The transcriptional regulation of a putative hemicellulose gene, PtrPARVUS2 in poplar.

The plant cell wall serves as a critical interface between the plant and its environment, offering protection against various stresses and contributing to biomass production. Hemicellulose is one of the major components of the cell wall, and understanding the transcriptional regulation of its production is essential to fully understanding cell wall formation. This study explores the regulatory mechanisms underlying one of the genes involved in hemicellulose biosynthesis, PtrPARVUS2. Six transcription factors (TFs) were identified from a xylem-biased library to negatively regulate PtrPARVUS2 expression. These TFs, belonging to diverse TF families, were confirmed to bind to specific cis-elements in the PtrPARVUS2 promoter region, as validated by Yeast One-Hybrid (Y1H) assays, transient expression analysis, and Chromatin Immunoprecipitation sequencing (ChIP-seq) assays. Furthermore, motif analysis identified putative cis-regulatory elements bound by these TFs, shedding light on the transcriptional regulation of SCW biosynthesis genes. Notably, several TFs targeted genes encoding uridine diphosphate glycosyltransferases (UGTs), crucial enzymes involved in hemicellulose glycosylation. Phylogenetic analysis of UGTs regulated by these TFs highlighted their diverse roles in modulating hemicellulose synthesis. Overall, this study identifies a set of TFs that regulate PARVUS2 in poplar, providing insights into the intricate coordination of TFs and PtrPARVUS2 in SCW formation. Understanding these regulatory mechanisms enhances our ability to engineer plant biomass for tailored applications, including biofuel production and bioproduct development.

Prevalence and genetic diversity of Anaplasma and Ehrlichia in ticks and domesticated animals in Suizhou County, Hubei Province, China.

Anaplasma and Ehrlichia are tick-borne bacterial pathogens that cause anaplasmoses and ehrlichioses in humans and animals. In this study, we examined the prevalence of Anaplasma and Ehrlichia species in ticks and domesticated animals in Suizhou County, Hubei Province in the central China. We used PCR amplification and DNA sequencing of the 16S rRNA, groEL, and gltA genes to analyze. We collected 1900 ticks, including 1981 Haemaphysalis longicornis and 9 Rhipicephalus microplus, 159 blood samples of goats (n = 152), cattle (n = 4), and dogs (n = 3) from May to August of 2023. PCR products demonstrated that Anaplasma bovis, Anaplasma capra, and an Ehrlichia species were detected in the H. longicornis with the minimum infection rates (MIR) of 1.11%, 1.32%, and 0.05%, respectively; A. bovis, A. capra, and unnamed Anaplasma sp. were detected in goats with an infection rate of 26.31%, 1.31% and 1.97%, respectively. Anaplasma and Ehrlichia species were not detected from cattle, dogs and R. microplus ticks. The genetic differences in the groEL gene sequences of the Anaplasma in the current study were large, whereas the 16S rRNA and gltA gene sequences were less disparate. This study shows that ticks and goats in Suizhou County, Hubei Province carry multiple Anaplasma species and an Ehrlichia species, with relatively higher infection rate of A. bovis in goats. Our study indicates that multiple Anaplasma and Ehrlichia species exist in ticks and goats in the central China with potential to cause human infection.

Analysis of population structure and genetic diversity of Camellia tachangensis in Guizhou based on SNP markers.

BACKGROUND: Camellia tachangensis F. C. Zhang is a five-compartment species in the ovary of tea group plants, which represents the original germline of early differentiation of some tea group plants. METHODS AND RESULTS: In this study, we analyzed single-nucleotide polymorphisms (SNPs) at the genome level, constructed a phylogenetic tree, analyzed the genetic diversity, and further investigated the population structure of 100 C. tachangensis accessions using the genotyping-by-sequencing (GBS) method. A total of 91,959 high-quality SNPs were obtained. Population structure analysis showed that the 100 C. tachangensis accessions clustered into three groups: YQ-1 (Village Group), YQ-2 (Forest Group) and YQ-3 (Transition Group), which was further consistent with the results of phylogenetic analysis and principal component analyses (PCA). In addition, a comparative analysis of the genetic diversity among the three populations (Forest, Village, and Transition Groups) detected the highest genetic diversity in the Transition Group and the highest differentiation between Forest and Village Groups. CONCLUSIONS: C. tachangensis plants growing in the forest had different genetic backgrounds from those growing in villages. This study provides a basis for the effective protection and utilization of C. tachangensis populations and lays a foundation for future C. tachangensis breeding.

