Evolutionary Relationships Research Articles

Genome-wide identification of the endonuclease family genes implicates potential roles of TaENDO23 in drought-stressed response and grain development in wheat

BackgroundEndonucleases play a crucial role in plant growth and stress response by breaking down nuclear DNA. However, the specific members and biological functions of the endonuclease encoding genes in wheat remain to be determined.ResultsIn this study, we identified a total of 26 TaENDO family genes at the wheat genome-wide level. These genes were located on chromosomes 2 A, 2B, 2D, 3 A, 3B, and 3D and classified into four groups, each sharing similar gene structures and conserved motifs. Furthermore, we identified diverse stress-response and growth-related cis-elements in the promoter of TaENDO genes, which were broadly expressed in different organs, and several TaENDO genes were significantly induced under drought and salt stresses. We further examined the biological function of TaENDO23 gene since it was rapidly induced under drought stress and exhibited high expression in spikes and grains. Subcellular localization analysis revealed that TaENDO23 was localized in the cytoplasm of wheat protoplasts. qRT-PCR results indicated that the expression of TaENDO23 increased under PEG6000 and abscisic acid treatments, but decreased under NaCl treatment. TaENDO23 mainly expressed in leaves and spikes. A kompetitive allele-specific PCR (KASP) marker was developed to identify single nucleotide polymorphisms in TaENDO23 gene in 256 wheat accessions. The alleles with TaENDO23-HapI haplotypes had higher grain weight and size compared to TaENDO23-HapII. The geographical and annual frequency distributions of the two TaENDO23 haplotypes revealed that the elite haplotype TaENDO23-HapI was positively selected in the wheat breeding process.ConclusionWe systematically analyzed the evolutionary relationships, gene structure characteristics, and expression patterns of TaENDO genes in wheat. The expression of TaENDO23, in particular, was induced under drought stress, mainly expressed in the leaves and grains. The KASP marker of TaENDO23 gene successfully distinguished between the wheat accessions, revealing TaENDO23-HapI as the elite haplotype associated with improved grain weight and size. These findings provide insights into the evolution and characteristics of TaENDO genes at the genome-wide level in wheat, laying the foundation for further biological analysis of TaENDO23 gene, especially in response to drought stress and grain development.

Gene expression analysis of Aquaporin genes in ruminants during growth phase in response to heat stress

Aquaporins (AQPs) are trans-membrane protein involved in water transport and different cellular functions such as cell adhesion, signalling and proliferation. These membrane proteins are essential for key physiological functions such as organ development, osmoregulation, tissue regeneration and metabolism. The regulation of AQP5 gene expression in ruminants during growth phase has not been analysed in-vivo. Therefore, the gene expression pattern was analysed in Jamunapari goats during 3 months to 12 month of age and adult age group in response to heat stress. The genotyping of the AQP5 gene was carried out by High-Resolution Melting (HRM) in four different goat breeds, which indicated four distinct genotypes in the population. The nucleotide diversity for the AQP5 gene ranged from 0.315 and 0.524 across the breeds. Additionally, a close evolutionary relationship between AQP5 and the HSP70 gene was observed, indicating a shared pathway for heat stress regulation. The m-RNA expression level of AQP5 at 3, 9, 12 month and adult age group exhibited 47.24, 1140, 43.17 and 12.55-fold higher expression than control. The m-RNA expression level of the AQP5 gene was up-regulated and significantly higher (P < 0.05) at 9-month age as compared to the other age groups. Heat stress phenotypes were classified based on respiration rate and heart rate, and the m-RNA expression of AQP5 was higher in heat stress-susceptible (HSS) individuals than heat stress-tolerant (HST) individuals at 3, 9, and 12 months of age. The AQP5 plays a significant role in thermoregulation during growth phases in response to heat stress in goats, however, it is required to understand the role of aquaporins at cellular level as well as to establish the association with production performance in ruminant system in-vivo.

