN 21.1 ± 1.3 and PSB-GEN 21.45 ± 1.0 mm) is observed. Also, significant bactericidal activity is observed in PSF-GEN and PSB-GEN as a reduction in the number of colonies (CFU/mL), more than 2 log₁₀ compared to control, PSF, and PSB, highlighting the potential of these biopolymers as effective carriers for gentamicin in combating bacterial infections. Full article

Toona ciliata is a deciduous or semi-deciduous tree species and belongs to the Toona genus of the Meliaceae family. Owing to low natural regeneration and over-exploitation, the species is listed as an endangered species at level II in China and its conservation has received increasing concern. Here, we sampled 447 individuals from 29 populations across the range-wide distribution of the T. ciliata complex in China and assessed their genetic variation using two chloroplast DNA markers. The results showed that the overall haplotype diversity and nucleotide diversity per site were high at h = 0.9767 and $\pi$ = 0.0303 for the psbA-trnH fragment and $h=$ 0.8999 and $\pi$ = 0.0189 for the trnL-trnL fragment. Phylogenetic analysis supported the division of the natural distribution of T. ciliata complex into western and eastern regions. The genetic diversity was higher in the western region than in the eastern region, showing significant phylogeographic structure. Genetic differentiation among populations was moderate (${\Phi }_{st}=42.87\%$), and the effects of isolation by distance (IBD) were significant. A neutrality test and mismatch distribution analysis indicated that the distribution of the T. ciliata complex generally did not expand, although a few local populations could likely expand after bottleneck effects. The overall results were complementary to and consolidated previous studies using mitochondrial and nuclear DNA markers. We finally discussed strategies for the genetic conservation of the T. ciliata complex. Full article

The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (Cichorium endivia var. latifolium and var. crispum) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar ‘Confiance’), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within Asteraceae with the well-separated C. endivia and intybus species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the ndhD, ndhA, and psbF genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress. Full article

Green alga Chlorella ohadii is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This structure revealed 64 subunits, which encompassed 386 chlorophylls, 86 carotenoids, four plastoquinones, and several structural lipids. At the luminal side of PSII, a unique subunit arrangement was observed to protect the oxygen-evolving complex. This arrangement involved PsbO (OEE1), PsbP (OEE2), PsbB, and PsbU (a homolog of plant OEE3). PsbU interacted with PsbO, PsbC, and PsbP, thereby stabilizing the shield of the oxygen-evolving complex. Significant changes were also observed at the stromal electron acceptor side. PsbY, identified as a transmembrane helix, was situated alongside PsbF and PsbE, which enclosed cytochrome b559. Supported by the adjacent C-terminal helix of Psb10, these four transmembrane helices formed a bundle that shielded cytochrome b559 from the surrounding solvent. Moreover, the bulk of Psb10 formed a protective cap, which safeguarded the quinone site and likely contributed to the stacking of PSII complexes. Based on our findings, we propose a protective mechanism that prevents Q_B (plastoquinone B) from becoming fully reduced. This mechanism offers insights into the regulation of electron transfer within PSII. Full article

The cyclic plastic deformation of polycrystals leads to the inhomogeneous distribution of the cyclic plastic strain. The cyclic plastic strain is concentrated in thin bands, called persistent slip bands (PSBs). The dislocation structure of these bands generally differs from the matrix structure and is characterized by alternating dislocation-rich and dislocation-poor regions. The mechanisms of the dislocation motion in the PSBs and the formation of the point defects and their migration are quantitatively described. It is shown that, due to localized cyclic plastic straining in the PSBs, persistent slip markings (PSMs) are produced where the PSBs emerge on the surface. They typically consist of a central extrusion accompanied by one or two parallel intrusions. The deep intrusion is equivalent to the crack-like surface defect. The concentration of the cyclic strain in the tip of an intrusion leads to intragranular fatigue crack initiation. The mechanism of the early crack growth in the primary slip plane is proposed and discussed. Numerous PSMs are produced on the surface of the cyclically loaded materials. PSMs contribute to the formation of the surface relief, as well as the relief on the grain boundary. PSMs from one grain impinging the grain boundary are sufficient to create sharp relief on the grain boundary. Void-like defects weaken the grain boundary cohesion and extra material push both grains locally apart. The conditions necessary for the weakening of the grain boundary are enumerated and examples of grain boundary crack initiations are shown. The relevant parameters affecting grain boundary initiation are identified and discussed. The collected experimental evidence and analysis is mostly based on the papers published by the author and his colleagues in the Institute of Physics of Materials in Brno. Full article

Eranthis Salisb. (Ranunculaceae) is a herbaceous plant genus, including few species disjunctively distributed throughout the temperate zone from Southeastern Europe to Eastern Asia. Until recently, only Eranthis sibirica DC. was known in South Siberia, being considered endemic and tertiary relict. Not long ago, Eranthis tanhoensis Erst was also described in Siberia. We report here a reconstruction of the phylogenetic relationships between the Siberian Eranthis species based on nuclear (ITS) and plastid (trnL + trnL-trnF + trnH-psbA) DNA. The phylogeographic structure of Siberian Eranthis is distinguished by the presence of the two “eastern” and “western” supergroups, which most likely formed as a result of disjunction caused by active mountain uplifts during the late Neogene–early Quaternary and subsequent progressive Pleistocene cooling. The eastern supergroup combines lineage I, containing populations from the eastern Khamar-Daban Ridge, the Eastern Sayan Mountains, and the Tannu-Ola Ridge, and lineage II containing western Khamar-Daban populations. The western supergroup includes only lineage III, containing Western Sayan populations. Our data clearly show that E. tanhoensis is nested in the E. sibirica clade, thereby indicating that its description as a separate species is unjustified, as it compromises the monophyletic status of E. sibirica. Therefore, we suggest here to consider E. tanhoensis as a synonym of E. sibirica. Full article

