Search Results (96)

Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article

This study focuses on a subtropical evergreen broad-leaved forest in China, utilizing a large permanent plot established in the Yaoluoping National Nature Reserve. By integrating data from a full-stem census and total station surveying, we analyzed the phylogenetic structure of the plant community as a whole and across different life-history stages (saplings, juveniles, and adults) while quantitatively assessing microtopographic variables and an interspecific competition index. The results indicate that the overall community in the Yaoluoping plot exhibited a weakly overdispersed pattern, and key microtopographic factors—including aspect, terrain position index (TPI), terrain ruggedness index (TRI), roughness, and flow direction—significantly influenced the evolution of phylogenetic structure. Distinctions were also observed among saplings, juveniles, and adults in phylogenetic structuring across life-history stages. Specifically, saplings displayed a higher degree of phylogenetic clustering, significantly influenced by density, elevation, TPI, and flow direction—suggesting that environmental filtering predominates at this stage, possibly due to lower environmental tolerance, limited dispersal ability, and conspecific negative density dependence. In contrast, juveniles and adults showed a more dispersed phylogenetic structure, with density, interspecific competition, aspect, TRI, TPI, and roughness significantly correlated with phylogenetic patterns, indicating that competition and niche differentiation become increasingly important as trees mature and establish within the community. Interspecific competition was found to play a crucial role in community structuring: the competition index was generally negatively correlated with the net relatedness index (NRI) and nearest taxon index (NTI) in juveniles and adults, implying that intense competition leads to the exclusion of some species and reduces overall diversity, with the strength and significance of competitive effects differing across stages. This study enhances our understanding of the complex interplay between microtopography and interspecific competition in shaping the phylogenetic structure and diversity of subtropical evergreen broad-leaved forests, elucidates the coupled mechanisms among microtopography, phylogenetic structure, and competition, and provides a scientific basis for forest conservation and management. Full article

Photosynthetic eukaryotes have shaped the Earth’s biosphere by producing oxygen and organic compounds using light energy in specialized organelles called plastids. Plastids evolved from free-living cyanobacteria ingested by heterotrophic unicellular eukaryotes. Two such independent engulfment processes, called cyanobacterial endosymbioses, have been reported. The first gave rise to primary plastids and three Archaeplastida lineages: glaucophytes, red algae, and green algae with land plants, whereas the second resulted in chromatophores in the rhizarian amoeba Paulinella. Importantly, Archaeplastidans donated their plastids to many protist groups, further spreading photosynthesis across the tree of life. To reveal complex plastid evolution, we performed comprehensive phylogenetic and molecular clock analyses using new fossil calibrations and the largest number yet of plastid-encoded proteins from 108 taxa, representing diverse photosynthetic organisms. Our results indicate that primary plastids evolved prior to 2.1–1.8 Ga, i.e., before glaucophytes diverged from other Archaeplastidans, and Paulinella chromatophores were likely before 292–266 Ma. Red and green algae were engulfed by cryptophyte and chlorarachniophyte ancestors between 1.7–1.4 Ga and 1.1–1.0 Ga, respectively; the former subsequently triggered plastid transfers to other eukaryotes. We also examined the impact of molecular clocks and calibration sets on age estimates, showing that clocks are the main source of variation. Full article

Colpodella species are free-living predatory protists that prey on algae, ciliates and bodonids using myzocytosis. Colpodella species have been reported in human and animal infections. Polymerase chain reaction (PCR) using primers targeting 18S rRNA genes of Cryptosporidium and piroplasms have identified Colpodella species in arthropods, host blood and feces, demonstrating the phylogenetic closeness of Colpodella species to the apicomplexa. However, in human, animal and arthropod hosts, the life cycle stages of Colpodella are unknown. In this literature review, we provide an overview of the widespread occurrence of Colpodella species in ticks, and pathogenicity in humans and animals. We discuss methods for culture and microscopy that can aid diagnosis. Phylogenetic tree analysis of Colpodella species identified using 18S rRNA demonstrates that the Colpodella species identified in different geographic regions represent different species and strains that may impact virulence and zoonotic transmission. There is a pressing need to culture Colpodella species, and to stain cells for morphological identification. This will aid molecular investigations aimed at identifying molecular markers of Colpodella spp. facilitating transmission, survival and pathogenesis in hosts, and will determine which species and strains to prioritize for the risk of zoonotic infections to humans and for infections in animals. Full article