The complete chloroplast genome of Calyptothecium philippinense Broth. (Pterobryaceae, Hypnales)

The genus Calyptothecium, currently comprising ca. 30 species worldwide, is the largest genus within the family Pterobryaceae. However, a comprehensive taxonomic revision of this genus is lacking. Calyptothecium philippinense Broth. 1899, a moss species widely found in the tropical regions of Asia, is characterized by the unique rugose leaves and large auriculate leaf bases. In this study, we sequenced the complete chloroplast genome (CPG) of C. philippinense using the Illumina NovaSeq 6000 platform. The length of the CPG of C. philippinense was determined to be 124,513 bp, with an AT content of 74%. The CPG of C. philippinense exhibited a standard quadripartite structure, consisting of one small single-copy (SSC) region (18,541 bp), one large single-copy region (LSC) (87,222 bp), and two inverted repeat (IR) regions (9375 bp each). A total of 126 genes from the CPG of C. philippinense were annotated, including 82 protein-coding genes, eight ribosomal RNA genes, and 36 transfer RNA genes. Phylogenetic analysis based on the CPGs of 25 bryophyte taxa revealed that the three Pterobryaceae species C. philippinense, Calyptothecium hookeri (Mitt.) Broth. and Pterobryopsis orientalis (Müll. Hal.) M. Fleisch. formed a robust clade. The findings could facilitate more accurate classification and help elucidate evolutionary relationships within Calyptothecium.

Characterization and phylogenetic analysis of the mitochondrial genome of Cylicostephanus longibursatus.

Cylicostephanus longibursatus is a common parasite in equine animals. Hosts infected by these nematodes might face disease or death. This study utilized next-generation sequencing technology to sequence the complete mitochondrial genome (mt genome) of C. longibursatus. Through bioinformatics techniques, the genomic base composition, codon usage, tRNA secondary structures, evolutionary relationships, and taxonomic status were analyzed. The results revealed that the mitochondrial genome of C. longibursatus is a double-stranded, 13,807-bp closed circular molecule with an AT content of 76.0%, indicating a clear preference for AT bases. The mitochondrial genome consisted of a total of 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. Among the 12 protein-coding genes, TTG and ATT were the common start codons. TAA was the predominant termination codon, except for the ND3 and ND6 coding genes, and the COШ genes used TAG and "T" as termination codons, respectively. All tRNAs exhibited atypical clover-leaf secondary structures, except for tRNALys and tRNALeu2, where two tRNASer genes lacked DHU arms and DHU loops, tRNAmet lacked the TΨC-arm, tRNAIle lacked the TΨC-loop, and the remaining 16 tRNAs lacked the TΨC-arm and TΨC loop, which were substituted by the "TV-replacement loop". Phylogenetic analyses, based on the 12 protein-coding genes and utilizing maximum likelihood (ML) and Bayesian inference (BI) analyses, indicated that C. longibursatus did not form a monophyletic group with other Cylicostephanus but was instead more closely related to Cyathostomum. These research findings provide fundamental data for exploring the population classification and phylogeny of strongylid nematodes.

Complete genome identified of clinical isolate Prototheca.

