Swiss-Prot Database Research Articles

Homology Modelling and Molecular Docking Studies of Spike Protein in SARS-CoV-2

ABSTRACT: The COVID-19 pandemic, caused by SARS-CoV-2, has posed substantial global health challenges, highlighting the urgent need for effective antiviral treatments. This study utilizes homology and molecular docking to identify potential natural compound inhibitors targeting the SARS-CoV-2 spike protein. The spike protein sequence was sourced from the Swiss-Prot database and modeled using MODELLER 10.3, employing templates from the Protein Data Bank (PDB). The constructed model underwent validation via Ramachandran plot analysis and MolProbity scores, confirming its reliability for subsequent analyses. Virtual screening of database was performed using AutoDock Vina. Compounds exhibiting the highest binding affinities were subjected to MD simulations to evaluate their stability. Tetrandrine (L1) and Tubocurarine (L2) emerged as the top candidates, with Tetrandrine demonstrating the lowest binding energy and the best fit. The ADMET properties of these compounds were assessed using SwissADME, affirming their drug-like potential. Molecular dynamics simulations further substantiated the stability of the Tetrandrine-spike protein complex, revealing significant interactions. This study identifies Tetrandrine as a promising inhibitor of SARS-CoV-2, warranting further exploration for antiviral drug development.

Towards the Albino Mutant Gene in Malus × Domestica Borkh.

Albino mutation is among the most common phenomena that often causes a water imbalance and disturbs physiological functions in higher species of trees. Albinism frequently occurs in hybridized apples, but almost all seedlings die shortly after germination. In this study, a spontaneous albino mutant on Fuji apple trees was obtained. After bud grafting, new albino shoots with greenish-white leaves grew, although they were slender, small, and died easily. Resequencing analysis indicated that a total of 49.37 Gbp clean data of the albino mutant samples was obtained; its Q30 reached 91.43%, the average rate mapped was 93.69%, and genome coverage was 96.47% (at least one base cover). Comparisons of the sequences for the albino mutants revealed 4,817,412 single-nucleotide polymorphisms (SNPs), 721,688 insertion/deletion markers (InDels), and 43,072 structural variations (SVs). The genes with non-synonymous SNPs, InDels, and SVs in CDS were compared with KEGG, GO, COG, NR, and SwissProt databases, and a total of 5700 variant genes were identified. A total of 1377 mutant genes had the GO annotation information. Among these, 1520 mutant genes had the pathway annotation and took part in 123 pathways. A total of 1935 variant genes were functionally classified into 25 COG categories. Further research on these variants could help understand the molecular regulatory mechanism of the apple albino mutant. Similarly, variations in the homologous MdAPG1 (Albino or pale-green mutant 1) gene, which was located on Chromosome 11 and belonged to the S-adenosyl-L-methionine-dependent methyltransferases superfamily, may have led to the generation of this apple albino mutant.

A Comprehensive Transcriptomic and Proteomics Analysis of Candidate Secretory Proteins in Rose Grain Aphid, Metopolophium dirhodum (Walker).

The Rose grain aphid, a notable agricultural pest, releases saliva while feeding. Yet, there is a need for a comprehensive understanding of the specific identity and role of secretory proteins released during probing and feeding. Therefore, a combined transcriptomic and proteomic approach was employed in this study to identify putative secretory proteins. The transcriptomic sequencing result led to the assembly of 18,030 unigenes out of 31,344 transcripts. Among these, 705 potential secretory proteins were predicted and functionally annotated against publicly accessible protein databases. Notably, a substantial proportion of secretory genes (71.5%, 69.08%, and 60.85%) were predicted to encode known proteins in Nr, Pfam, and Swiss-Prot databases, respectively. Conversely, 27.37% and 0.99% of gene transcripts were predicted to encode known proteins with unspecified functions in the Nr and Swiss-Prot databases, respectively. Meanwhile, the proteomic analysis result identified, 15 salivary proteins. Interestingly, most salivary proteins (i.e., 60% of the proteins) showed close similarity to A. craccivora, while 46.67% showed close similarity to A. glycines, M. sacchari and S. flava. However, to verify the expression of these secretory genes and characterize the biological function of salivary proteins further investigation should be geared towards gene expression and functional analysis.