We describe a new species of snake of the genus Tachymenoides using molecular and morphological evidence. The description is based on 21 specimens (4 females, 17 males) obtained in the regions of Pasco, Junín, and Puno between 2190 and 3050 m elevation. A maximum likelihood phylogenetic tree based on two mitochondrial (12S and cyt-b) genes and one nuclear (c-mos) gene shows that the new species is the sister taxon of T. affinis and distinct from Galvarinus tarmensis, which we transfer back to Tachymenis. The new species has smooth dorsal scales without apical pits usually in 19/17/15 series, 1 preocular, 2 postoculars, 1 loreal undivided nasal scale, 8 supralabials (4th and 5th in contact with the eye), 9 infralabials, 1–2+2–3 temporals, 139–157 ventrals, 52–67 subcaudals, and a divided cloacal scale. The longest specimen, a male, had a total length of 559 mm. Two females contained six and five eggs with small embryos. In life, the dorsum and flanks are olive brown to pale grayish brown with scattered black and cream flecks and no longitudinal stripes. Ventral coloration is highly variable, nearly uniformly black, mottled gray and dark-gray, mottled pale gray and tan, or pale grayish tan. Usually, three irregularly shaped, narrow, longitudinal ventral stripes are present. The iris is brown with a distinct yellowish-tan ringlet. Full article

Cymothoidae (Crustacea: Isopoda) infest fish in marine, brackish, and freshwater environments. Cymothoa pulchrum Lanchester, 1902 is a cymothoid commonly found in the buccal cavity of mainly Tetraodontiformes fishes, distributed in the central and western Indo-Pacific region. This study describes the morphology of each life cycle stage of C. pulchrum: adult female, transitional, adult male, juvenile, and manca. In addition, we obtained DNA sequences linked to the morphological information of this species. We compared it with the sequences in the database using the neighbor-joining tree based on cytochrome c oxidase subunit I (COI) and 16S rRNA. Prior to this study, morphological data on the immature stages of Japanese Cymothoa was limited to juveniles of Cymothoa indica Schioedte and Meinert, 1884. The research identified 12 distinct morphological features that differentiate juvenile C. pulchrum from juvenile C. indica. Molecular analysis revealed that the COI sequences obtained in this study matched some of the C. pulchrum sequences in the database, whereas other sequences in the database formed a clade with Cymothoa eremita (Brünnich, 1783). In the phylogenetic tree based on 16S rRNA, C. pulchrum was also divided into two groups. In the COI phylogenetic tree, C. pulchrum and C. eremita form a total of five groups, and these two species might need to be re-examined taxonomically and molecularly. Full article

Forest trees significantly affect human life. The spread of pathogens, including bacterial ones, poses a serious threat to their health. Despite this, however, the species composition and distribution of pathogenic bacteria, as well as the etiology of common diseases affecting forest trees, remain virtually unstudied. In this study, we, for the first time, describe different species of Pseudomonas and Pantoea as new etiological agents associated with the symptoms of leaf spotting and wood darkening on Acer tataricum L., Fraxinus pennsylvanica L., Ulmus minor Mill. Ulmus laevis Pallas. and Populus tremula L. For the identification of bacteria species, we used an integrated approach based on the characterization of their morphology, biochemistry, physiology and genetics. Phylogenetic analysis was performed using multilocus typing for five genes for Pseudomonas and six genes for Pantoea. Leaf spotting on A. tataricum, F. pennsylvanica, U. minor and U. laevis was shown to be caused by Pseudomonas cerasi, Pseudomonas congelans, Pseudomonas graminis, Pseudomonas syringae and Pantoea agglomerans both in monoinfection and coinfection. Wood darkening in U. minor U. laevis and P. tremula was found to be associated with the presence of Pantoea sp. and P. agglomerans. The coinfection of forest trees with bacteria of the genera Pseudomonas and Pantoea indicates a complex mechanism of interaction between the two populations, which will be the subject of future studies. Full article

The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) Kahl, 1932, and Metopus major Kahl, 1932, were investigated by live observation, protargol staining and 18S rRNA gene sequencing. B. abnormalis sp. nov. can be separated from its congeners by a combination of the following features: bullet-shaped cell with a life size of about 130–190 × 90–120 μm, dikinetids distributed along dorsal dome kineties, highly developed adoral zone comprised of 87–107 polykinetids, making about 450° spiralization around the long axis. The present work demonstrates that two known species, M. contortus and M. major, have a special trait never previously reported, viz. short, regularly arranged preoral dome dikinetids. Species with short, regularly arranged dome dikinetids appear in divergent clades in SSU rRNA gene trees, which may infer that this trait evolved several times. Phylogenetic analyses based on SSU rRNA gene sequence data also support the monophyly of the genus Brachonella and the paraphyly of the order Metopida, respectively. Full article