Introduction. Prototheca is an opportunistic pathogen that can infect both humans and animals, of which Prototheca wickerhamii (P. wickerhamii) being the most significant pathogenic green algae.Gap statement. The incidence of human diseases caused by Prototheca has been on the rise, yet there is a significant gap in genetic research pertaining to the pathophysiological aspects of these infections.Aim. The aim of this study is to present the whole genome data from the clinical isolate InPu-22_FZ strain and to understand its genomic characteristics through comparative genomic analysis and phylogenetic tree analysis. Functional annotation of protein-coding genes and analysis of their pathogenicity are also conducted.Methodology. We described the high-quality de novo genome assembly of the clinical isolate InPu-22_FZ strain, achieved by combining Nanopore ONT and Illumina NovaSeq sequencing technologies. Phylogenetic tree was constructed to study the evolutionary relationship between the InPu-22_FZ strain and other species. The average nucleotide identity (ANI) analysis was used to assess the similarity between different species. Additionally, the size, distribution and composition of synteny blocks were also analysed to infer the evolutionary relationships of the genomes.Results. The size of the assembled nuclear genome was 18.47 Mb with 48 contigs. Key features of the genome include high overall GC content (63.31%), high number (5478) and proportion (62.24%) of protein-coding genes and more than 96.71% of genes annotated for gene function. Phylogenetic analyses showed that the InPu-22_FZ strain and other P. wickerhamii clustered into one clade with a bootstrap value of 99% and collinearity analysis revealed high levels of collinearity with ATCC 16529. The ANI analysis revealed only a relatively high similarity (89-93%) to available P. wickerhamii genomes, suggesting the overall genomic novelty of InPu-22_FZ strain. Interestingly, the analysis of the pathogen-host interaction database unveiled and demonstrated reduced virulence of this strain, albeit it was isolated from a chronic upper-limb cutaneous infection.Conclusion. The study provides an in-depth insight into the genomic structure and biological function of the InPu-22_FZ strain, revealing the genetic basis of its pathogenicity and virulence.

Development of in silico methodologies to predict the toxicity of novel proteins in the context of food and feed risk assessment

Abstract This report is the outcome of an EFSA procurement (OC/EFSA/GMO/2021/02 – LOT1) aiming at developing an in silico strategy to predict the toxicity of (novel) proteins. Up‐to‐date, commercially available tools predicting protein toxicity based on primary structures were evaluated for their accuracy and usability, using a curated dataset of annotated toxins and non‐toxins from UniProt. ToxinPred2 and Toxify emerged as the top performers, showing both high accuracy and suitability for integration into an automated pipeline. Additional bioinformatics methods were explored, which provide sequence similarity‐based information rather than direct predictions (BLAST, InterPro HMM profiles). By converting their outputs into features for machine learning models, a high prediction accuracy was achieved, though there is potential for improvement to reduce overfitting risks. An Artificial Intelligence (AI)‐based consensus pipeline, integrating results from ToxinPred2, Toxify, and our machine learning models was developed. This consensus model reached a 95% accuracy rate in distinguishing toxins from non‐toxins. Noteworthy, our BLAST‐based machine learning model ‐ although performance‐wise comparable to BLAST ‐ offers higher sensitivity and specificity across diverse queries than BLAST; it relies on database‐based evolutionary relationships, which may significantly limit its applicability to novel or mutated toxins. Structure‐based prediction methods are deemed impractical due to their resource intensity and reliance on accurate structural data; AI‐driven structure prediction methods ‐ like Rosetta and AlphaFold ‐ are promising, however they are still under development and may not be suitable for the regulatory context yet. Recommendations are provided, including enhancement of the proposed consensus pipeline to create an independent open‐source, user‐friendly tool for evaluating the safety of (novel) proteins in food and feed; regular updates of the proposed databases and models; incorporation of 3D structures and in general validation of AI and machine learning models for regulatory uses.

Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold

Advancements in genome-wide sequence analysis have led to the discovery of numerous novel bacterial non-coding RNAs (ncRNAs). These ncRNAs have been categorized into various RNA families and classes based on their size, structure, function, and evolutionary relationships. One such ncRNA family, raiA, is notably abundant in the bacterial phyla Firmicutes and Actinobacteria and is remarkably well-conserved across many Gram-positive bacteria. In this study, we integrated cryo-electron microscopy single-particle analysis with computational modeling and biochemical techniques to elucidate the structural characteristics of raiA from Clostridium sp. CAG 138. Our findings reveal the globular 3D fold of raiA, providing valuable structural insights. This analysis paves the way for future investigations into the functional properties of raiA, potentially uncovering new regulatory mechanisms in bacterial ncRNAs.