Transcriptome sequencing and SSR prediction of Clematis calyx based on SMRT sequencing platform

Clematis is an excellent vertical greening plant for garden viewing vines, with great ornamental and high medicinal value. To obtain transcriptome information and functional gene data for the Clematis calyx, this study utilized three biological replicates of the calyx from each of the three Clematis varieties: ‘Henryi’, ‘Polish spirit’, and ‘Mme Julia Correvon’ Single-molecule real-time sequencing technology was employed for full-length transcriptome sequencing. The study revealed that 21,673,173 non-chimeric sequences were identified through full-length transcriptome sequencing. After clustering, correction, and redundancy removal, 40,465 high-quality, full-length transcripts were obtained. Among these transcripts, there were 15,488 long non-coding RNA (lncRNA), 9,212 simple sequence repeats (SSR) sites, 1,247 transcription factors (TFs), 1,228 alternative splicing events, and 7,189 selectively polyadenylation sites predicted. In addition, 7,442 primer pairs were designed based on the SSR sites, covering 80.76% of the total SSR. 15 primer pairs were randomly selected for amplification, and 73.3% of them were successfully amplified. Transcript annotation results showed that 38,439, 38,094, 26,815, and 33,407 transcripts were annotated to the Nr, KEGG, KOG, and SwissProt databases, respectively. Among these, the KEGG database identified 137 metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and amino acid biosynthesis. 104 and 7 transcripts are involved in the flavonoid and anthocyanin metabolism pathways, respectively. The above results provide initial insights into the transcriptome information and functional characteristics of Clematis calyx. This critical data supports future research on marker primers for the color mechanism of Clematis calyx, the pathways and regulatory mechanisms of flavonoids and other products, as well as specific trait genes.

A Novel Method to Profile Transcripts Encoding SH2 Domains in the Patiria miniata Mature Egg Transcriptome.

The critical mechanism to restart zygote metabolism and prevent polyspermy during fertilization is the intracellular Ca2+ increase. All of the signaling molecules leading to the Ca2+ rise are not fully known in any species. In the sea star Patiria miniata, SFK1, SFK3, and PLCγ participate in this fertilization Ca2+ increase. These proteins share common regulatory features, including signaling via tyrosine phosphorylation and their SH2 domains. In this study, we explore two different bioinformatic strategies to identify transcripts in the Patiria miniata mature egg transcriptome (Accession PRJNA398668) that code for proteins possessing an SH2 domain. The first identified the longest open reading frame for each transcript and then utilized similarity searching tools to provide identities for each transcript. The second, novel, method involved a six-frame translation of the entire transcriptome to identify SH2 domain-containing proteins. The identified transcripts were aligned against the NCBI non-redundant database and the SwissProt database. Eighty-two transcripts that encoded SH2 domains were identified. Of these, 33 were only found using the novel method. This work furthers research into egg activation by providing possible target proteins for future experiments and a novel method for identifying specific proteins of interest within a de novo transcriptome.

SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study.

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence of systematic pan-genomic analyses. To address these gaps, we developed the Solanaceae Information Resource (SoIR, https://soir.bio2db.com), a comprehensive genomics database for the Solanaceae family. SoIR integrates genomic data from 81 species and transcriptomic data from 41 species, encompassing a total of 3908408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases. The resource also includes 3437115 CRISPR guide sequences, 212395 transcription factorsand 19086 genes associated with methylation modification. In addition to species-specific analyses, SoIR provides extensive bioinformatics tools for investigating gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes. With advanced tools such as Blast, Synteny and Sequence Alignment, the platform provides users with interactive and intuitive visualizations for conducting cross-species comparative genomics. As the first comprehensive pan-genomic resource for the entire Solanaceae family, SoIR facilitates in-depth cross-species analysis, supporting global research initiatives in plant evolution, functional genomics and crop improvement.