Cyanobacteria are major contributors to global carbon fixation and primarily use visible light (400−700 nm) to drive oxygenic photosynthesis. When shifted into environments where visible light is attenuated, a small, but highly diverse and widespread number of cyanobacteria can express modified pigments and paralogous versions of photosystem subunits and phycobiliproteins that confer far-red light (FRL) absorbance (700−800 nm), a process termed far-red light photoacclimation, or FaRLiP. During FaRLiP, alternate photosystem II (PSII) subunits enable the complex to bind chlorophylls d and f, which absorb at lower energy than chlorophyll a but still support water oxidation. How the FaRLiP response arose remains poorly studied. Here, we report ancestral sequence reconstruction and structure-based molecular evolutionary studies of the FRL-specific subunits of FRL-PSII. We show that the duplications leading to the origin of two PsbA (D1) paralogs required to make chlorophyll f and to bind chlorophyll d in water-splitting FRL-PSII are likely the first to have occurred prior to the diversification of extant cyanobacteria. These duplications were followed by those leading to alternative PsbC (CP43) and PsbD (D2) subunits, occurring early during the diversification of cyanobacteria, and culminating with those leading to PsbB (CP47) and PsbH paralogs coincident with the radiation of the major groups. We show that the origin of FRL-PSII required the accumulation of a relatively small number of amino acid changes and that the ancestral FRL-PSII likely contained a chlorophyll d molecule in the electron transfer chain, two chlorophyll f molecules in the antenna subunits at equivalent positions, and three chlorophyll a molecules whose site energies were altered. The results suggest a minimal model for engineering far-red light absorbance into plant PSII for biotechnological applications. Full article

A profile of endogenous hormones and sugars in leaves and pseudobulbs of Laelia anceps subsp. anceps (Orchidaceae) plants induced and non-induced to flowering by the effect of different doses of exogenous gibberellic acid (GA₃), considering the current and back growth structures (CGS and BGS), were investigated. A factorial experiment with five doses of GA₃ and two growth structures was designed. Adult plants with undifferentiated vegetative buds were selected and sprayed with doses of 0, 400, 600, 800, and 1000 mg GA₃ L⁻¹. The main results showed a strong interaction between GA₃ dose and growth structures, which promoted the highest kinetin (KIN) concentration in CGS. Exogenous GA₃ increased endogenous GA₃ in leaves and pseudobulbs induced (I-Leaf and I-PSB) and non-induced (NI-Leaf and NI-PSB) to flowering. For sugar concentration, the 400 mg L⁻¹ GA₃ dose promotes significant interaction with the CGS in NI-PSB. In general, the hormone profile revealed opposite balances of endogenous hormone concentrations for KIN, zeatin (ZEA), trans-zeatin (T-ZEA), indoleacetic acid (IAA), indole-3-butyric acid (IBA) and GA₃, not only for growth structures but also for vegetative organs analyzed, depending on whether the plants were induced or not induced to flowering, with the highest concentration of endogenous hormones in pseudobulbs. Likewise, different sugar concentration balances were observed. These balances of both endogenous hormones and sugars are likely to be involved in the flowering of L. anceps. Full article

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage. Full article

The simple thalloid liverwort Apopellia endiviifolia is a widespread Holarctic species belonging to the family Pelliaceae. European populations of this species comprise two distinct evolutionary lineages named “species A”, known also as water form, and typical, mainly terrestrial forms named “species B”. Newly sequenced, assembled and annotated chloroplast genomes of six European specimens belonging to the two cryptic lineages occupying different microhabitats, revealed the structure typical for liverworts and previously sequenced reference. The plastomes of A. endiviifolia are 120,537–120,947 bp long with a structure typical for most plants, including a pair of IR regions (each of 9,092–9,207 bp) separated by LSC (82,506–82,609 bp) and SSC (19,854–19,924 bp) regions and consist of 121 unique genes, including 81 protein-coding genes, 6 genes of unknown function (ycf genes), 4 ribosomal RNAs and 30 transfer RNAs. Comparative analysis of typical, terrestrial and water forms revealed 4971 molecular diagnostic characters (MDCs), which exceeds numbers found in many well recognized liverworts taxa. Moreover, beside the presence of evolutionary hotspots like ycf1 and ycf2 genes and several intergenic spacer like ndhB-psbM, rps4-ndhJ and ndhC-atpE, the molecular identification of Apopellia cryptic species was possible by almost 98% of 500 bp long frames simulating mini barcodes. The different ecological niches can be driven by different pressures of positive selection, which was detected in nine genes including ccsA, ndhD, ndhF, petA, psbB, psbC, rpoB, ycf1 and ycf2. Despite clearly genetic differences and ecological preferences, the current observation of morphological differentiation does not no allow to separate terrestrial and water forms into taxonomic species. Full article

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima. Full article