Background: 20-Hydroxyecdysone (20E) is the most ubiquitous ecdysteroid (Ecd) and plays critical roles during the life cycle of arthropods. To elucidate the metabolism pathway of 20E in the economically important species, Scylla paramamosain, we conducted a comprehensive exploration of the genes involved in the 20E metabolism pathway. Methods: A comprehensive exploration of genes involved in the 20E metabolism pathway was conducted, including gene annotation, local blast using the Drosophila ortholog as query, and TreeFam ortholog genes identification. Bioinformatics and expression profiling of the identified genes were performed to assess their roles in the 20E metabolism of green mud crabs. Results: This experiment indicated that, except for CYP306a1 and CYP314a1, all other ortholog genes involved in the Drosophila 20E metabolism can be found in the mud crab, suggesting that the function of these two genes might be replaced by other CYP genes or the “active” Ecd in mud crabs was not the 20E. All genes had the typical features of each gene family, clustered with the specific clade in the phylogenetic trees. In addition, all the identified genes had the highest expression level in the Y-organ, and sex-biased gene expression was observed in these genes. Conclusions: This study provided some valuable insights into the metabolism and diversity of ecdysteroids in crustaceans. Full article

During the last few decades, the main focus of numerous studies has been on the human breast milk microbiota and its influence on the infant intestinal microbiota and overall health. The presence of lactic acid bacteria in breast milk affects both the quantitative and qualitative composition of the infant gut microbiota. The aim of this study was to assess the most frequently detected cultivable rod-shaped lactobacilli, specific for breast milk of healthy Bulgarian women and fecal samples of their infants over the first month of life, in 14 mother–infant tandem pairs. Additionally, we evaluated the strain diversity among the most common isolated species. A total of 68 Gram-positive and catalase-negative strains were subjected to identification using the MALDI-TOF technique. Predominant cultivable populations belonging to the rod-shaped lactic acid bacteria have been identified as Lacticaseibacillus rhamnosus, Limosilactobacillus fermentum, Lacticaseibacillus paracasei, and Limosilactobacillus reuteri. Also, we confirmed the presence of Lactiplantibacillus plantarum and Lactobacillus gasseri. Up to 26 isolates were selected as representatives and analyzed by 16S rRNA sequencing for strain identity confirmation and a phylogenetic tree based on 16S rRNA gene sequence was constructed. Comparative analysis by four RAPD primers revealed genetic differences between newly isolated predominant L. rhamnosus strains. This pilot study provides data for the current first report concerning the investigation of the characteristic cultivable lactobacilli isolated from human breast milk and infant feces in Bulgaria. Full article

Watermelon is one of the most important edible plants worldwide. Owing to its special cultivation conditions, watermelon is exposed to many biological and abiotic stresses during its development. Lectin receptor-like kinases (LecRLKs) are plant-specific membrane proteins that play important roles in sensing and responding to environmental stimuli. Although the LecRLK gene family has been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in watermelon. In this study, 61 putative LecRLK genes were identified in watermelon, consisting of 36 G-type, 24 L-type, and 1 C-type LecRLK genes. They were distributed in clusters on chromosomes, and members from the same subfamily were mostly clustered together. The analysis of the phylogenetic tree and conserved motif indicated that there were obvious differences among three ClaLecRLK subfamilies, and there was also rich diversity in the C-terminal within subfamilies. A collinear analysis revealed that the evolution of the ClaLecRLK gene family in different Cucurbitaceae crops was asynchronous. Furthermore, the analysis of the ClaLecRLK protein structure showed that not all proteins contained signal peptides and a single transmembrane domain. A subcellular localization assay confirmed that the number and position of transmembrane domains did not affect ClaLecRLK protein localization in cells. Transcriptome data revealed distinct expression patterns of LecRLK genes of watermelon in various tissues, and their responses to different fungi infection were also significantly different. Finally, the potential binding sites of the ClaLecRLK genes targeted by miRNA were predicted. This study enhances the understanding of the characteristics and functions of the LecRLK gene family in watermelon and opens up the possibility of exploring the roles that LecRLK genes may play in the life cycle of Cucurbitaceae plants. Full article

Comparing phylogenetic trees is a prominent problem widely used in applications such as clustering and building the Tree of Life. While there are many well-developed distance measures for phylogenetic trees defined on the same set of taxa, the situation is contrasting for trees defined on different but mutually overlapping sets of taxa. This paper presents a new polynomial-time algorithm for completing phylogenetic trees and computing the distance between trees defined on different but overlapping sets of taxa. This novel approach considers both the branch lengths and the topology of the phylogenetic trees being compared. We demonstrate that the distance measure applied to completed trees is a metric and provide several properties of the new method, including its symmetrical nature in tree completion. Full article