CUDASW++4.0: ultra-fast GPU-based Smith–Waterman protein sequence database search

BackgroundThe maximal sensitivity for local pairwise alignment makes the Smith-Waterman algorithm a popular choice for protein sequence database search. However, its quadratic time complexity makes it compute-intensive. Unfortunately, current state-of-the-art software tools are not able to leverage the massively parallel processing capabilities of modern GPUs with close-to-peak performance. This motivates the need for more efficient implementations.ResultsCUDASW++4.0 is a fast software tool for scanning protein sequence databases with the Smith-Waterman algorithm on CUDA-enabled GPUs. Our approach achieves high efficiency for dynamic programming-based alignment computation by minimizing memory accesses and instructions. We provide both efficient matrix tiling, and sequence database partitioning schemes, and exploit next generation floating point arithmetic and novel DPX instructions. This leads to close-to-peak performance on modern GPU generations (Ampere, Ada, Hopper) with throughput rates of up to 1.94 TCUPS, 5.01 TCUPS, 5.71 TCUPS on an A100, L40S, and H100, respectively. Evaluation on the Swiss-Prot, UniRef50, and TrEMBL databases shows that CUDASW++4.0 gains over an order-of-magnitude performance improvements over previous GPU-based approaches (CUDASW++3.0, ADEPT, SW#DB). In addition, our algorithm demonstrates significant speedups over top-performing CPU-based tools (BLASTP, SWIPE, SWIMM2.0), can exploit multi-GPU nodes with linear scaling, and features an impressive energy efficiency of up to 15.7 GCUPS/Watt.ConclusionCUDASW++4.0 changes the standing of GPUs in protein sequence database search with Smith-Waterman alignment by providing close-to-peak performance on modern GPUs. It is freely available at https://github.com/asbschmidt/CUDASW4.

First De Novo genome assembly and characterization of Gaultheria prostrata.

Gaultheria Kalm ex L. (Ericaceae), a type of evergreen shrub, known as a natural source of methyl salicylate, possesses rich germplasm resources, strong habitat adaptability, significant ornamental value, and noteworthy pharmacological activities. However, due to the paucity of whole genomic information, genetically deep research in these areas remains limited. Consequently, we intend to obtain genome data through high-throughput sequencing, gene annotation, flow cytometry, transcription factors prediction and genetic marker analysis for a representative species of this genus, with Gaultheria prostrata selected for our study. In this study, we preliminarily obtained the genome of G. prostrata through next-generation sequencing methods. Utilizing 47.94 Gb of high-quality sequence data (108.95× coverage), assembled into 114,436 scaffolds, with an N50 length of 33,667 bp. The genome size assembled by SOAPdenovo, approximately 417 Mb, corresponded closely to predictions by flow cytometry (440 Mb) and k-mer analysis (447 Mb). The genome integrity was evaluated using BUSCO with 91%. The heterozygosity ratio was 0.159%, the GC content was 38.85%, and the repetitive regions encompassed over 34.6% of the genome. A total of 26,497 protein-coding genes have been predicted and annotated across Nr, Swissprot, GO, KEGG, and Pfam databases. Among these, 14,377 and 2,387 genes received functional annotation in Nr and Swissprot, respectively; 21,895, 24,424, and 22,330 genes were similarly annotated in GO, KEGG, and Pfam. Moreover, A total of 279,785 SSRs were identified and 345,270 primers for these SSRs were designed. Within the various nucleotide types of SSRs, AG/CT and AAG/CTT constituted the predominant dinucleotide and trinucleotide repeat types in G. prostrata. In addition, 1,395 transcription factors (TFs) from 75 TF families, 462 transcription regulators (TRs) from 33 TR families and 840 protein kinase (PKs) from 118 PK families were identified in this genome. We also performed phylogenetic analyses of G. prostrata and related species, including estimation of divergence times and expansion and contraction analyses, followed by positive selection analyses of orthologous gene pairs of G. prostrata and its close relative Vaccinium corymbosum. These results provide a reference for in-depth study of genus Gaultheria, contributing to future functional and comparative genomics analyses and providing supporting data for the development of molecular markers.

