Search Results (567)

In this study, a systematic taxonomic analysis was carried out on the lichen genus Peltula, collected from Helan Mountain in China; three new species (Peltula helanense, P. overlappine, and P. reticulata) and a new record (P. crispatula (Nyl.) Egea) for China were identified. Four species were identified by morph-anatomical, chemical, and phylogenetic analyses by combining two gene loci (ITS and LSU). Peltula helanense is with tiny individual thalli up to 1mm, attached by creamy-white cylindrical rhizoids and apothecia filling the whole squamule. Peltula overlappine is characterized by thallus squamulose forming rosette-shaped patches and squamules with distinctive thickened margins. Peltula reticulata is characterized by brownish brown thallus and squamules with densely reticulate upper surface. P. crispatula is characterized by irregular squamules attached to a tuft of hyphae. The four species are described in detail, compared, and discussed with similar species, and images of morpho-anatomical structures of the four species are also provided. Moreover, a key to the species of Peltula from Helan Mountain is provided. The results enrich the data of the genus Peltula and also indicate that the rich diversity of lichen species in Helan Mountain is worthy of in-depth study. Full article

Species of the Rhodnius genus have a complex taxonomy because the events of phenotypic plasticity and cryptic speciation make it difficult to correctly classify these vectors. During the taxonomic history of the genus, five synonymization events occurred. Additionally, some authors suggest that R. milesi possibly represent only phenotypic polymorphisms of R. neglectus. Thus, we analyzed the specific status of R. milesi in relation to R. neglectus using phylogenetic studies with the mitochondrial gene cytochrome B and the study of reproductive barriers. The phylogenetic reconstruction grouped R. milesi together with R. neglectus from different localities, demonstrating that these taxa represent the same species based on the phylogenetic species concept. Experimental crosses demonstrate the absence of pre- and postzygotic barriers under laboratory conditions. Additionally, when the hatch rates of crosses are compared to intraspecific crosses, it can be noted that they are high and very similar. Finally, the mortality rate of the hybrids does not indicate hybrid inviability, the absence of chromosome pairing errors does not indicate hybrid sterility, and the proportion between male and female hybrids demonstrates that Haldane’s rule was not acting. Therefore, we perform the formal synonymization of R. milesi with R. neglectus. Full article

The genus Hedysarum L. (Fabaceae) includes about 200 species of annual and perennial herbs distributed in Asia, Europe, North Africa, and North America. Many species of this genus are valuable medicinal, melliferous, and forage resources. In this review, we consider the taxonomic history of the genus Hedysarum, the chromosomal organization of the species from the sections Hedysarum and Multicaulia, as well as phylogenetic relationships between these sections. According to morphological, genetic, and phylogenetic data, the genus Hedysarum is divided into three main sections: Hedysarum (= syn. Gamotion), Multicaulia, and Stracheya. In species of this genus, two basic chromosome numbers, x = 7 (section Hedysarum) and x = 8 (sections Multicaulia and Stracheya), were determined. The systematic positions of some species within the sections are still uncertain due to their morphological similarities. The patterns of distribution of molecular chromosomal markers (45S rDNA, 5S rDNA, and different satellite DNAs) in karyotypes of various Hedysarum species made it possible to determine their ploidy status and also specify genomic relationships within the sections Hedysarum and Multicaulia. Recent molecular phylogenetic studies clarified significantly the taxonomy and evolutionary development of the genus Hedysarum. Full article

In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management. Full article

Ammonium transporters (AMTs) are vital plasma membrane proteins facilitating NH₄⁺ uptake and transport, crucial for plant growth. The identification of favorable AMT genes is the main goal of improving ammonium-tolerant algas. However, there have been no reports on the systematic identification and expression analysis of Chlamydomonas reinhardtii (C. reinhardtii) AMT genes. This study comprehensively identified eight CrAMT genes, distributed across eight chromosomes, all containing more than 10 transmembrane structures. Phylogenetic analysis revealed that all CrAMTs belonged to the AMT1 subfamily. The conserved motifs and domains of CrAMTs were similar to those of the AMT1 members of OsAMTs and AtAMTs. Notably, the gene fragments of CrAMTs are longer and contain more introns compared to those of AtAMTs and OsAMTs. And the promoter regions of CrAMTs are enriched with cis-elements associated with plant hormones and light response. Under NH₄⁺ treatment, CrAMT1;1 and CrAMT1;3 were significantly upregulated, while CrAMT1;2, CrAMT1;4, and CrAMT1;6 saw a notable decrease. CrAMT1;7 and CrAMT1;8 also experienced a decline, albeit less pronounced. Transgenic algas with overexpressed CrAMT1;7 did not show a significant difference in growth compared to CC-125, while transgenic algas with CrAMT1;7 knockdown exhibited growth inhibition. Transgenic algas with overexpressed or knocked-down CrAMT1;8 displayed reduced growth compared to CC-125, which also resulted in the suppression of other CrAMT genes. None of the transgenic algas showed better growth than CC-125 at high ammonium levels. In summary, our study has unveiled the potential role of CrAMT genes in high-ammonium environments and can serve as a foundational research platform for investigating ammonium-tolerant algal species. Full article

