Search Results (42)

Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the RBCS gene family in C3 and C4 grasses to identify genetic targets for improved crop photosynthesis. Triticeae/Aveneae phylogeny groups exhibited a syntenic tandem duplication array averaging 326.1 Kbp on ancestral chromosomes 2 and 3, with additional copies on other chromosomes. Promoter analysis revealed a paired I-box element promoter arrangement in chromosome 5 RBCS of H. vulgare, S. cereale, and A. tauschii. The I-box pair was associated with significantly enhanced expression, suggesting functional adaptation of specific RBCS gene copies in Triticaeae. H. vulgare-derived pan-transcriptome data showed that RBCS expression was 50.32% and 28.44% higher in winter-type accessions compared to spring types for coleoptile (p < 0.05) and shoot, respectively (p < 0.01). Molecular dynamics simulations of a mutant H. vulgare Rubisco carrying a C4-like amino acid substitution (G59C) in RBCS significantly enhanced the stability of the Rubisco complex. Given the known structural efficiency of C4 Rubisco complexes, G59C could serve as an engineering target for enhanced RBCS in economically crucial crop species which, in comparison, possess less efficient Rubisco complexes. Full article

The sustainable growth of finfish farming relies heavily on reducing the high ecological footprint of sourcing and producing fish feeds that accounts for almost 50% of the total ecological footprint of finfish farming. Sustainable alternatives to fishmeal often pose challenges due to the presence of antinutritional factors and nutrient imbalances that impair fish health and growth. Screening for alternative nutrient sources and adapting to global commodity fluctuations requires modern tools that can predict the physiological responses of fish early and reliably. The present study explores for the first time the potential of fish red blood cell (RBC) transcriptome as a minimally invasive biomarker of physiological responses in gilthead seabream (Sparus aurata) fed either a fishmeal-based (FM) or a plant-protein-based (PP) diet. Blood samples were collected at multiple time points (15, 20, and 30 days post-diet initiation) from genetically diverse full-sib families reared under commercial conditions, integrating transcriptomic analysis with long-term growth assessments. Differential gene expression analysis revealed significant dietary effects on oxidative phosphorylation, ribosomal capacity, and lipid metabolism pathways, highlighting metabolic plasticity and cellular adaptations to plant-based feeds. The downregulation of oxidative phosphorylation genes suggests a metabolic shift in response to altered nutrient composition, while ribosomal pathway modulation indicates potential constraints on protein synthesis. These transcriptomic shifts, conserved across two independent experiments, reinforce the utility of RBCs as a real-time indicator of fish physiological status, offering a tool for monitoring dietary impacts and optimizing feed formulations. Such insights are essential for advancing sustainable, nutritionally balanced aquaculture feeds that support fish welfare and productivity. The minimally invasive sample collection respects the 3Rs (Reduce, Refine, Replace) principle in animal experimentation and allows for frequent screening and generation of refined data. Full article

Banisteriopsis is a genus in the Malpighiaceae family with 61 species, notable for including ritualistic taxa such as B. caapi (Spruce ex Griseb.) C.V. Morton, one of the main components of Ayahuasca tea. We analyzed 38 Banisteriopsis species, representing more than 60% of the genus, to investigate its geographical origin, diversification period, and colonization routes in the Neotropics. Plastid genes (matK, ndhF, and rbcL) and nuclear regions (ETS, ITS, and PHYC) were used in our analyses. Divergence time analyses were performed using Bayesian inference with a relaxed molecular clock and ancestral area reconstruction. Our results show that Banisteriopsis originated in the Miocene approximately 22 million years ago, and its diversification coincides with the expansion of dry areas in South America. Banisteriopsis began colonizing the Cerrado earlier than most other plants, and the history of the genus reveals that the biome served as a source of species for Neotropical rainforests. Our results also indicate a probable ancient origin for B. caapi, with no evidence of human manipulation in its diversification, and they reinforce archaeological evidence of a millennia-old exchange of uses among Amazonian peoples. Full article

Myeloid leukaemia (ML) is a cancer that occurs by the accumulation of abnormally multiplied myeloid cells in bone marrow, peripheral blood, and other related tissue. MST3 is a gene of the GCK family that has a role in apoptosis, along with other cellular functions like cellular differentiation, cell cycle, metabolism, and others. Objectives: The objectives of this study were to count RBCs and WBCs, study MST3 expression in ML and control samples, and perform an in silico correlation study on the KRAS and NRAS genes. Methods: The counting of RBCs and WBCs was carried out using a hemacytometer, the expression of MST3 was studied using RT-PCR, and a correlation study was carried out using GEPIA. Results: RBC and WBC levels in ML differed from the control levels, and the expression of MST3 was found to be upregulated in ML in comparison to controls, with a 2.90–8.65-fold change, with a significant p-value > 0.05. A positive correlation in expression was also found between MST3 and KRAS and NRAS genes, with a significant r value correlation. Conclusions: From this study, it could be deduced that MST3 might have a role in ML pathogenesis, but further research is needed to study its role in the progression of the disease. Full article