NADPH-cytochrome P450 reductase involved in the lambda-cyhalothrin susceptibility on the green mirid bug Apolygus lucorum.

NADPH-cytochrome P450 reductase (CPR) is crucial for the detoxification process catalysed by cytochrome P450, which targets various exogenous xenobiotics, as well as pesticides. In our research, we successfully obtained the complete cDNA sequence of Apolygus lucorum's CPR (AlCPR) using reverse transcription PCR along with rapid amplification of cDNA ends technology. Bioinformatics analysis exhibited that the inferred amino acid sequence of AlCPR is characteristic of standard CPRs, featuring an N-terminal membrane anchor and three conserved FMN, FAD and NADP binding sites. Phylogenetic result revealed that AlCPR was positioned within the Hemiptera cluster, showing a close evolutionary relationship with the CPR of Cimex lectularius. The real-time quantitative PCR results demonstrated widespread expression of AlCPR across various life stages and tissues of A. lucorum, with the most prominent expression in adults and the abdominal region. Injecting double-stranded RNA of AlCPR only significantly increased the lambda-cyhalothrin susceptibility in lambda-cyhalothrin-resistant strain rather than the susceptible strain. These findings suggest a potential link between AlCPR and the P450-dependent defence mechanism against lambda-cyhalothrin in A. lucorum.

Advancements and prospects in reconstructing the genetic genealogies of ancient and modern human populations using ancestral recombination graphs.

With the release of large-scale genomic resources from ancient and modern populations, advancements in computational biology tools, and the enhancement of data mining capabilities, the field of genomics is undergoing a revolutionary transformation. These advancements and changes have not only significantly deepened our understanding of the complex evolutionary processes of human origins, migration, and admixture but have also unveiled the impact of these processes on human health and disease. They have accelerated research into the genetic basis of human health and disease and provided new avenues for uncovering the evolutionary trajectories recorded in the human genome related to population history and disease genetics. The ancestral recombination graph (ARG) reconstructs the evolutionary relationships between genomic segments by analyzing recombination events and coalescence patterns across different regions of the genome. An ARG provides a record of all coalescence and recombination events since the divergence of the sequences under study and specifies a complete genealogy at each genomic position, which is the ideal data structure for genomic analysis. Here, we review the theoretical foundations and research advancements of the ARG, and explore its translational applications and future prospects across various disciplines, including forensic genomics, population genetics, evolutionary medicine, and medical genomics. Our goal is to promote the application of this technique in genomic research, thereby deepening our understanding of the human genome.

Fossilized soft tissues in tentaculitids from the Upper Devonian of Armenia: Towards solving the mystery of their phylogenetic affinities

The tentaculitids represent a significant and diverse group of mysterious fossils found in Palaeozoic strata. Their biology and evolutionary relationships remain poorly understood due to limited information about their soft body anatomy. The discovery of fossilized soft tissues in tentaculitids from the Upper Devonian of Armenia helps to resolve the old mystery of tentaculitid phylogenetic affinities. The thick bundles of phosphatic bars in the tentaculitid interior closely resemble the musculature of several tubicolous invertebrates, such as phoronids and bryozoans. Based on this similarity, we interpret these structures as fossilized muscles of the tentaculitid animal. The attachment of tentaculitid body muscles in a honeycomb pattern to the body wall is unlike that of any mollusc. Based on this muscle arrangement, molluscan affinities of tentaculitoids can be refuted. The muscle arrangement in tentaculitids is more akin to that of bryozoans than to phoronids. Presumably, tentaculitids and bryozoans shared a common ancestor. This ancestor was probably a solitary animal, with coloniality emerging later in the bryozoan branch of the phylogenetic tree. Alternatively, tentaculitoids might have evolved from a bryozoan-like ancestor by losing their coloniality.