The dinoflagellate genus Karlodinium J. Larsen is well known to form harmful algal blooms (HABs), some of which can produce karlotoxins or other ichthyotoxins and thus cause fish-killing events. Among the 16 currently accepted species of Karlodinium (about half of which are reported to be toxic), six species (K. australe, K. decipiens, K. digitatum, K. elegans, K. veneficum, and K. zhouanum) have been reported or described in the coastal waters of China. However, a fine morphological and molecular characterization of the seldom-observed species K. decipiens has not been conducted; moreover, the negative effects of this species on aquatic animals have not been investigated. This work reports the morphological and phylogenetic characterization of a strain of K. decipiens isolated from Jiaozhou Bay, China, in 2019. The characterization of the strain was conducted using light and scanning electron microscopy, LSU, SSU rDNA, and ITS sequences-based systematic analyses, pigment analysis, and a detailed investigation of its potential toxic/harmful activity on aquatic animals. We observed the typical diagnostic features of K. decipiens, including its relatively large size, ellipsoidal or ovoid cell shape, ventral pore, ventral ridge connecting the two displaced ends of the cingulum, cingulum with a displacement of about one-third of the cell length, numerous polyhedral or slightly elongated chloroplasts distributed peripherally, and large nucleus located centrally. However, we also observed a large amphiesmal vesicle at the dorsal end of the ASC at the dorsal epicone, which is a novel feature that has never been reported from any species of the genus. Based on the results of this study, it is not clear whether this feature is a specific structure of the species or a common characteristic of the genus; therefore, this novel feature is worthy of further examination. Fucoxanthin was the most abundant pigment among all the carotenoids detected. The phylogenies inferred using Bayesian inference (BI) and maximum likelihood (ML) techniques confirmed the conspecificity of our isolate with the holotype K. decipiens (accession no. EF469236). In molecular trees, K. decipiens and K. antarcticum form a separate clade from other species of Karlodinium, and it should be examined whether a large amphiesma vesicle may be a characteristic of this clade. The exposure bioassays using brine shrimp (Artemia salina) indicated that K. decipiens exhibited toxicity to zooplankton, with 100% and 68% mortality observed in brine shrimp using live cell cultures and cell culture lysates over 120 h, respectively. Our work provides a detailed morphological and molecular characterization of K. decipiens from China. The results of this study broaden the known geographical distribution of this species and demonstrate it to be a harmful dinoflagellate. Full article

The TIFY family is a plant-specific gene family that is involved in regulating a variety of plant processes, including developmental and defense responses. The Cymbidium species have certain ornamental and ecological value. However, the characteristics and functions of TIFY genes in Cymbidium remain poorly understood. This study conducted a genome analysis of the TIFY gene family in Cymbidium goeringii, C. ensifolium, and C. sinense and investigated their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns under heat stress in C. goeringii. C. goeringii (26), C. ensifolium (19), and C. sinense (21). A total of 66 TIFY genes were identified, and they were classified into four subfamilies (JAZ, ZML, PPD, and TIFY) based on their systematic evolutionary relationships. Sequence analysis showed that TIFYs contained a conserved TIFY domain and that genes within the same subfamily had structural similarity. Analysis of cis-regulatory elements revealed that these genes contain numerous light-responsive elements and stress-responsive elements. We subjected C. goeringii (16 h light/8 h dark) to 24 h of 38 °C high-temperature stress in a climate chamber. Additionally, results from RT-qPCR experiments showed that under heat stress, the expression levels of eight genes in C. goeringii show significant differences. Among them, the JAZ subfamily exhibited the strongest response to heat stress, initially showing upregulation followed by a downregulation trend. In conclusion, this study investigated the role of TIFY genes in three Cymbidium species, providing insights into C. goeringii under heat stress. Full article