Phytoplasmas are a group of plant-pathogenic, cell-wall-less bacteria vectored primarily by leafhoppers (Hemiptera Cicadellidae), one of the most diverse families of insects. Despite the importance of documenting associations between phytoplasmas, their insect vectors, and plant hosts to prevent disease outbreaks, such knowledge is currently highly incomplete and largely neglects the diversity of the system in natural areas. Here, we used anchored hybrid enrichment (AHE) to recover the DNA of five plant genes (rbcL, matK, ITS1, ITS2, and trnH-psbA) in 58 phloem-feeding leafhoppers from around the world that had previously tested positive for phytoplasma infection. Using BLASTn and a strict filtering approach, we assigned taxonomic classifications to the plant sequences and tested for cophylogenetic signals between potential Deltocephalinae leafhopper vectors and their associated plants. We observed incongruence between plant and insect phylogenies. Many leafhopper species, including presumed grass specialists, fed on distantly related plant lineages; 66% of sampled leafhoppers fed on plants from at least two different orders. By disentangling phytoplasma–leafhopper–plant interactions, we identify locations at risk of phytoplasma disease outbreaks. Furthermore, the observed wide diet breadth raises questions about how phytoplasma infection may manipulate the feeding preference of their insect host and helps fill the gaps in understanding the ecology and diversification of the tripartite association. Full article

This study evaluates the potential of using pond water eDNA to reflect the surrounding terrestrial plant communities, aiming to develop a sustainable, large-scale, and long-term monitoring method for plant diversity in forest ecosystems. Water samples were collected four times from two ponds with different vegetation types during the late spring to autumn seasons in Japan. eDNA was extracted from dissolved particles fractionated by sequential filtration through pore sizes of 200 µm, 5 µm, and 0.45 µm, followed by high-throughput amplicon sequencing targeting the plant rbcL gene. By comparing field surveys with the eDNA data, we identified 79% and 63% of plant families and genera, respectively, suggesting that pond water eDNA may reflect the surrounding terrestrial plant ecosystem. Additionally, different trends were observed in the seasonal variation of plant taxa and their composition detected in eDNA, based on particle size. This study highlights the potential of pond water eDNA to provide valuable insights into forest plant richness and seasonal dynamics, offering a novel approach for ecological monitoring. Full article

Background: Xi Junecry (Pinellia ternata), a perennial herb of the Araceae family, is indigenous to Xinxian County, Henan Province, China, and is regarded as a premium variety among similar medicinal materials. However, the lack of comprehensive genetic information on Xi Junecry germplasm resources has constrained the cultivation and identification of high-quality varieties. Methods: In this study, six chloroplast genomes of Xi Junecry were assembled and annotated using high-throughput sequencing. Subsequently, comparative analyses were conducted, and a phylogenetic tree was constructed. Results: The six Xi Junecry chloroplast genome lengths ranged from 157,456 to 158,406 bp, and the GC content was between 36.0% and 36.2%. A total of 265 single nucleotide polymorphism sites were identified across the six genomes, with a whole-genome nucleotide diversity (Pi) value of 0.00084. Among the four genomic regions, the small single-copy region exhibited the highest Pi, followed by the large single-copy region, while the inverted repeat region showed the lowest. Nucleotide polymorphism in coding regions was significantly lower than in non-coding regions. Nine hypervariable regions were identified, as follows: ndhE-ndhG, trnN-GUU-ndhF, trnS-GCU-trnG-UCC, atpB-rbcL, psaI, accD-ycf4, psbE-petL, psaC-ndhE, and psbI-trnG-UCC. Positive selection sites were detected in the accD and rbcL genes. Phylogenetic analysis clustered the six Xi Junecry samples into a distinct clade, separating them from other regional Pinellia samples. Conclusions: These findings elucidate the genetic variation levels in Xi Junecry and provide high-variability loci for population history inference, genetic diversity assessment, species domestication studies, and new cultivar development. Full article

