Genomic Analysis Research Articles

Breast cancer identification using machine learning and hyperparameter optimization

Breast cancer identification can be analyzed through genomic analysis using gene expression data, one type of which is mRNA. This involves analyzing gene expression patterns of breast tissue samples to distinguish breast cancer from healthy tissue or to differentiate subtypes of different breast cancers. This research developed the right computational model for breast cancer classification using machine learning and hyperparameter optimization algorithms. The primary objective of this research is to utilize various machine learning algorithms to classify breast cancer based on gene expression and enhance the models developed in previous studies. This paper provides an extensive literature review of prior breast cancer classification research and offers new theoretical perspectives. This research used a problem-solving approach with conventional machine learning techniques, most notably the decision tree. It also evaluates other machine learning algorithms for comparison, including k-nearest neighbor, naïve bayes, random forest, extra tree classifier, and support vector machine. The evaluation process used classification reports that provide insight into the precision, recall, F1-score, and accuracy of each machine learning model. The evaluation results show that the performance of the decision tree algorithm model is superior and impressive, achieving 99.73% accuracy and a score of 1 for precision, recall, and F1-score.

Multi-omics analyses of the mechanism for formation of key aroma-active compounds in blood orange wine fermented by Pichia kudriavzevii

Pichia kudriavzevii is an emerging non-Saccharomyces yeast recognized for its ability to enhance aroma quality in fermented foods, though the precise mechanisms underlying its effects remain poorly understood. This study delves into the influence of P. kudriavzevii BP15 on the formation of key aroma-active compounds (KAACs) and metabolic pathways during the fermentation of blood orange wine. By integrating multi-omics approaches, including volatilomics, genomics, and transcriptomics, this work systematically evaluated the profile of volatile organic compounds (VOCs), pinpointed the genes implicated in KAACs metabolism, and elucidated the biotransformation pathways of KAACs. The volatilomics results demonstrated that inoculation with P. kudriavzevii BP15 significantly improved the complexity and desirability of aroma by promoting the accumulation of diverse VOCs, particularly esters. The genomics analysis further revealed that a substantial portion of P. kudriavzevii BP15 genome was dedicated to carbohydrate, amino acid, and energy metabolisms. The transcriptomics data identified the high expression of multiple genes (e.g., ARO8, ACC1, ALD4, ILV5) during the early stages of fermentation by P. kudriavzevii BP15 that are integral to the biosynthesis of KAACs. These insights provide a deeper understanding of P. kudriavzevii BP15′s potential application in the production of high-quality blood orange wine, underscoring its role in enhancing the aroma profile through sophisticated metabolic interventions.

Multi-omic profiling of a novel Myrothecium species reveals its potential mechanism of lignin degradation

Lignin utilization is one of the key challenges in the valorziation of lignocellulose. Filamentous fungi are promising candidates for lignin degradation and mineralization. However, novel lignin-degrading species are underexplored and the mechanism of lignin degradation is not fully understood. Here we isolated and characterized a novel species, Myrothecium wuxin, capable of utilizing lignosulfonate as the sole carbon source. To understand the mechanism of lignin degradation, genomic, transcriptomic and metabolic analyses were performed. The genome was sequenced, and assembled to a size of 48.55 Mb, with a contig N50 size of 5.67Mb. A total of 14,221 protein-coding genes were predicted, including a high number of potential ligninolytic enzymes. Transcriptomic analysis revealed a pronounced effect of lignosulfonate on gene expression profiles. More than twenty intermediate aromatic metabolites were identified during lignosulfonate utilization. Through genomic annotation, the genes potentially involved in lignin degradation were identified, and more than nine metabolic pathways of lignin-derived aromatic intermediates were predicted, including the homogentisate pathway, benzoic acid pathway, as well as the tree-branched β-ketoadipate pathway. The genomic information will provide a valuable resource for lignin degradation, while the elucidated catabolic pathways and associated enzymes provide exciting biotechnological opportunities for lignin valorization and production of valuable chemicals.