Epichloë fungal endophytes hold promise in sustainable agriculture by fortifying cool-season grasses such as Elymus spp. against various stresses. Elymus spp. are widely distributed in Northwest China with a high incidence of endophyte infections. In this study, we identified 20 Epichloë endophytic fungal strains carried by five Elymus spp. from five areas of Northwest China and systematically characterized their morphology, molecular phylogeny, mating type, and alkaloid diversity for the first time. The morphological characterization underscores strain diversity, with variable colony textures and growth rates. A phylogenetic analysis confirms all strains are E. bromicola, emphasizing their taxonomic status. Alkaloid-encoding gene profiling delineates distinct alkaloid synthesis capabilities among the strains, which are crucial for host adaptability and resistance. A mating-type analysis reveals uniformity (mtAC) across the Epichloë strains, simplifying breeding strategies. Notably, the Epichloë strains exhibit diverse alkaloid synthesis gene profiles, impacting host interactions. This research emphasizes the ecological significance of Epichloë endophytes in Elymus spp. ecosystems, offering insights into their genetic diversity and potential applications in sustainable agriculture. Full article

Soluble sugars, as an indispensable source of energy, play crucial roles in plant growth and development. However, to date, scant information about the sucrose metabolism-related gene families is available in kiwifruit (Actinidia rufa Planch). Here, we systematically identified the members of various gene families encoding crucial enzymes or transporters involved in sucrose metabolism, re-analyzed their expression patterns under different fruit development stages, and determined the regulatory mechanism involving key transcription factors. A total of sixty-two genes from six gene families (thirty-one ArINVs, two ArSPPs, four ArSPSs, nine ArSUSs, six ArSUCs/SUTs, and ten ArSWEETs) were identified in the A. rufa genome. The characterization of these members, including gene structure, motifs, conserved domains, and cis-acting elements, were analyzed. Phylogenetic analysis revealed that these gene families could be categorized into six distinct subgroups. These six gene families have undergone strong purifying selection during domestication. In addition, expression analysis of the 62 genes indicated that differential expression patterns are highly regulated by developmental processes. Specifically, we identified 11 transcription factors that were rigorously correlated (r > 0.98) with key gene expression profiles. This represents a comprehensive analysis of the genes involved in sucrose metabolism in kiwifruit, which provides useful information for further functional analysis of these genes. Full article

The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties. Full article

Hsp40–Hsp70 typically function in concert as molecular chaperones, and their roles in post-infection immune responses are increasingly recognized. However, in the economically important fish species Scophthalmus maximus (turbot), there is still a lack in the systematic identification, interaction models, and binding site analysis of these proteins. Herein, 62 Hsp40 genes and 16 Hsp70 genes were identified in the turbot at a genome-wide level and were unevenly distributed on 22 chromosomes through chromosomal distribution analysis. Phylogenetic and syntenic analysis provided strong evidence in supporting the orthologies and paralogies of these HSPs. Protein–protein interaction and expression analysis was conducted to predict the expression profile after challenging with Aeromonas salmonicida. dnajb1b and hspa1a were found to have a co-expression trend under infection stresses. Molecular docking was performed using Auto-Dock Tool and PyMOL for this pair of chaperone proteins. It was discovered that in addition to the interaction sites in the J domain, the carboxyl-terminal domain of Hsp40 also plays a crucial role in its interaction with Hsp70. This is important for the mechanistic understanding of the Hsp40–Hsp70 chaperone system, providing a theoretical basis for turbot disease resistance breeding, and effective value for the prevention of certain diseases in turbot. Full article

Sucrose transporters (SUTs) play vital roles in phloem sucrose unloading and transportation in wheat grains. However, the genomic information regarding the SUT gene family and their expression patterns in response to heat stress in grains of male-sterile wheat (Triticum aestivum L.) lines has not been systematically studied. In this study, a thorough examination of the wheat SUT gene family was conducted, focusing on their expression patterns in male-sterile lines under heat stress conditions in grain tissues. A total of 19 SUT genes were identified, with phylogenetic analysis indicating their classification into five distinct groups. Polyploidization was identified as a substantial factor in the expansion of SUT genes, with segmental duplication being the predominant mechanism driving the evolutionary expansion of the SUT gene family in wheat. Transcriptome data indicate that the expression levels of TaSUT1 and TaSUT2 were higher than other SUT genes in grains of male-sterile lines. The TaSUT1 expression showed a gradual decreasing trend, while TaSUT2 showed a reverse trend with the process of grain filling. After heat stress, the TaSUT1 expression in grains of male-sterile lines was first significantly increased and then significantly decreased with the filling stage extension, aligning with the observed trend of sucrose levels, indicating that heat stress may decrease the grain weight by reducing sucrose unloading and transportation process in grains. These results provide a systematic analysis of the SUT gene family and lay a theoretical foundation for us to study the grain filling of male-sterile lines in response to abiotic stress. Full article