Transcriptome Profile and Gene Expression During Different Ovarian Maturation Stages of Macrobrachium rosenbergii (De Man, 1879).

Macrobrachium rosenbergii, or giant river prawn, is the most economically crucial cultured freshwater crustacean. A predominant challenge in developing crustacean aquaculture is reproduction management, particularly ovary maturation, where identifying regulative mechanisms at the molecular level is critical. Ovary is the primary tissue for studying gene and protein expressions involved in crustacean growth and reproduction. Despite significant interest in M. rosenbergii, its gene discovery has been at a relatively small scale compared to other genera. In this study, comprehensive transcriptomic sequencing data for different maturation stages of the ovary of M. rosenbergii were observed. The 20 female M. rosenbergii samples evaluated were categorised into four maturation stages, 1 to 4. A total of 817,793,14, 841,670,70, 914,248,78 and 878,085,88 raw reads were obtained from stages 1, 2, 3 and 4, respectively. The assembled unique sequences (unigenes) post-clustering (n = 98013) was 131,093,546 bp with an average size of 1,338 bp. The BLASTX unigene search against National Centre for Biotechnology Information (NCBI), non-redundant (NR), nucleotide sequence (NT), Kyoto Encyclopaedia of Genes and Genomes Orthology (KO), Swiss-Prot, Protein Family (PFAM), Gene Ontology (GO), and euKaryotic Orthologous Groups (KOG) databases yielded 27,680 (28.24%), 7,449 (7.59%), 13,026 (13.29%), 22,606 (23.06%), 29,907 (30.51%), 30,025 (30.63%) and 14,368 (14.65%) significant matches, respectively, totalling to 37,338 annotated unigenes (38.09%). The differentially expressed genes (DEG) analysis conducted in this study led to identifying cyclin B, insulin receptor (IR), oestrogen sulfotransferase (ESULT) and vitellogenin (Vg), which are critical in ovarian maturation. Nevertheless, some M. rosenbergii ovarian maturation-related genes, such as small ubiquitin-like modifier (SUMO)-activating enzyme subunit 1, E3 ubiquitin-protein ligase RNF25, and neuroparsin, were first identified in this study. The data obtained in the present study could considerably contribute to understanding the gene expression and genome structure in M. rosenbergii ovaries throughout its developmental stage.