Impact of prescribed fire on fungal communities in Scots pine (Pinus sylvestris) forests in Mediterranean transitional zones

The Mediterranean region is renowned for its natural susceptibility to wildfires. In recent years, this risk has intensified due to various factors, including climate change and rural abandonment. Castilla y Leon stands out as one of the most severely impacted areas grappling with rural exodus. This evolving scenario accentuates the urgency of implementing forest management strategies to mitigate the escalating threat of wildfires, with a primary focus on fuel reduction. Although prescribed fires represent an efficient and cost-effective tool for wildfire prevention, they remain a contentious subject in Europe. Fungi not only contribute significantly to rural economies but also play a pivotal role in maintaining the equilibrium of forest ecosystems. The main objective of this study was to examine the effects of prescribed burning on Pinus sylvestris soils, with a specific focus on the recovery of fungal populations after such fires. To assess the short-term effects of prescribed fires on soil fungal communities, we collected soil samples from both burned and unburned plots 12 months post-burning to perform genomic DNA analyses. Our findings indicate that prescribed burning does not significantly alter fungal diversity or composition, with only litter saprotrophs showing significantly higher levels of abundance in burned areas than in unburned areas. Valuable edible fungi persisted post-burning, suggesting that prescribed burning could be used to reduce wildfire fuel loads while preserving fungal biodiversity and valuable edible fungi. These results advocate for the use of prescribed burning as a viable, myco-friendly forest management practice, offering a balance between fire prevention and ecological conservation.

Convergence of mcr-1 and broad-spectrum β-lactamase genes in Escherichia coli strains from the environmental sector

The mcr-type gene encodes the main plasmid-mediated mechanism of colistin resistance and has been reported in several bacterial species obtained from different sources. Anthropogenic activities in the environment favor the evolution of antimicrobial resistance. Indeed, mcr-1-positive Escherichia coli strains were susceptible to non-polymyxins antimicrobials, but now emerging as multidrug-resistant (MDR) lineages. In this regard, hundreds of surface water and agricultural soil samples were screened for the presence of E. coli carrying the mcr-type genes and mcr-1-positive strains were subjected to in-depth genomic analysis. Almost all colistin-resistant strains were classified as MDR, highlighting those obtained from soils that showed resistance to extended-spectrum cephalosporins and carbapenems. International and high-risk clones of E. coli were identified, with ST10 and ST1720 shared between water and soil samples. Resistome analysis showed a broad resistome (AMR, metal tolerance, and biocide resistance). The mcr-1.1 and mcr-1.26 allelic variants were detected on IncX4 and IncI2 plasmids. Curiously, mcr-1-positive E. coli strains from agricultural soils harbored plasmid-mediated blaCTX-M-1, blaCTX-M-8, or blaKPC-2 genes. Virulome analysis demonstrated traits of a high putative virulence potential, with the presence of extraintestinal pathogenic E. coli. Comparative analysis revealed the persistence and dissemination of plasmid-mediated antimicrobial resistance genes in genetically diversity E. coli strains at the human-animal-environmental interface. These findings demonstrate a possible emerging AMR trend with the convergence of resistance to colistin and broad-spectrum β-lactams in environmental-derived E. coli strains.

Chromosome-scale assembly and analysis of yellow Camellia (Camellia limonia) genome reveal plant adaptation mechanism and flavonoid biosynthesis in karst region