The fructose-1,6-bisphosphate aldolase (FBA) gene family exists in higher plants, with the genes of this family playing significant roles in plant growth and development, as well as response to abiotic stresses. However, systematic reports on the FBA gene family and its functions in cucumber are lacking. In this study, we identified five cucumber FBA genes, named CsFBA1-5, that are distributed randomly across chromosomes. Phylogenetic analyses involving these cucumber FBAs, alongside eight Arabidopsis FBA proteins and eight tomato FBA proteins, were conducted to assess their homology. The CsFBAs were grouped into two clades. We also analyzed the physicochemical properties, motif composition, and gene structure of the cucumber FBAs. This analysis highlighted differences in the physicochemical properties and revealed highly conserved domains within the CsFBA family. Additionally, to explore the evolutionary relationships of the CsFBA family further, we constructed comparative syntenic maps with Arabidopsis and tomato, which showed high homology but only one segmental duplication event within the cucumber genome. Expression profiles indicated that the CsFBA gene family is responsive to various abiotic stresses, including low temperature, heat, and salt. Taken together, the results of this study provide a theoretical foundation for understanding the evolution of and future research into the functional characterization of cucumber FBA genes during plant growth and development. Full article

As an important genus in Orchidaceae, Cymbidium has rich ecological diversity and significant economic value. DNA binding with one zinc finger (Dof) proteins are pivotal plant-specific transcription factors that play crucial roles in the growth, development, and stress response of plants. Although the Dof genes have been identified and functionally analyzed in numerous plants, exploration in Orchidaceae remains limited. We conducted a thorough analysis of the Dof gene family in Cymbidium goeringii, C. ensifolium, and C. sinensis. In total, 91 Dof genes (27 CgDofs, 34 CeDofs, 30 CsDofs) were identified, and Dof genes were divided into five groups (I–V) based on phylogenetic analysis. All Dof proteins have motif 1 and motif 2 conserved domains and over half of the genes contained introns. Chromosomal localization and collinearity analysis of Dof genes revealed their evolutionary relationships and potential gene duplication events. Analysis of cis-elements in CgDofs, CeDofs, and CsDofs promoters showed that light-responsive cis-elements were the most common, followed by hormone-responsive elements, plant growth-related elements, and abiotic stress response elements. Dof proteins in three Cymbidium species primarily exhibit a random coil structure, while homology modeling exhibited significant similarity. In addition, RT-qPCR analysis showed that the expression levels of nine CgDofs changed greatly under heat stress. CgDof03, CgDof22, CgDof27, CgDof08, and CgDof23 showed varying degrees of upregulation. Most upregulated genes under heat stress belong to group I, indicating that the Dof genes in group I have great potential for high-temperature resistance. In conclusion, our study systematically demonstrated the molecular characteristics of Dof genes in different Cymbidium species, preliminarily revealed the patterns of heat stress, and provided a reference for further exploration of stress breeding in orchids. Full article

Seagrass serves as a quintessential reservoir for obligate marine Lulworthiaceae fungi. Our current knowledge of the mycological diversity associated with seagrass in Hong Kong remains poor. We analyzed the diversity of fungi associated with the most widely distributed seagrass species in Hong Kong Halophila ovalis (Hydrocharitaceae), using a combination of culture-based methods and high-throughput amplicon sequencing. Halophilomyces hongkongensis, a novel fungal species in a newly proposed genus within the Lulworthiaceae family, was isolated from H. ovalis roots and rhizomes. The novel fungus showed distinct morphological characteristics, while both combined 18S-28S and internal transcribed spacer (ITS) phylogenetic trees based on maximum likelihood and Bayesian methods supported its discrimination from other existing Lulworthiaceae members. The ITS2 region in the Illumina sequencing results of multiple H. ovalis compartments, water, and adjacent non-seagrass sediments revealed continuous recruitment of H. hongkongensis by H. ovalis throughout the year despite dramatically fluctuating environmental conditions, with remarkably high proportions of this taxon found in root and rhizome internal tissues, possibly indicating a strong and specialized relationship established between the Lulworthiaceae fungal partner and its seagrass host. The inhibitory abilities exhibited by H. hongkongensis against Staphylococcus aureus SA29213 and ATCC 43300 (methicillin-resistant) may imply its capacity in producing (novel) antibacterial compounds. The discovery of H. hongkongensis as the first novel Lulworthiaceae taxon in Hong Kong, along with its distributional pattern in the seagrass meadow, provides valuable insights into the systematics and ecology of this strictly marine fungal family. Full article