Between 2020 and 2023, rust fungus specimens were collected from the primary forested regions of the Sanjiangyuan area in Qinghai Province, resulting in over 300 samples. A taxonomic and phylogenetic study of the rust fungi from these forests was conducted using morphological and molecular biological techniques. The investigation identified rust fungi from 7 families, 12 genera, 56 species and varieties, including 10 new host records, 1 new record for China, and 2 novel species. The host plants involved belonged to 26 families, 48 genera, and 78 species. Pucciniaceae and Coleosporiaceae were the dominant families, with the genera Puccinia, Melampsora, and Gymnosporangium being prevalent. The rust fungi in the Sanjiangyuan forests showed a biogeographical affinity with the North Temperate Zone. Floristic comparisons revealed a higher similarity with rust fungi from Inner Mongolia, Gansu, and Tibet and a lower similarity with those from Hainan. An analysis of the life forms of rust fungus host plants indicated that herbaceous plants were the most common, followed by shrubs and trees. In different regions of Sanjiangyuan, rust fungi were found as follows: Golog Prefecture with 6 families, 9 genera, and 28 species; Yushu Prefecture with 5 families, 8 genera, and 31 species; Huangnan Prefecture with 5 families, 9 genera, and 26 species; and Hainan Prefecture with 4 families, 5 genera, and 10 species. The families Pucciniaceae, Melampsoraceae, and Coleosporiaceae were common across all four regions. Moreover, the families Rosaceae, Asteraceae, Ranunculaceae, Salicaceae, and Caprifoliaceae were shared among the host plants in these regions. Full article

Exoglycosidase enzymes hydrolyze the N-glycosylations of cell wall enzymes, releasing N-glycans that act as signal molecules and promote fruit ripening. Vesicular exoglycosidase α-mannosidase enzymes of the GH38 family (EC 3.2.1.24; α-man) hydrolyze N-glycans in non-reduced termini. Strawberry fruit (Fragaria × ananassa) is characterized by rapid softening as a result of cell wall modifications during the fruit ripening process. Enzymes acting on cell wall polysaccharides explain the changes in fruit firmness, but α-man has not yet been described in F. × ananassa, meaning that the indirect effects of N-glycan removal on its fruit ripening process are unknown. The present study identified 10 GH38 α-man sequences in the F. × ananassa genome with characteristic conserved domains and key residues. A phylogenetic tree built with the neighbor-joining method and three groups of α-man established, of which group I was classified into three subgroups and group III contained only Poaceae spp. sequences. The real-time qPCR results demonstrated that FaMAN genes decreased during fruit ripening, a trend mirrored by the total enzyme activity from the white to ripe stages. The analysis of the promoter regions of these FaMAN genes was enriched with ripening and phytohormone response elements, and contained cis-regulatory elements related to stress responses to low temperature, drought, defense, and salt stress. This study discusses the relevance of α-man in fruit ripening and how it can be a useful target to prolong fruit shelf life. Full article

The Lanzhou lily (Lilium davidii var. unicolor) is a variant of the Sichuan lily of the lily family and is a unique Chinese ‘medicinal and food’ sweet lily. Somatic cell embryogenesis of Lilium has played an important role in providing technical support for germplasm conservation, bulb propagation and improvement of genetic traits. Somatic embryogenesis receptor-like kinases (SERKs) are widely distributed in plants and have been shown to play multiple roles in plant life, including growth and development, somatic embryogenesis and hormone induction. Integrating the results of KEGG enrichment, GO annotation and gene expression analysis, a lily LdSERK1 gene was cloned. The full-length open reading frame of LdSERK1 was 1875 bp, encoding 624 amino acids. The results of the phylogenetic tree analysis showed that LdSERK1 was highly similar to rice, maize and other plant SERKs. The results of the subcellular localisation in the onion epidermis suggested that the LdSERK1 protein was localised at the cell membrane. Secondly, we established the virus-induced gene-silencing (VIGS) system in lily scales, and the results of LdSERK1 silencing by Tobacco rattle virus (TRV) showed that, with the down-regulation of LdSERK1 expression, the occurrence of somatic embryogenesis and callus tissue induction in scales was significantly reduced. Finally, molecular assays from overexpression of the LdSERK1 gene in Arabidopsis showed that LdSERK1 expression was significantly enhanced in the three transgenic lines compared to the wild type, and that the probability of inducing callus tissue in seed was significantly higher than that of the wild type at a concentration of 2 mg/L 2,4-D, which was manifested by an increase in the granularity of the callus tissue. Full article