Yellow Camellia is an endangered and protected wild plant with unique medicinal value. Among the Camellia Sect. Chrysantha Chang, certain species (e.g. Camellia limonia) can grow in karst regions. The karst region is a highly sensitive ecosystem with low environmental capacity. However, the molecular mechanisms underlying the adaptation of yellow camellia to karst regions remain unclear. Here, we present a high-quality genome with 15 chromosome groups with an N50 of 198.92Mb. The divergence between C. limonia and Camellia sinensis occurred approximately 6 million years ago, indicating that the Himalayan uplift event may led to species differentiation. This enables C. limonia to thrive in a unique ecological environment like the karst region. Flavonoid compounds play a significant role in the interaction between plants and their environment. In comparison to Theaceae family genomes, C. limonia exhibits an increased number of gene family members involved in the flavonoid biosynthesis pathway, including UDP-glycosyltransferases and chalcone reductase. Additionally, two gene clusters associated with flavonoid biosynthesis were identified in the genome of C. limonia. Furthermore, comparative genomics analysis revealed the expansion of genes associated with karst environment adaptation in the genome of C. limonia, such as calmodulin genes and genes related to Calcium ion transmembrane transport. Additionally, at the gene expression level, it was observed that the secondary metabolism-related genes may be involved in the calcium tolerance of C. limonia. These findings provide important insights into the evolution of C. limonia, offering references for the study of plants in karst areas.

Major depressive disorder is associated with mitochondrial ND6 T14502C mutation in two Han Chinese families

BACKGROUND Globally, the World Health Organization ranks major depressive disorder (MDD) as the leading cause of disability. However, MDD molecular etiology is still poorly understood. AIM To explore the possible association between mitochondrial ND6 T14502C mutation and MDD. METHODS Clinical data were collected from two pedigrees, and detailed mitochondrial genomes were obtained for the two proband members. The assessment of the resulting variants included an evaluation of their evolutionary conservation, allelic frequencies, as well as their structural and functional consequences. Detailed mitochondrial whole genome analysis, phylogenetic, and haplotype analysis were performed on the probands. RESULTS Herein, we reported the clinical, genetic, and molecular profiling of two Chinese families afflicted with MDD. These Chinese families exhibited not only a range of onset and severity ages in their depression but also extremely low penetrances to MDD. Sequence analyses of mitochondrial genomes from these pedigrees have resulted in the identification of a homoplasmic T14502C (I58V) mutation. The polymorphism is located at a highly conserved isoleucine at position 58 of ND6 and distinct mitochondrial DNA (mtDNA) polymorphisms originating from haplogroups M10 and H2. CONCLUSION Identifying the T14502C mutation in two individuals with no genetic relation who exhibit symptoms of depression provides compelling evidence that this mutation may be implicated in MDD development. Nonetheless, the two Chinese pedigrees that carried the T14502C mutation did not exhibit any functionally significant mutations in their mtDNA. Therefore, the phenotypic expression of the T14502C mutation related to MDD may be influenced by the nuclear modifier gene(s) or environmental factors.

Identification of Recombinant Aichivirus D in Cattle, Italy

Kobuviruses (KoVs) are a group of small, non-enveloped RNA viruses classified in the genus Kobuvirus within the Picornaviridae family, comprising Aichivirus species A to F. KoVs have been identified in humans and several mammals, including domestic ungulates. This study investigated the presence of KoVs in a collection of bovine stool samples (n = 38) obtained from animals with enteritis or without clinical signs. By RT-PCR screening, KoV RNA was detected in 10/ 38 animals (26.3%). Six of the ten positive animals had enteric signs. On sequence analysis of the amplicons, eight strains were related to species Aichivirus B, commonly identified in cattle. In contrast, two strains (ITA/2019/572-1 and ITA/2020/bovine/30-2), displayed the highest nt identity (up to 97.1%) to cattle, yak, and goat Aichivirus D strains. On whole genome analysis, strains ITA/2019/572-1 and ITA/2020/30-2 showed 88.9% nt identity to each other and 87.8–90.3% nt to the bovine kobuvirus strain CHN/2021/ON730709 identified in China. Interestingly these three Aichivirus D strains showed a recombinant makeup, clustering with D1 genotype in the capsid region and with D2 genotype in the non-structural genes. These findings suggest that Aichivirus D KoVs are common components of livestock virome. Understanding the genetic diversity of KoVs in animals will be useful to improve the diagnostics and gather epidemiological data.