PRODUCTION OF RECOMBINANT SALMONELLA ABORTUS EQUI PROTEINS

The cause of mare abortions of salmonellosis etiology is pathogen Salmonella abortusequi. The economic damage caused by this infection is due to the loss of reproductive capacity of the sires, litter failure, reduced productivity and veterinary costs. High level of infection of horses is registered in many countries, including Kazakhstan. The main method of diagnosis is bacteriological, but its disadvantages are low sensitivity and duration of results. The OIE recommends the use of PCR and ELISA for diagnosis of infection, however, due to the high cost of test systems, the use of PCR in veterinary laboratories is not always justified, and the effectiveness of the ELISA method depends largely on the structure and purity of the antigen. Currently, genetic engineering methods make it possible to obtain recombinant antigens of animal pathogens containing separate proteins, which excludes the occurrence of nonspecific reactions. These antigens can be used in tests for serological diagnostics, immunization of laboratory animals, and in the development of vaccines. According to literature data, it is known that diagnostically significant antigens in bacteria of the genus Salmonella are outer membrane proteins. Therefore, the outer membrane protein OmpX of S. abortusequi, which has high immunogenicity and conservativeness was selected as a target. The aim of this work is to obtain recombinant OmpX antigens of S. abortusequi and study their properties. As a result, E. coli strains producing recombinant OmpX protein of S. abortusequi were created. The synthesized genes were cloned into expression vectors and transformed into competent E. coli BL21 cells. The rOmpX of Salmonella abortusequi was produced and purified; electrophoretic analysis showed the purity of the preparation with a molecular mass of 23 kDa. The recombinant protein was analyzed by LC/MC-MC spectrometry, and peptides containing QTTDYPTYKHDTSDYGFSYGAGLQFN amino acid sequences were identified. A search of the peptide spectrum in the SwissProt database showed that they corresponded to the OmpX protein of Salmonella abortusequi. To determine the quality of protein refolding and the conservation of antigenic epitopes of the protein, Western blot was used with control positive sera that specifically reacted with a protein of molecular mass 23kDa. The resulting recombinant OmpX protein was then used as an antigen in an indirect ELISA to detect antibodies in serum samples from aborted mares. The results of n-ELISA showed the presence of antibodies in serum at a titer of 1:1600 (+26.6; - 21.1). Thus, rOmpX of S. abortusequiwith a molecular mass of 23 kDa was obtained and its main properties were studied. The correctness of protein refolding was confirmed by Western blot and ELISA with positive control sera. The specificity of recombinant proteins was proved by interaction with positive serum samples of horses from unfavorable farms. The obtained recombinant antigens can be used in the creation of tests for the diagnosis of salmonellosis abortion of horses in the Republic of Kazakhstan. WPM с добавлением БАП 1,0 мг/л, ИМК 0,1 мг/л, ГК 0,2 мг/л, где было в среднем образовано 7,36 микропобегов на один эксплант.

Full-Length Transcriptome Construction and Systematic Characterization of Virulence Factor-Associated Isoforms in Vairimorpha (Nosema) Ceranae.

Vairimorpha (Nosema) ceranae is a single-cellular fungus that obligately infects the midgut epithelial cells of adult honeybees, causing bee microsporidiosis and jeopardizing bee health and production. This work aims to construct the full-length transcriptome of V. ceranae and conduct a relevant investigation using PacBio single-molecule real-time (SMRT) sequencing technology. Following PacBio SMRT sequencing, 41,950 circular consensus (CCS) were generated, and 25,068 full-length non-chimeric (FLNC) reads were then detected. After polishing, 4387 high-quality, full-length transcripts were gained. There are 778, 2083, 1202, 1559, 1457, 1232, 1702, and 3896 full-length transcripts that could be annotated to COG, GO, KEGG, KOG, Pfam, Swiss-Prot, eggNOG, and Nr databases, respectively. Additionally, 11 alternative splicing (AS) events occurred in 6 genes were identified, including 1 alternative 5' splice-site and 10 intron retention. The structures of 225 annotated genes in the V. ceranae reference genome were optimized, of which 29 genes were extended at both 5' UTR and 3' UTR, while 90 and 106 genes were, respectively, extended at the 5' UTR as well as 3' UTR. Furthermore, a total of 29 high-confidence lncRNAs were obtained, including 12 sense-lncRNAs, 10 lincRNAs, and 7 antisense-lncRNAs. Taken together, the high-quality, full-length transcriptome of V. ceranae was constructed and annotated, the structures of annotated genes in the V. ceranae reference genome were improved, and abundant new genes, transcripts, and lncRNAs were discovered. Findings from this current work offer a valuable resource and a crucial foundation for molecular and omics research on V. ceranae.

Sex Differences in Antennal Transcriptome of Hyphantria cunea and Analysis of Odorant Receptor Expression Profiles.