The Shangqiu Yellow River Ancient Course National Forest Park, the only national forest park in China created entirely from man-made forests, plays a critical role in ecological conservation. Our research employed plot surveys and quantitative ecological methods, including a diversity index analysis and importance value analysis, to investigate the diversity of arboreal, shrub, and herbaceous plants. This study revealed the composition and distribution of plant communities and analyzed invasive species. It identified dominant plant families, genera, and species and evaluated the types, distribution, and characteristics of invasive plants. We documented 70 families, 177 genera, and 254 species, highlighting that local environmental factors and human activities significantly affect the composition and distribution of plant communities. The presence of 29 invasive plant species poses a risk to the ecosystem. We constructed a phylogenetic tree of the plant community based on rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit) gene sequences, revealing the evolutionary relationships among species, and evaluated the community’s stability using the NTI (nearest taxon index) and NRI (net relatedness index). This research aims to provide a scientific foundation for conserving plant diversity and promoting sustainable development, and it can inform ecological protection and biodiversity studies in similar regions. 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

N6–methyladenosine (m⁶A) is a widespread post–transcriptional modification in eukaryotic mRNAs. Proteins with the YTH structural domain act as m⁶A–binding proteins by recognizing the m⁶A modification and regulating mRNA through this recognition. In this study, SlYTHDF2, a prototypical m⁶A –binding protein gene in the YTH family was expressed in various tissues, and subcellular localization analyses indicated that the SlYTHDF2 protein was localized in the nucleus and cytoplasm. SlYTHDF2 knockout lines were obtained using CRISPR/Cas9 technology and showed the senesced leaves prematurely increased endogenous ABA accumulation compared with the wild type. Moreover, we found that dark promoted leaf senescence in SlYTHDF2 knockout lines and exogenous ABA further accelerated leaf senescence under dark conditions. The qRT–PCR analysis revealed significant alterations in the expression of genes associated with the ABA pathway. Relative to the wild type, the CR–slythdf2 plants exhibited reduced levels of photosynthetic pigments, higher accumulation of reactive oxygen species, and increased damage to cell membranes. Additionally, we discovered that SlYTHDF2 interacts with the chloroplast–binding protein SlRBCS3 through yeast two–hybrid and BiFC experiments. Overall, our data suggest the important role of SlYTHDF2 in regulating tomato leaf senescence. Full article

Chlorellacean members are common in aquatic or subaerial habitats, and many of them have significant economic value. Taxonomic reports and organelle genome data for the Nannochloris clade, an important subgroup within this family, are limited, hindering the understanding and exploitation of this clade. In this study, a fusiform-celled strain, FACHB-3607, was isolated from a pond in China. Through examination of morphological characteristics and phylogenetic analyses of rbcL, 18S rDNA, and ITS, it was identified as a new species within the Nannochloris clade, named Koliella bifissiva sp. nov. In addition, this study provided a first insight into the organellar genomes of the genus Koliella. The K. bifissiva chloroplast had a 99.8 kb genome, and the mitochondrion had a 40.8 kb genome, which are moderate sizes within the Nannochloris clade. Phylogenomic analysis showed that K. bifissiva is most closely related to Nannochloris sp. “desiccata”, followed by Marvania. In contrast, Picochlorum was the most distantly related species. The organelle genomes of the Nannochloris clade display dynamic evolution, reflected in variations in genome size, gene content and order, and selection pressure. This research enhances our knowledge of species diversity and evolutionary history in the Nannochloris clade. Full article

Rubisco small subunit (RbcS), a core component with crucial effects on the structure and kinetic properties of the Rubisco enzyme, plays an important role in response to plant growth, development, and various stresses. Although Rbcs genes have been characterized in many plants, their muti-functions in soybeans remain elusive. In this study, a total of 11 GmRbcS genes were identified and subsequently divided into three subgroups based on a phylogenetic relationship. The evolutionary analysis revealed that whole-genome duplication has a profound effect on GmRbcSs. The cis-acting elements responsive to plant hormones, development, and stress-related were widely found in the promoter region. Expression patterns based on the RT-qPCR assay exhibited that GmRbcS genes are expressed in multiple tissues, and notably Glyma.19G046600 (GmRbcS8) exhibited the highest expression level compared to other members, especially in leaves. Moreover, differential expressions of GmRbcS genes were found to be significantly regulated by exogenous plant hormones, demonstrating their potential functions in diverse biology processes. Finally, the function of GmRbcS8 in enhancing soybean resistance to soybean mosaic virus (SMV) was further determined through the virus-induced gene silencing (VIGS) assay. All these findings establish a strong basis for further elucidating the biological functions of RbcS genes in soybeans. Full article