Expression of Concern for Nazir et al., “Characterization, taxonomic classification, and genomic analysis of two newly isolated bacteriophages with potential to infect Escherichia coli ”

Expression of Concern for Nazir et al., “Characterization, taxonomic classification, and genomic analysis of two newly isolated bacteriophages with potential to infect <i>Escherichia coli</i> ”

Genome sequences of toxigenic cyanobacteria from a bloom in Lake Mattamuskeet, North Carolina (United States)

AbstractLake Mattamuskeet, the largest lake in North Carolina, USA, has undergone decades‐long eutrophication causing reduced water quality and promoting cyanobacterial blooms that may produce toxins. It is therefore necessary to evaluate the cyanobacterial diversity of the lake and their toxigenic potential. We present draft genomes of Microcystis, Pelatocladus, Raphidiopsis, and Umezakia strains isolated from Lake Mattamuskeet. The whole‐genome shotgun projects for Umezakia ovalisporum BLCC‐F208, Microcystis sp. BLCC‐F209, Microcystis sp. BLCC‐F210, Pelatocladus sp. BLCC‐F211, U. ovalisporum BLCC‐F215, and Raphidiopsis BLCC‐F218 have been deposited in GenBank under accession numbers JBHFLK000000000, CP169647, JBHFLL000000000, JBHFLM000000000, JBHFLN000000000, and JBHFLO000000000, respectively. Based on the genomic analysis, several biosynthetic gene clusters (BCGs) with varying degrees of similarity to known toxic and bioactive compound gene clusters were identified across the different cyanobacterial strains.

High-grade B-cell lymphoma not otherwise specified, with diffuse large B-cell lymphoma gene expression signatures: Genomic analysis and potential therapeutics.

High-grade B-cell lymphoma not otherwise specified (HGBCL, NOS) has overlapping morphological and genetic features with diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL), leading to uncertainty in its diagnosis and clinical management. Using functional genomic approaches, we previously characterized HGBCL and NOS, that demonstrate gene expression profiling (GEP), and genetic signatures similar to BL. Herein, we characterize distinct HGBCL, NOS, cohort (n = 55) in adults (n = 45) and in children (n = 10), and compared the GEP, genomic DNA copy number (CN), and mutational spectrum with de novo DLBCL (n = 85) and BL (n = 52). This subgroup, representing ~60% of HGBCL, NOS, lack gene-expression signature of BL and double hit/dark zone lymphoma, but express DLBCL like signatures and are characterized by either GCB- or ABC-like mRNA signatures and exhibit higher genomic complexity, similar to de novo DLBCL, and show alteration in genes regulating B-cell activation (CD79B, MYD88, PRDM1, TBLIXR1, CARD11), epigenome (KMT2D, TET2) and cell cycle transition (TP53, ASPM). However, recurrent mutations in genes often mutated in BL (DDX3X, GNA13, CCND3), but rare in DLBCL, are also present in HGBCL-NOS, highlighting genetic heterogeneity. Consistent with mutation spectrum, frequent genomic CN alterations in genes regulating B-cell activation (del-PRDM1, gain-BCL6, -REL, -STAT3) and cell cycle regulators (del-TP53, del-CDKN2A, del-RB1, gain-CCND3) were observed. Pediatric cases showed GCB-DLBCL-like mRNA signatures, but also featured hallmark mutations of pediatric BL. Frequent oncogenic PIM1 mutations were present in adult HGBCL, NOS. In vitro analyses with pharmacologic or genetic inhibition of PIM1 expression triggered B-cell activation and NF-κB-induced apoptosis, suggesting that PIM1 is a rational therapeutic target.

Genomic Single Nucleotide Polymorphism (SNP) markers and mitochondrial haplotypes illuminate the origins of Crown-of-Thorns Starfish (Acanthaster solaris) outbreaks in the South China Sea.