Complete mitochondrial genome and phylogenetic analysis of Chloris chloris (Passeriformes: Fringillidae)

In this study, we employed high-throughput metagenomic data to assemble the mitochondrial genome (mitogenome) of the European greenfinch (Chloris chloris; Linnaeus 1758). The circular mitogenome was 16,813 base pairs (bp) in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region. The base composition of the mitogenome is 30.6% A, 30.7% C, 14.2% G, and 24.5% T, resulting in a GC content of 44.9%. Phylogenetic analysis, utilizing the concatenation of the 13 mitochondrial PCGs from 32 related species of the order Passeriformes, indicated a closer relationship between C. chloris and C. sinica. Moreover, the genus Chloris was closely related to the genera of Serinus, Crithagra, Carduelis, and Acanthis. This mitogenomic data of C. chloris not only be helpful for species identification but also facilitates our understanding of the evolutionary relationship among different species in genus Chloris, which experienced rapid radiation evolution.

Resequencing reveals population structure and genetic diversity in Tibetan sheep

BackgroundThe Tibetan sheep is one of the three major primitive sheep breeds in China, representing a unique and high-quality genetic resource in the Qinghai-Tibet Plateau and neighboring high-altitude regions, exhibiting exceptional adaptability to high-altitude climatic environments. However, research on the genetic relationships among different populations of Tibetan sheep at the whole-genome level remains insufficient. This study aims to explore the population structure and historical dynamics among 11 Tibetan sheep populations, accurately assess the genetic diversity within the populations, and providing a theoretical basis for the development of targeted genetic breeding strategies for Tibetan sheep.ResultsIn this study, a total of 10,884,454 high-quality SNPs were obtained. All Tibetan sheep populations exhibited varying degrees of linkage disequilibrium, with similar decay rates; among them, the WT population showed the fastest decay, while the TS population exhibited the slowest decay rate. Analyses using Tajima’s D and π indicated that the genetic diversity levels of the Tibetan sheep populations are generally low. Fst results revealed that most populations exhibited moderate to low levels of genetic differentiation. The effective population size among Tibetan sheep populations showed an increasing trend over time. The evolutionary relationships among Tibetan sheep populations reflect the correlation between their geographical locations and genomic genetic distances, while also indirectly confirming the impact of historical activities such as early human migration, admixture, fusion, and expansion on the population sizes and distributions of Tibetan sheep.ConclusionsThe results indicate that the genetic diversity levels and genetic differentiation among Tibetan sheep populations are relatively low. In this study, we identified the genetic characteristics of Tibetan sheep populations, which exhibit low levels of diversity, genetic differentiation, and a strong population structure. A deeper genomic exploration of the population structure and diversity status of Tibetan sheep populations will provide theoretical support for subsequent genetic breeding and diversity conservation efforts.

Rare occurrence of Blastocystis in sea turtles and insects (cockroaches, houseflies, and crickets) from several states in Peninsular Malaysia.

Blastocystis a single-celled eukaryotic protist, is known to inhabit the intestines of various hosts, including humans, and has been implicated in a wide spectrum of symptoms, ranging from gastrointestinal issues to skin disorders, thereby establishing its status as an emerging infectious agent. In this study, the prevalence of Blastocystis infection was investigated in insects, including cockroaches, houseflies, and crickets, as well as sea turtles. Additionally, the genotypic characteristics of the isolated Blastocystis strains were examined, and the evolutionary relationships between Blastocystis species found in sea turtles, and animals/humans were determined. Microscopic techniques and molecular methods were utilized in this study. The results showed that four out of 90 insects (4.44%) and one out of 13 sea turtles (7.7%) were infected by Blastocystis. Furthermore, detailed observations revealed the presence of characteristic morphological features, such as vacuolar forms in the cockroach, cricket and sea turtle samples and binary fission from cockroach samples, indicative of Blastocystis' mode of reproduction. While the ST8 of Blastocystis in sea turtles were successfully identified, no subtyping was achieved for the infected insects. This study not only establishes the occurrence of Blastocystis infection in sea turtles but also uncovers its ability to infect insects, suggesting a potential reservoir role for these organisms. Overall, this research emphasizes the significance of comprehending the prevalence, genotypic diversity, and evolutionary relationships of Blastocystis across various hosts. Such insights are instrumental in developing effective control measures and public health interventions to mitigate the associated symptoms and prevent future outbreaks.

Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering.

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue 'The evolution of plant metabolism'.

A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus).

COI-barcode-like sequences appear to show substantially more species diversity among Mesoamerican bumblebees than had been reported previously from morphological studies. Closer examination shows that some of this apparent diversity may be pseudospecies (groups falsely misinterpreted as separate species), often supported by paralogous 'numts' (nuclear copies of mitochondrial sequences). For the well-sampled weisi-complex, we seek to filter out pseudogenes in order to use the orthologous COI-barcode sequences for identifying estimates of evolutionary relationships and likely species' gene coalescents for candidate species. Even after this filtering, in contrast to recent purely morphological studies our results from an integrative assessment of species' gene coalescents together with skeletal morphology support that 'Bombus weisi' Friese in its recent broad sense consists of two species: B. weisi (which includes the taxon montezumae Cockerell); and B. nigrodorsalis Franklin. Our interpretation rejects likely numts-based pseudospecies and a candidate species that are unsupported by skeletal morphology. This shows that careful attention needs to be paid to both barcode analysis and to skeletal morphology, to avoid describing pseudospecies.

Genome-Wide Analysis Elucidates the Roles of AhLBD Genes in Different Abiotic Stresses and Growth and Development Stages in the Peanut (Arachis hypogea L.).

The lateral organ boundaries domain (LBD) genes, as the plant-specific transcription factor family, play a crucial role in controlling plant architecture and stress tolerance. However, the functions of AhLBD genes in the peanut plant (Arachis hypogea L.) remain unclear. In this study, 73 AhLBDs were identified in the peanut plant and divided into three groups by phylogenetic tree analysis. Gene structure and conserved protein motif analysis supported the evolutionary conservation of AhLBDs. Tandem and segment duplications contributed to the expansion of AhLBDs. The evolutionary relationship analysis of LBD gene family between A. hypogaea and four other species indicated that the peanut plant had a close relationship with the soybean plant. AhLBDs played a very important role in response to growth and development as well as abiotic stress. Furthermore, gene expression profiling and real-time quantitative qRT-PCR analysis showed that AhLBD16, AhLBD33, AhLBD67, and AhLBD72 were candidate genes for salt stress, while AhLBD24, AhLBD33, AhLBD35, AhLBD52, AhLBD67, and AhLBD71 were candidate genes for drought stress. Our subcellular localization experiment revealed that AhLBD24, AhLBD33, AhLBD67, and AhLBD71 were located in the nucleus. Heterologous overexpression of AhLBD33 and AhLBD67 in Arabidopsis significantly enhanced tolerance to salt stress. Our results provide a theoretical basis and candidate genes for studying the molecular mechanism for abiotic stress in the peanut plant.

Characterization of the complete mitochondrial genome of the medical fungus Ganoderma resinaceum Boud., 1889 (Polyporales: Ganodermataceae)

The medical mushroom Ganoderma resinaceum Boud., 1889, is of great interest in pharmacy due to its diverse functional active ingredients. However, the mitochondrial genome of G. resinaceum remains unexplored. Here, we present the complete mitochondrial genome of G. resinaceum, which spans 67,458 bp and has a GC content of 25.65%. This genome encompasses 15 core protein-coding genes, 8 independent ORFs, 15 intronic ORFs, 27 tRNAs, and 2 rRNA genes. Through phylogenetic analysis using Bayesian inference (BI), we elucidated the evolutionary relationships among 34 Basidiomycota fungi, revealing distinct clades and indicating a close relationship between G. resinaceum and G. subamboinense.