Mucor thermorhizoides-A New Species from Post-mining Site in Sudety Mountains (Poland).

Mucor representatives are mostly rapidly growing cosmopolitan soil saprotrophs of early diverged Mucoromycotina subphylum. Although this is the most speciose genus within the group, some lineages are still understudied. In this study, new species of Mucor was isolated from the post-mining area in southwestern Poland, where soil chemical composition analysis revealed high concentration of hydrocarbons and heavy metals. Phylogenetic analysis based on multigene phylogeny showed that the new isolate clusters distinctly from other Mucor species as a sister group to Mucor microsporus. New species Mucor thermorhizoides Abramczyk (Mucorales, Mucoromycota) is characterized by the extensive rhizoid production in elevated temperatures and formation of two layers of sporangiophores. It also significantly differs from M. microsporus in the shape of spores and the size of sporangia. M. thermorhizoides was shown to be able to grow in oligotrophic conditions at low temperatures. Together with M. microsporus they represent understudied and highly variable lineage of the Mucor genus.

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats.

The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while ß-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. KEY POINTS: • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest ß-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.

A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses.

Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order Pimascovirales of the phylum Nucleocytoviricota. However, they were not classified previously by the International Committee on Taxonomy of Viruses (ICTV). Here, we present a comprehensive analysis of the gene content, morphology, and phylogenomics of these viruses, providing data that underpinned the recent proposal to establish new taxa for their initial classification. The new taxonomy, which has now been ratified by the ICTV, includes the family Orpheoviridae and genus Alphaorpheovirus, the family Pithoviridae and genus Alphapithovirus, and the family Cedratviridae and genus Alphacedratvirus, aiming to formally catalogue the isolates covered in this study. Additionally, as per the newly adopted rules, we applied standardized binomial names for the virus species created to classify isolates with complete genome sequences available in public databases at the time of the proposal. The specific epithet of each virus species was chosen as a reference to the location where the exemplar virus was isolated.

Characterization of Pseudomonas spp. contamination and in situ spoilage potential in pasteurized milk production process.

To investigate the prevalence of Pseudomonas in the pasteurized milk production process and its effect on milk quality, 106 strains of Pseudomonas were isolated from the pasteurized milk production process of a milk production plant in Shaanxi Province, China. The protease, lipase and biofilm-producing capacities of the 106 Pseudomonas strains were evaluated, and the spoilage enzyme activities of their metabolites were assessed by simulating temperature incubation in the refrigerated (7 °C) and transport environment (25 °C) segments and thermal treatments of pasteurization (75 °C, 5 min) and ultra-high temperature sterilization (121 °C, 15 s). A phylogenetic tree was drawn based on 16S rDNA gene sequencing and the top 5 strains were selected as representative strains to identify their in situ spoilage potential by examining their growth potential and ability to hydrolyze proteins and lipids in milk using growth curves, pH, whiteness, Zeta-potential, lipid oxidation, SDS-PAGE and volatile flavor compounds. The results showed that half and more of the isolated Pseudomonas had spoilage enzyme production and biofilm capacity, and the spoilage enzyme activity of metabolites was affected by the culture temperature and sterilization method, but ultra-high temperature sterilization could not completely eliminate the enzyme activity. The growth of Pseudomonas lundensis and Pseudomonas qingdaonensis was less affected by temperature and time, and the hydrolytic capacity of extracellular protease and lipase secreted by Pseudomonas lurida was the strongest, which had the greatest effect on milk quality. Therefore, it is crucial to identify the key contamination links of Pseudomonas, the main bacteria responsible for milk spoilage, and the influence of environmental factors on its deterioration.

Genomic and taxonomic evaluation of 38 Treponema prophage sequences.

BACKGROUND: Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage. RESULTS: We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes. CONCLUSIONS: In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.

Emergence of Eurasian Avian-Like Swine Influenza A (H1N1) virus in a child in Shandong Province, China.