Outbreaks of the coral predator Crown-of-Thorns Starfish (CoTS) pose a severe threat to coral reefs in the Indo-Pacific Ocean. In 2018, the South China Sea (SCS) experienced significant CoTS outbreaks, leading to extensive coral mortality across the Xisha, Zhongsha, Dongsha, and Nansha Islands, severely impacting the coral reef ecosystem. To explore the origins of these outbreaks, we conducted a comprehensive genomic analysis using data from genomic single nucleotide polymorphism sites (SNPs) and mitochondrial haplotypes. Our analysis reveals that CoTS populations in the SCS, which exhibit moderate genetic diversity and may have undergone positive selection or population expansion. There was limited genetic differentiation among CoTS populations from XS, ZS, and NS groups. Especially between the XS and ZS groups, there was almost no genetic differentiation. The populations from XS, ZS, and NS groups have strong genetic connections with populations in Vietnam and the Philippines. There was high gene flow from Vietnam to the Xisha Islands and from the Philippines to the Nansha Islands, suggesting that the CoTS populations in these regions primarily originate from these neighboring countries. The comprehensive analyses of SNP and mitochondrial genomes have provided valuable insights into the population genetics of CoTS. This research has generated significant genomic resources and facilitated important studies on the genetics of the CoTS species. By identifying potential source populations and understanding the genetic basis of their spread, managers can develop more effective conservation strategies to protect vulnerable coral reef ecosystems in the SCS.

Clonal and horizontal transmission of carbapenem-resistant Enterobacterales strains and genes via flies.

Antimicrobial resistance (AMR) is one of the most pressing global public health challenges; in particular, the rapid dissemination of carbapenem-resistant Enterobacterales (CRE) is emerging as a significant concern worldwide. Flies, serving as carriers of pathogens, pose a potential threat in the transmission of antibiotic-resistant bacteria (ARB) between animals and humans. The aim of this study was to evaluate and reveal the potential risk of AMR spread by flies. A total of 450 flies were collected from four farms, four rural areas, and four urban areas in Dengfeng, Henan, China. To select CRE strains on the surface of flies, three flies sampled from the same geographical location were arbitrarily selected and placed into one tube of brain heart infusion broth (BHI), and the supernatant was screened using CHROMagar™ mSuperCARBA culture medium. Different colors and shapes of colonies were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA sequencing. Antimicrobial susceptibility testing for CRE strains was performed using broth microdilution. All CRE strains were whole-genome sequenced. Short-read sequencing was performed using MGISEQ-2000 and long-read sequencing was conducted using GridION. Totally, 150 BHI tubes were screened for CRE strains, and 33 strains were identified as CRE positive. In 24 mSuperCARBA plates, only one species of CRE strain was isolated from each plate. In three plates, two different species of CRE strains were identified in each plate. In one plate, three different species of CRE strains were simultaneously isolated. Carbapenem resistance genes were detected in 81.8% of CRE strains, and blaNDM-1 was predominant (66.7%). No significant correlations between carbapenem-resistant phenotypes and carbapenem resistance genes were observed. The complete genomes of all 33 strains were obtained. Genome analysis revealed that clonal transmission events may have occurred among different farms and rural areas. Phylogenetic analysis revealed that blaNDM-1 IncFII plasmids could break bacterial species barrier for cross-host transmission in diverse areas. To understand and control the transmission of AMR from the perspective of One Health, it is imperative to enhance surveillance of ARB, antibiotic resistance genes, and antibiotic-resistant plasmids in flies.

Orchid phylogenetics and evolution: history, current status and prospects.

Orchidaceae are one of the two largest families of angiosperms; they exhibit a host of changes -- morphological, ecological and molecular -- that make them excellent candidates for evolutionary study. Such studies are most effectively performed in a phylogenetic context, which provides direction to character change. Understanding of orchid relationships began in the pre-evolutionary classification systems of the 1800's that were based solely on morphology, and now is largely based on genomic analysis. The resulting patterns have been used to update family classification and to test many evolutionary hypotheses in the family. Recent analyses with dense sampling and large numbers of nuclear loci have yielded well-supported trees that have confirmed many longstanding hypotheses and overturned others. They are being used to understand evolutionary change and diversification in the family. These include dating the origination of the family, analysis of change in ecological habit (from terrestrial to epiphytic and back again in some cases), revealing significant plastid genome change in leafless holomycotrophs, studying biogeographic patterns in various parts of the world, and interpreting patterns of fungal associations with orchids. Understanding of orchid relationships has progressed significantly in recent decades, especially since DNA sequence data have been available. These data have contributed to an increasingly refined classification of orchids and the pattern has facilitated many studies on character evolution and diversification in the family. Whole genome studies of the family are just beginning and promise to reveal fine-level details underlying structure and function in these plants, and, when set in a phylogenetic context, provide a much richer understanding of how the family has been so successful in diversification.