Insects rely on olfaction for mating, finding oviposition sites, and locating hosts. Hyphantria cunea is a serious pest that severely damages forests. Differential expression analysis of olfactory-related genes between males and females is the basis for elucidating the functions of olfactory-related proteins in H. cunea. In this study, Illumina HiSeqTM 4000 high-throughput sequencing technology was used to perform transcriptome sequencing of the antennal tissues of adult male and female H. cunea. Functional annotation was conducted using the NR, Swiss-Prot, KOG, KEGG, and GO databases, and the results showed that the antennal transcriptome of adult H. cunea contained 50,158 unigenes. Differential expression analysis identified 3923 genes that were significantly differentially expressed between male and female antennae. A total of 221 olfactory-related genes were annotated, and 96 sex-biased genes were identified, including 13 odorant receptors (ORs), 48 odorant binding proteins (OBPs), 7 chemosensory proteins (CSPs), 10 ionotropic receptors (IRs), 10 sensory neuron membrane proteins (SNMPs), 2 gustatory receptors (GRs), and 6 odorant-degrading enzymes (ODEs), indicating that there were differences in olfaction between male and female H. cunea. Quantitative real-time PCR was used to verify the expression levels of 21 putative general odorant receptor genes in male and female antennae. HcunOR4 and HcunOR5 showed female-biased expression; HcunOR48, HcunOR49 and HcunOR50 showed male-biased expression. The results were consistent with the transcriptome differential analysis. The screening of male-biased odorant receptor genes might provide a theoretical basis for the functional characterization of odorant receptors for recognizing sex pheromones in H. cunea.

Characterization, whole-genome sequence analysis, and protease production of a new thermophilic Bacillus licheniformis strain isolated from Debagh hot spring, Algeria.

A new thermophilic strain, designated as Bacillus sp. LMB3902, was isolated from Hammam Debagh, the hottest spring in Algeria (up to 98°C). This isolate showed high protease production in skim milk media at 55°C and exhibited significant specific protease activity by using azocasein as a substrate (157.50 U/mg). Through conventional methods, chemotaxonomic characteristics, 16S rRNA gene sequencing, and comparative genomic analysis with the closely related strain Bacillus licheniformis DSM 13 (ATCC 14580T), the isolate Bacillus sp. LMB3902 was identified as a potentially new strain of Bacillus licheniformis. In addition, the gene functions of Bacillus sp. LMB3902 strain were predicted using the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups, Non-Redundant Protein Sequence Database, Swiss-Prot, and Pfam databases. The results showed that the genome size of Bacillus sp. LMB3902 was 4.279.557bp, with an average GC content of 46%. The genome contained 4.760 predicted genes, including 8 rRNAs, 78 tRNAs, and 24 sRNAs. A total of 235 protease genes were annotated including 50 proteases with transmembrane helix structures and eight secreted proteases with signal peptides. Additionally, the majority of secondary metabolites found by antiSMASH platform showed low similarity to identified natural products, such as fengicin (53%), lichenysin (57%), and surfactin (34%), suggesting that this strain may encode for novel uncharacterized natural products which can be useful for biotechnological applications. This study is the first report that describes the complete genome sequence, taxono-genomics, and gene annotation as well as protease production of the Bacillus genus in this hydrothermal vent.

Mitochondrial proteome analysis reveals that an augmented cytochrome c oxidase assembly and activity potentiates respiratory capacity in sarcoma

Mitochondrial oxidative phosphorylation (OXPHOS) is an obligatory process in sarcoma. Despite that, the metabolic programming of sarcoma mitochondria is still unknown. To obtain a comprehensive metabolic insight of mitochondria, we developed a mouse fibrosarcoma model by injecting 3-methylcholanthrene and compared mitochondrial proteomes between sarcoma and its contralateral normal muscle using mass spectrometry. Our study identified ∼449 proteins listed in the SwissProt databases, and all the data sets are available via ProteomeXchange with the identifier PXD044903. In sarcoma, 49 mitochondrial proteins were found differentially expressed, including 36 proteins up-regulated and 13 proteins down-regulated, with the significance of p-value <0.05 and the log2[fold change] > 1 and < −1 as compared to normal muscle. Our data revealed that various anaplerotic reactions actively replenish the TCA cycle in sarcoma. The comparative expression profile and Western blotting analysis of OXPHOS subunits showed that complex-IV subunits, MT-CO3 and COX6A1, were significantly up-regulated in sarcoma vs. normal muscle. Further, biochemical and physiological assays confirmed enhanced complex-IV specific enzymatic and supercomplex activities with a concomitant increase of oxygen consumption rate in sarcoma mitochondria compared to normal muscle. Validation with human post-operative sarcoma tissues also confirms an increased MT-CO3 expression compared to normal tissue counterparts. Thus, our data comprehensively analyses the mitochondrial proteome and identifies augmented complex-IV assembly and activity in sarcoma.