BACKGROUND: Influenza A virus infections can occur in multiple species. Eurasian avian-like swine influenza A (H1N1) viruses (EAS-H1N1) are predominant in swine and occasionally infect humans. A Eurasian avian-like swine influenza A (H1N1) virus was isolated from a boy who was suffering from fever; this strain was designated A/Shandong-binzhou/01/2021 (H1N1). The aims of this study were to investigate the characteristics of this virus and to draw attention to the need for surveillance of influenza virus infection in swine and humans. METHODS: Throat-swab specimens were collected and subjected to real-time fluorescent quantitative polymerase chain reaction (RT‒PCR). Positive clinical specimens were inoculated onto Madin-Darby canine kidney (MDCK) cells to isolate the virus, which was confirmed by a haemagglutination assay. Then, whole-genome sequencing was carried out using an Illumina MiSeq platform, and phylogenetic analysis was performed with MEGA X software. RESULTS: RT‒PCR revealed that the throat-swab specimens were positive for EAS-H1N1, and the virus was subsequently successfully isolated from MDCK cells; this strain was named A/Shandong-binzhou/01/2021 (H1N1). Whole-genome sequencing and phylogenetic analysis revealed that A/Shandong-binzhou/01/2021 (H1N1) is a novel triple-reassortant EAS-H1N1 lineage that contains gene segments from EAS-H1N1 (HA and NA), triple-reassortant swine influenza H1N2 virus (NS) and A(H1N1) pdm09 viruses (PB2, PB1, PA, NP and MP). CONCLUSIONS: The isolation and analysis of the A/Shandong-binzhou/01/2021 (H1N1) virus provide further evidence that EAS-H1N1 poses a threat to human health, and greater attention should be given to the surveillance of influenza virus infections in swine and humans.

Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria.

BACKGROUND: Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS: The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS: The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.

Decoding huge phage diversity: a taxonomic classification of Lak megaphages.

High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the 'Grandevirales'. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order 'Grandevirales'. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.

Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea.

Background: Despite the Caridean shrimps' vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P.  ortmanni, P. izumiae and P. lophotes. Methods: The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina's next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results: The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species-P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions: Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.).

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

Ultrastructure of the Jurassic serpulid tubes-phylogenetic and paleoecological implications.

The ultrastructural diversity of the Middle and Late Jurassic serpulid tubes from the Polish Basin has been investigated. The inspection of 12 taxa representing the two major serpulid clades allowed for the identification of three ultrastructure types-irregularly oriented prismatic structure (IOP), spherulitic prismatic structure (SPHP), and simple prismatic structure (SP). Six of the studied species are single-layered and six species possess two distinct layers. Ultrastructural diversity corresponds to certain serpulid clades. The members of Filograninae have single-layered tube walls composed of possibly plesiomorphic, irregularly oriented prismatic structure (IOP). Two-layered tubes occur solely within the clade Serpulinae, where the external, denser layer is built of either the ordered spherulitic (SPHP) or simple prismatic microstructure (SP), and the internal layer is composed of irregularly oriented prismatic structure (IOP). Apart from phylogenetic signals provided by the tube ultrastructure, it can be used in analyzing paleoecological aspects of tube-dwelling polychaetes. Compared to the more primitive, irregularly oriented microstructures of Filograninae, the regularly oriented microstructures of Serpulinae need a higher level of biological control over biomineralization. The advent of the dense outer protective layer (DOL) in serpulids, as well as the general increase in ultrastructure diversity, was likely a result of the evolutionary importance of the tubes for serpulids. Such diversity of the tube ultrastructural fabrics allowed for maximizing functionality by utilizing a variety of morphogenetic programs. The biomineralization system of serpulids remains more complex compared to other tube-dwelling polychaetes. Physiologically more expensive tube formation allows for mechanical strengthening of the tube by building robust, strongly ornamented tubes and firm attachment to the substrate. Contrary to sabellids, which perform a fugitive strategy, an increased tube durability allows serpulids a competitive advantage over other encrusters.

Distinctive color variation in Rhinolepadichthys geminus (Gobiesocidae: Diademichthyinae) from Alor Islands, Indonesia: morphological and molecular insights.

Rhinolepadichthys geminus, one of three recently described species in the genus Rhinolepadichthys (previously known as Lepadichthys lineatus complex), is characterized by several distinct diagnostic morphological and color features, including a pair of yellow stripes on the body ventral midline. However, one of three specimens recently collected from the Alor Islands, Indonesia, possessed a yellow circular line, instead of a pair of yellow stripes, indicating that the latter were not an invariable feature. Morphological and molecular evidence confirmed the identity of the specimen and intraspecific significance of the color variation.