Harnessing AI for advancing pathogenic microbiology: a bibliometric and topic modeling approach

IntroductionThe integration of artificial intelligence (AI) in pathogenic microbiology has accelerated research and innovation. This study aims to explore the evolution and trends of AI applications in this domain, providing insights into how AI is transforming research and practice in pathogenic microbiology.MethodsWe employed bibliometric analysis and topic modeling to examine 27,420 publications from the Web of Science Core Collection, covering the period from 2010 to 2024. These methods enabled us to identify key trends, research areas, and the geographical distribution of research efforts.ResultsSince 2016, there has been an exponential increase in AI-related publications, with significant contributions from China and the USA. Our analysis identified eight major AI application areas: pathogen detection, antibiotic resistance prediction, transmission modeling, genomic analysis, therapeutic optimization, ecological profiling, vaccine development, and data management systems. Notably, we found significant lexical overlaps between these areas, especially between drug resistance and vaccine development, suggesting an interconnected research landscape.DiscussionAI is increasingly moving from laboratory research to clinical applications, enhancing hospital operations and public health strategies. It plays a vital role in optimizing pathogen detection, improving diagnostic speed, treatment efficacy, and disease control, particularly through advancements in rapid antibiotic susceptibility testing and COVID-19 vaccine development. This study highlights the current status, progress, and challenges of AI in pathogenic microbiology, guiding future research directions, resource allocation, and policy-making.

Characterization and genome analysis of Klebsiella phages with lytic activity against Klebsiella pneumoniae.

Klebsiella pneumoniae is an important gram-negative opportunistic pathogen that causes a variety of infectious diseases. As K. pneumoniae are becoming increasingly resistant to antibiotics, the use of bacteriophages may offer a non-antibiotic-based approach to treat these infections. In the present study, five lytic bacteriophages, 2044307w, k2044hw, k2044ew, k2044302 and 2146hw specific to K. pneumoniae were isolated from hospital sewage and characterized. They belong to group A of the KP32viruses based on transmission electron microscopy (TEM) and genome analysis. These bacteriophages have an extremely narrow host spectrum. The phenotypic characteristics of the phages were determined using lysis assay, pH, and temperature stability tests. This contributes to expanding our understanding of K. pneumoniae phages.

Artificial intelligence-enhanced biosurveillance for antimicrobial resistance in sub-Saharan Africa.

Antimicrobial resistance (AMR) remains a critical global health threat, with significant impacts on individuals and healthcare systems, particularly in low-income countries. By 2019, AMR was responsible for >4.9 million fatalities globally, and projections suggest this could rise to 10 million annually by 2050 without effective interventions. Sub-Saharan Africa (SSA) faces considerable challenges in managing AMR due to insufficient surveillance systems, resulting in fragmented data. Technological advancements, notably artificial intelligence (AI), offer promising avenues to enhance AMR biosurveillance. AI can improve the detection, tracking and prediction of resistant strains through advanced machine learning and deep learning algorithms, which analyze large datasets to identify resistance patterns and develop predictive models. AI's role in genomic analysis can pinpoint genetic markers and AMR determinants, aiding in precise treatment strategies. Despite the potential, SSA's implementation of AI in AMR surveillance is hindered by data scarcity, infrastructural limitations and ethical concerns. This review explores what is known about the integration and applicability of AI-enhanced biosurveillance methodologies in SSA, emphasizing the need for comprehensive data collection, interdisciplinary collaboration and the establishment of ethical frameworks. By leveraging AI, SSA can significantly enhance its AMR surveillance capabilities, ultimately improving public health outcomes.

Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes.

Genome-based analysis allows for large-scale classification of diverse bacteria and has been widely adopted for delineating species. Unfortunately, for higher taxonomic ranks such as genus, establishing a generally accepted approach based on genome analysis is challenging. While core-genome phylogenies depict the evolutionary relationships among species, determining the correspondence between clades and genera may not be straightforward. For genotypic divergence, the percentage of conserved proteins and genome-wide average amino acid identity are commonly used, but often do not provide a clear threshold for classification. In this work, we investigated the utility of global comparisons and data visualization in identifying clusters of species based on their overall gene content and rationalized that such patterns can be integrated with phylogeny and other information such as phenotypes for improving taxonomy. As a proof of concept, we selected 177 representative genome sequences from the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes for a case study. We found that the clustering patterns corresponded to the current understanding of these organisms, namely the split into three above-genus groups: Hominis, Pneumoniae and Spiroplasma-Entomoplasmataceae-Mycoides. However, at the genus level, several important issues were found. For example, recent taxonomic revisions that split the Hominis group into three genera and Entomoplasmataceae into five genera are problematic, as those newly described or emended genera lack clear differentiations in gene content from one another. Moreover, several cases of misclassification were identified. These findings demonstrated the utility of this approach and its potential application to other bacteria.

The chloroplast genome of Cephalanthera nanchuanica (Orchidaceae): comparative and phylogenetic analysis with other Neottieae species.

Cephalanthera nanchuanica is a terrestrial orchid species and has been red listed as a second-grade protected plant due to its limited distributions in China. Initially classified within a monotypicgenus Tangtsinia, this species was later reassigned to Cephalanthera based on morphological and molecular data. However, previous phylogenetic analyses of Cephalanthera using several segment sequences exhibited alow discriminatory power in delineating its relationships. In this study, we characterized and comparatively analyzed the complete chloroplast (cp) genome of C. nanchuanica with those of six previously reported Cephalanthera species. Our findings revealed that the cp genome of C. nanchuanica had the typical quadripartite structure, with a size of 161,365bp and a GC content of 37.27%. A total of 113 unique genes were annotated, among which nearly half of protein-encoding genes (RSCU > 1) showed a preference in codon usage. No structural rearrangements were observed among the cp genomes of Cephalanthera species, except for C. humilis, which displayed structural alterations due to gene loss, relocation, and inverted repeat (IR) expansion/contraction. The cp genomes of Cephalanthera species were highly conserved, with only a small number of SSRs detected, most of which preferred A/T bases. Comparative analysis of cp genomes indicated that IR and coding regions were less divergent than single copy and non-coding regions and eight mutational hotspots were identified. Phylogenetic analysis suggested that the tribe Neottieae was a monophyletic group, divided into five clades. Palmorchis was the earliest-diverging lineage, followed by Cephalanthera. Diplandrorchis was deeply nested within Neottia, forming a clade. Aphyllorchis and Limodorum formed another clade, sister to Epipactis. Within the Cephalanthera clade, C. nanchuanica was sister to C. falcata with astrong support. This study demonstrated that the cp genome characters of C. nanchuanica are highly similar to those of other Cephalanthera species, except for the mycoheterotrophic species C. humilis. Although the cp genomes of Cephalanthera species (excluding C. humilis) exhibited conservation in genome structure and sequence, SSR repeats and mutational hotspots were identified, which could potentially serve as as molecular markers for distinguishing Cephalanthera species. The phylogenetic analysis based on the protein-coding genes provided high-resolution support for the infrageneric classification. Therefore, cp genome data will be instrumental in resolving the phylogeny of the genus Cephalanthera.

Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages.

Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications. Here, we report a comparative genomics analysis of Xenorhabdus griffiniae, including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus, the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species. Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X. griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.