Establishment of Novel Simple Sequence Repeat (SSR) Markers from Chimonanthus praecox Transcriptome Data and Their Application in the Identification of Varieties.

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag-simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits.

ToxTeller: Predicting Peptide Toxicity Using Four Different Machine Learning Approaches.

Examining the toxicity of peptides is essential for therapeutic peptide-based drug design. Machine learning approaches are frequently used to develop highly accurate predictors for peptide toxicity prediction. In this paper, we present ToxTeller, which provides four predictors using logistic regression, support vector machines, random forests, and XGBoost, respectively. For prediction model development, we construct a data set of toxic and nontoxic peptides from SwissProt and ConoServer databases with existence evidence levels checked. We also fully utilize the protein annotation in SwissProt to collect more toxic peptides than using keyword search alone. From this data set, we construct an independent test data set that shares at most 40% sequence similarity within itself and with the training data set. From a quite comprehensive list of 28 feature combinations, we conduct 10-fold cross-validation on the training data set to determine the optimized feature combination for model development. ToxTeller's performance is evaluated and compared with existing predictors on the independent test data set. Since toxic peptides must be avoided for drug design, we analyze strategies for reducing false-negative predictions of toxic peptides and suggest selecting models by top sensitivity instead of the widely used Matthews correlation coefficient, and also suggest using a meta-predictor approach with multiple predictors.

Chromosome-Scale Genome Assembly Provides Insights into Fresh Pine Wood Decay Strategies of the Wolfiporia hoelen

The sclerotia of Wolfiporia hoelen (Fr.) Y.C. Dai &amp; V. Papp is an important traditional Chinese medicine with diverse pharmacological properties. This study utilized a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing to generate a high-quality chromosome-level genome assembly of a W. hoelen strain Minling A5. There were 112 contigs in the genome, with 62.95 Mb in total length and 4.21 Mb in length for the contig N50. The average GC content was 51.89%. Based on Hi-C data, we corrected the CCS data and scaffolded them into 14 pseudo-chromosomes. The genome contained 44.37% repetitive sequences and 12,670 protein-coding genes, 86.53% (10,963) of which could be functionally annotated in at least one of the KOG, GO, Pfam, Swissprot, TrEMBL, NR, and KEGG databases. In addition, 240 transfer RNAs, 97 ribosomal RNAs, and 103 other non-coding RNAs were identified in the W. hoelen genome. A total of 755 pseudogenes were also identified, with an average length of 2665.51 bp. Further, there were 398, 100, 2837, 519, and 2068 genes annotated by CAZymes, TCDB, PHI, P450, and DFVF databases, respectively. One notable attribute of W. hoelen is its capacity to thrive in a substrate of fresh pine sawdust. Through an analysis of the growth on various pure wood sawdust culture media, we found that the growth of W. hoelen and Sparassis latifolia on pine sawdust was similar to that on broad-leaved wood sawdust, while the growth of Pleurotus ostreatus, P. eryngii, and Cyclocybe aegerita was slower than that on broad-leaved wood sawdust. By the functional annotation analysis of orthogroups in these five mushroom-forming fungi, it was determined that 645 orthogroups were specifically common in W. hoelen and S. latifolia. The genes in these specific orthogroups were significantly enriched in 12 pathways, including steroid biosynthesis, biosynthesis of antibiotics, and tyrosine metabolism. The high-quality genome and comparative genome analysis results significantly contribute to advancing our foundational knowledge of W. hoelen biology, while also offering valuable insights for the development of innovative biotechnological approaches aimed at enhancing the efficient and sustainable utilization of Pinus.