Bulbophyllum is one of the largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae, including species of ornamental and medical importance. The lack of knowledge regarding the characterization of Bulbophyllum chloroplast (cp) genomes has imposed current limitations on our study. Here, we report the complete cp genomes of seven Bulbophyllum species, including B. ambrosia, B. crassipes, B. farreri, B. hamatum, B. shanicum, B. triste, and B. violaceolabellum, and compared with related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. A total of 28 Bulbophyllum cp genomes exhibit typical quadripartite structures with lengths ranging from 145,092 bp to 165,812 bp and a GC content of 36.60% to 38.04%. Each genome contained 125–132 genes, encompassing 74–86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The genome arrangements, gene contents, and length were similar, with differences observed in ndh gene composition. It is worth noting that there were exogenous fragment insertions in the IR regions of B. crassipes. A total of 18–49 long repeats and 38–80 simple sequence repeats (SSRs) were detected and the single nucleotide (A/T) was dominant in Bulbophyllum cp genomes, with an obvious A/T preference. An analysis of relative synonymous codon usage (RSCU) revealed that leucine (Leu) was the most frequently used codon, while cysteine (Cys) was the least used. Six highly variable regions (rpl32-trnL^UAG > trnT^UGU-trnL^UAA > trnF^GAA-ndhJ > rps15-ycf1 > rbcL-accD > psbI-trnS^GCU) and five coding sequences (ycf1 > rps12 > matK > psbK > rps15) were identified as potential DNA markers based on nucleotide diversity. Additionally, 31,641 molecular diagnostic characters (MDCs) were identified in complete cp genomes. A phylogenetic analysis based on the complete cp genome sequences and 68 protein-coding genes strongly supported that 28 Bulbophyllum species can be divided into four branches, sects. Brachyantha, Cirrhopetalum, and Leopardinae, defined by morphology, were non-monophyly. Our results enriched the genetic resources of Bulbophyllum, providing valuable information to illustrate the complicated taxonomy, phylogeny, and evolution process of the genus. Full article

Cattle can be severely infected with the tick-borne protozoa Babesia bovis, giving rise to serious economic losses. Invasion of the host’s RBCs by the parasite merozoite/sporozoites depends largely on the MSA (merozoite surface antigens) gene family, which comprises various fragments, e.g., MSA-1, MSA-2a1, MSA-2a2, MSA-2b and MSA-2c, highlighting the importance of these antigens as vaccine candidates. However, experimental trials documented the failure of some developed MSA-based vaccines to fully protect animals from B. bovis infection. One reason for this failure may be related to the genetic structure of the parasite. In the present study, all MSA-sequenced B. bovis isolates on the GenBank were collected and subjected to various analyses to evaluate their genetic diversity and population structure. The analyses were conducted on 199 MSA-1, 24 MSA-2a1, 193 MSA-2b and 148 MSA-2c isolates from geographically diverse regions. All these fragments displayed high nucleotide and haplotype diversities, but the MSA-1 was the most hypervariable and had the lowest inter- and intra-population gene flow values. This fragment also displayed a strong positive selection when testing its isolates for the natural selection, which suggests the potential occurrence of more genetic variations. On the contrary, the MSA-2c was the most conserved in comparison to the other fragments, and displayed the highest inter- and intra-population gene flow values, which was evidenced by a significantly negative selection and negative neutrality indices (Fu’s Fs and Tajima’s D). The majority of the MSA-2c tested isolates had two conserved amino acid repeats, and earlier reports have found these repeats to be highly immunogenic, which underlines the importance of this fragment in developing vaccines against B. bovis. Results of the MSA-2a1 analyses were also promising, but many more MSA-2a1 sequenced isolates are required to validating this assumption. The genetic analyses conducted for the MSA-2b fragment displayed borderline values when compared to the other fragments. Full article

Potamogetonaceae are aquatic plants divided into six genera. The largest genus in the family is Potamogeton, which is morphologically diverse with many hybrids and polyploids. Potamogetonaceae plastomes were conserved in genome size (155,863 bp–156,669 bp), gene contents (113 genes in total, comprising 79 protein-coding genes and 30 tRNA and 4 rRNA genes), and GC content (36.5%). However, we detected a duplication of the trnH gene in the IR region of the Potamogeton crispus and P. maakianus plastomes. A comparative analysis of Alismatales indicated that the plastomes of Potamogetonaceae, Cymodaceae, and Ruppiaceae have experienced a 6-kb inversion of the rbcL-trnV region and the ndh complex has been lost in the Najas flexilis plastome. Five divergent hotspots (rps16-trnQ, atpF intron, rpoB-trnC, trnC-psbM, and ndhF-rpl32) were identified among the Potamogeton plastomes, which will be useful for species identification. Phylogenetic analyses showed that the family Potamogetonaceae is a well-defined with 100% bootstrap support and divided into two different clades, Potamogeton and Stuckenia. Compared to the nucleotide substitution rates among Alismatales, we found neutral selection in all plastid genes of Potamogeton species. Our results reveal the complete plastome sequences of Potamogeton species, and will be helpful for taxonomic identification, the elucidation of phylogenetic relationships, and the plastome structural analysis of aquatic plants. Full article