La anatomía de la raíz como evidencia filogenética para los helechos Cheilanthoides (Pteridaceae)

Background and aims: To our hypothesis on the evolutionary relationships of Cheilanthoid ferns, based on molecular data and partially on morphological and reproductive data, we add here a study of root anatomy in the genera of the subfamily occurring in South America. M&amp;M: Root characters were analyzed anatomically in 48 South American species representing the 12 genera of Cheilanthoideae occurring in South America. Techniques of plant histology were used for anatomical analysis and tissue characterization. Characters with possible diagnostic value were identified and mapped on a molecular phylogeny of Cheilanthoideae based on three plastidial markers (rbcL, trnL-F and rps4). Results: The character "type of root cortex" showed a distribution of states that fit to the major clades or genera in the phylogeny of the subfamily. The homogeneous cortex state was plesiomorphic for Cheilanthoideae, whereas the heterogeneous bark state was acquired by some genera of the hemionitoid clade: Hemionitis and the genera of the Adiantopsis-Doryopteris clade (except Mineirella). In addition, we discuss the role of different tissues in the root mechanics of this group. Conclusions: The character "type of root cortex" could contribute to the characterization of genera and the generic assignment of confusing species in the classification of Cheilanthoideae. However, the complete resolution of the relationship of hemionitds clade in the global phylogeny of the subfamily is necessary.

Characterization and phylogenetic analysis of the chloroplast genome in Elaeocarpus duclouxii

Elaeocarpus duclouxii, an evergreen tree species, is renowned for its fruits rich in flavonoids exhibiting potent antioxidant properties. Despite its significance, the chloroplast genome of this plant has remained unexplored until now. Our study presents the first comprehensive sequencing and analysis of the E. duclouxii chloroplast genome, revealing a circular DNA molecule of 158,148 base pairs. This genome comprises a large single-copy region of 85,700 base pairs, a small single-copy region of 17,672 base pairs, and a pair of inverted repeat regions totaling 27,388 base pairs. The genome encodes 132 genes, including 87 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analyses indicate a close evolutionary relationship between E. duclouxii and E. sylvestris. This study not only represents the first phylogenetic investigation of E. duclouxii but also establishes a crucial genomic foundation for future research area such as conservation genetics, evolutionary biology, and potential biotechnological applications.

Genome-wide comparative analysis of CC1 Staphylococcus aureus between colonization and infection

BackgroundStaphylococcus aureus is one of the most important bacteria in human colonization and infection. Clonal complex1 (CC1) is one of the largest and most important S. aureus CCs, and it is a predominant clone in S. aureus colonization and can cause a series of S. aureus infections including bloodstream infections. No studies on the relationship of CC1 S. aureus between colonization and infection have been published.MethodsTo figure out if there are some significant factors in CC1 S. aureus help its colonization or infection, 15 CC1 S. aureus isolates including ten from colonization and five from bloodstream infections were enrolled in this study. Whole-genome sequencing and bioinformatics analysis were performed.ResultsVirulence factor regulators XdrA, YSIRK signal peptide, CPBP family and OmpR family specifically found in infection isolates can promote virulence factors and enhance the pathogenicity of S. aureus. In addition, some significant differences in metabolism and human diseases were discovered between colonization and infection. Fst family of type I toxin–antitoxin system that mainly maintains stable inheritance was specifically found in CC1 S. aureus colonization isolates and might help S. aureus survive for colonization. No significant differences in genomic evolutionary relationship were found among CC1 S. aureus isolates between colonization and infection.ConclusionsVirulence factor regulators and metabolic state can promote CC1 S. aureus pathogenic process compared with colonization, and it seems that the strains of colonization origin cannot have pathogenic potential. Experimental confirmation and a bigger number of CC1 S. aureus strains are necessary for further study about the details and mechanism between colonization and infection.