Two Distinct Enzymes Have Both Phytoene Desaturase and 3,4-Desaturase Activities Involved in Carotenoid Biosynthesis by the Extremely Halophilic Archaeon Haloarcula japonica.

The extremely halophilic archaeon Haloarcula japonica accumulates the C50 carotenoid, bacterioruberin (BR). To reveal the BR biosynthetic pathway, unidentified phytoene desaturase candidates were functionally characterized in the present study. Two genes encoding the potential phytoene desaturases, c0507 and d1086, were found from the Ha. japonica genome sequence by a homology search using the Basic Local Align Search Tool. Disruption mutants of c0507 and d1086 and their complemented strains transformed with expression plasmids for c0507 and d1086 were subsequently constructed. High-performance liquid chromatography (HPLC) ana-lyses of carotenoids produced by these strains revealed that C0507 and D1086 were both bifunctional enzymes with the same activities as both phytoene desaturase (CrtI) and 3,4-desaturase (CrtD). C0507 and D1086 complemented each other during BR biosynthesis in Ha. japonica. This is the first study to identify two distinct enzymes with both CrtI and CrtD activities in an extremely halophilic archaeon.

Molecular characterization and phylogenetic analysis of babA gene of Helicobacter pylori isolated from Indian patients with gastrointestinal diseases.

INTRODUCTION: Outer membrane protein (OMP) of Helicobacter pylori (H. pylori) i.e., blood group antigen binding adhesin (babA) is responsible for the attachment of H. pylori in the gastric epithelium. Its adherence is causative for gastric pathology such as gastritis, peptic ulcer disease (PUD), or digestive tract disorders like erosive reflux disease (ERD) and (NERD) non-erosive reflux disease and together called Gastroesophageal reflux disease (GERD). BabA manifests rapid and varied selection via substitution of amino acid in its Leb-carbohydrate binding domain (CBD) which enables better binding preferences for distinct human populations and ABO blood group phenotypes. The positive evolutionary selection of the pathogenic factor of this genetically diverse bacterium has enabled it to adapt to the host gastric environment. Analyzing the association of virulent genes (cagA, vacA) and babA will help us better understand bacteria's pathogenicity. METHOD: 109 H. pylori strains from patients with distinct gastrointestinal diseases were genotyped using Polymerase Chain Reaction(PCR) for cagA, vacA, and babA followed by Sanger sequencing and phylogenetic analysis. RESULT: In the babA + ve genotype, a statistically significant association with p = 0.04 and < 0.0001 is seen in gastritis and ERD respectively. A significant association of genotype vacAs1m2 (p = 0.0002) was seen in gastritis, vacAs1m1 (p = 0.02) in NERD, vacAs1m1 (p < 0.0001) and vacAs1m2 (p = 0.002) in ERD. This relationship helps to detect gastritis or ERD where BabA gene can be used as an independent marker for detecting their presence. CONCLUSION: The appearance of variants within distinct disease categories is due to local genetic variation.

Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping.

Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens.

Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for Phytophthora sojae, Globisporangium ultimum, Pythium oligandrum, and G. spinosum. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with Copia-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in P. sojae. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.

An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function.

NLR family proteins act as intracellular receptors. Gene duplication amplifies the number of NLR genes, and subsequent mutations occasionally provide modifications to the second gene that benefits immunity. However, evolutionary processes after gene duplication and functional relationships between duplicated NLRs remain largely unclear. Here, we report that the rice NLR protein Pit1 is associated with its paralogue Pit2. The two are required for the resistance to rice blast fungus but have different functions: Pit1 induces cell death, while Pit2 competitively suppresses Pit1-mediated cell death. During evolution, the suppression of Pit1 by Pit2 was probably generated through positive selection on two fate-determining residues in the NB-ARC domain of Pit2, which account for functional differences between Pit1 and Pit2. Consequently, Pit2 lost its plasma membrane localization but acquired a new function to interfere with Pit1 in the cytosol. These findings illuminate the evolutionary trajectory of tandemly duplicated NLR genes after gene duplication.