Genome- and Toxicology-Based Safety Assessment of Probiotic Akkermansia muciniphila ONE Isolated from Humans.

In this study, the genome of Akkermansia muciniphila ONE (designated AKK ONE) was sequenced, assembled, and analyzed. In addition, the safety of this strain was further evaluated by toxicological studies. The results showed that the AKK ONE genome is contained on a single chromosome with a total length of 2,817,524 bp and an average GC content of 55.48%. In total, 2411, 1131, 1168, 1745, and 1402 genes were annotated to the NR, GO, KEGG, COG, and SwissProt database, respectively. Potential resistance genes, adeF, tetW, ANT(3″)-IIa, and aadA1 were detected. AKK ONE was sensitive to ampicillin, ceftriaxone, cefotaxime, meropenem, tetracycline, and chloramphenicol and resistant to moxifloxacin. No potential virulence-related genes were detected. The PathogenFinder database analysis showed that AKK ONE was a non-potential human pathogen. This strain had good gastroenteric fluid tolerance and a weak ability to colonize the gut. No test item-related adverse effects were observed in the acute and subchronic toxicity test. AKK ONE did not display mutagenic activity either. This strain did not change the hematological and clinical biochemical parameters of mice. The weights of the organs were not affected by AKK ONE treatment. These results support that AKK ONE is safe for use as a probiotic at a dose of 8.28 × 109 CFU/kg bw/day.

Distinct signatures of gut microbiota and metabolites in primary biliary cholangitis with poor biochemical response after ursodeoxycholic acid treatment

BackgroundAbout 1/3 of primary biliary cholangitis (PBC) patients suffered from poor response worldwide. And these patients present intestinal disturbances. We aimed to identify signatures of microbiota and metabolites in PBC patients with poor response, comparing to patients with response.MethodsThis study enrolled 25 subjects (14 PBC patients with response and 11 PBC patients with poor response). Metatranscriptomics and metabolomics analysis were carried out on their fecal.ResultsPBC patients with poor response had significant differences in the composition of bacteria, characterized by decreased Gemmiger etc. and increased Ruminococcus etc. The differential microbiota functions characterized by decreased abundance of elongation factor Tu and elongation factor G base on the KO database, as well as decreased abundance of Replicase large subunit etc. based on the SWISS-PROT database. PBC with poor response also had significant differences in 17 kinds of bacterial metabolites, characterized by decreased level of metabolites vital in bile acids metabolism pathway (L-Cysteine etc.) and the all-trans-Retinoic acid, a kind of immune related metabolite. The altered microbiota was associated with the differential expressed metabolites and clinical liver function indicators. 1 bacterial genera, 2 bacterial species and 9 metabolites simultaneously discriminated PBC with poor response from PBC with response with high accuracy.ConclusionPBC patients with poor response exhibit unique changes in microbiota and metabolite. Gut microbiota and metabolite-based algorithms could be used as additional tools for differential prediction of PBC with poor prognosis.

Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing.

A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The genome of the B. cereus SCL10 strain was sequenced and assembled, revealing a size of 4,979,182 bp and 5167 coding genes. The genes involved in biological functions were annotated by using the GO, COG, KEGG, NR, and Swiss-Prot databases. The results showed that genes related to alkyl hydroperoxide reductase (ahpC, ahpF), DNA-binding proteins from starved cells (dps), spore and biofilm formation (spoVG, spo0A, gerP), cold shock-like protein (cspC, cspE), ATP-dependent chaperone (clpB), and photolyase, small, acid-soluble spore protein (SASP) and DNA repair protein (recA, radD) could explain the stress resistance. These findings suggest that antioxidant activity, sporulation, biofilm formation, and DNA protection may be considered as the main resistance mechanisms under exposure to radiation in the B. cereus SCL10 strain.