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We present the genome assembly of the pennate diatom Epithemia pelagica strain UHM3201 (Ochrophyta; Bacillariophyceae; Rhopalodiales; Rhopalodiaceae) and that of its cyanobacterial endosymbiont (Chroococcales: Aphanothecaceae). The genome sequence of the diatom is 60.3 megabases in span, and the cyanobacterial genome has a length of 2.48 megabases. Most of the diatom nuclear genome assembly is scaffolded into 15 chromosomal pseudomolecules. The organelle genomes have also been assembled, with the mitochondrial genome 40.08 kilobases and the plastid genome 130.75 kilobases in length. A number of other prokaryote MAGs were also assembled.

Background: Directly discharging livestock and poultry slaughter blood without proper treatment can cause severe ecological damage. Exploring the use of microorganisms to break down waste blood into smaller molecules such as peptides and amino acids, as well as investigating the possibility of transforming these small molecules into water-soluble fertilizers containing amino acids, holds significant research value in the comprehensive utilization of livestock and poultry blood. Results: In this study, a single strain of Bacillus pumilus NWMCC0302, which has effectively degraded bovine blood, was isolated from abattoir blood sludge using casein agar plates and Columbia blood agar plates. The degradation test was carried out using bovine raw blood as a nitrogen source in the medium, and the results showed that the strain degraded 53.83% of bovine blood under optimal degradation conditions. The whole genome sequencing of Bacillus pumilus NWMCC0302 was conducted using the second-generation DNBSEQ platform and the third-generation PacBio platform, employing high-throughput sequencing technology. The size of the strain's entire genome was determined to be 3 868 814 bp with a G-C content of 41.63%. The total gene length accounted for 88.98% of the genome length at 3 442 341 bp and encoded 4 113 genes. The strain contained 79 tRNAs, 24 rRNAs, 7 sRNAs, and 296 repetitive sequences. The gene data obtained from sequencing were also functionally annotated using the COG, KEGG, and VFDB databases. In the COG database, 310 genes were involved in amino acid transport and metabolism, including 10 catabolic proteins related to COGs. In the KEGG database, were 201 genes involved in amino acid metabolism pathways, including 8 genes in nitrogen metabolism pathways and 2 genes in oxidative pathways. The VFDB database contains two lysostaphin genes and one serine protease-hydrolyzed ClpP gene. Conclusions: In summary, Bacillus pumilus NWMCC0302 was screened for its efficient ability to degrade bovine blood. Additionally, the genetic information of Bacillus pumilus NWMCC0302 was revealed at the genetic level, providing a feasible experimental method for applying this strain to the degradation of blood from slaughtered livestock and poultry. Moreover, it is a potential functional strain for producing amino acid-containing water-soluble fertilisers. [ABSTRACT FROM AUTHOR]

Avian leukosis is a significant viral disease affecting chicken populations globally, including Bangladesh, resulting in high mortality and morbidity rates and causing substantial economic losses in the commercial poultry industry. This study aimed to detect avian leukosis virus (ALV) during recent outbreaks in Bangladesh, utilising a molecular‐based approach. A total of 14 liver samples were collected from the suspected layer flocks in Bangladesh. The diagnosis of ALV infection in chickens was confirmed through necropsy, histopathological examinations, reverse transcription‐polymerase chain reaction (RT‐PCR), and sequence analysis. Gross observations revealed severe liver enlargement with scattered white nodules on the surface in the infected chickens. Histopathological observations showed the infiltration of huge mononuclear inflammatory cells in the periportal area of liver and microvesicular fatty degeneration and necrosis of some hepatocytes. RT‐PCR results identified three samples positive for the env gene of ALV. Sequence analysis of the env genes demonstrated high homology among the identified strains (97%–98%) and with reference strains (92%–96%) at the nucleotide level. The phylogenetic tree revealed close relatedness of the three identified strains to reference strains from India, USA, and China. Mutational analysis indicated several mutations throughout the envelope glycoprotein of the identified strains. Protein structure analysis showed minor changes in the hydrophobic region of the envelope protein of the identified strains. In conclusion, this study, the first detailed investigation in Bangladesh, contributes to understanding ALV epidemiology, highlights genetic diversity, and emphasises the necessity for further investigations and the implementation of effective control measures in the affected regions. [ABSTRACT FROM AUTHOR]

Koji mold (Aspergillus oryzae) is a key microorganism in brewing and fermentation in Japan. We isolated koji molds from the environment in Niigata Prefecture. Eighty-one environmental samples were placed on isolation medium made from steamed rice with wood ash and 36 Aspergillus section Flavi -like strains were obtained. Of those, 26 strains did not produce aflatoxin. We studied their morphology, sequence of ITS region, calmodulin gene, aflatoxin biosynthetic homologous gene cluster and α-amylase gene and fermentation-related enzyme activities. Furthermore, DNA-seq analysis of 14 strains from 26 non-aflatoxin producing strains were conducted and compared the three mycotoxin biosynthetic gene clusters (aflatoxin, cyclopiazonic acid, and aflatrem) and fermentation-related genes against those of reference strain A. oryzae RIB40. In some strains, gene sequences confirmed the absence of mycotoxin production, but differences in fermentation-related enzyme activities could not be explained well by amino acid substitutions. We classified the 26 isolates into 6 morphology types based on the appearance of colonies and mating types, and it was found that strains of the same morphology type had similar enzymatic profiles and gene sequences. Our results show that koji molds with various properties occur in the environment, and it will expand the possibilities of koji mold in industrial use. [ABSTRACT FROM AUTHOR]

Diplocarpon coronariae is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual morph of this pathogen, a phenomenon hitherto unobserved in Europe. Diplocarpon coronariae reproduces through a heterothallic mating system requiring at least two different mating types for sexual reproduction. Genes determining the mating types are located on the mating-type locus. In this study, D. coronariae strain DC1_JKI from Dresden, Germany, was sequenced and used to unravel the structure of the mating type locus. Using short-read and long-read sequencing methods, the first gapless and near-complete telomere-to-telomere genome assembly of D. coronariae was achieved. The assembled genome spans 51.2 Mbp and comprises 21 chromosome-scale contigs of high completeness. The generated genome sequence was used to in silico elucidate the structure of the mating-type locus, identified as MAT1-2. Furthermore, an examination of MAT1-1 and MAT1-2 frequency across a diverse set of samples sourced from Europe and Asia revealed the exclusive presence of MAT1-2 in European samples, whereas both MAT loci were present in Asian counterparts. Our findings suggest an explanation for the absence of the sexual morph, potentially linked to the absence of the second mating idiomorph of D. coronariae in European apple orchards. [ABSTRACT FROM AUTHOR]

Candida tropicalis (C. tropicalis) is a zoonotic pathogen that is widespread in the environment and in recent years an increasing number of dairy cows have been infected with the fungus causing mastitis in cows.In this study, 37 milk samples from the udders of cows with clinical mastitis were collected from a dairy farm in Guangxi Province, China, from which C. tropicalis was isolated and identified, and then the isolated fungi were subjected to genome frame map sequencing, genome functional analysis as well as comparative genome analysis of the sequencing results, and combined with the virulence test of the fungi and drug sensitivity test of the fungi determined in infected mice, the resistance genes and pathogenicity of the fungi were Analysis of resistance genes and pathogenicity.Our study results revealed the isolation and characterisation of C. tropicalis from diseased cows, with a genome length of approximately 14.27 Mb. Functional annotation of the genome identified 4068 genes associated with C. tropicalis. The strain exhibited a chemoresistance mutation in the gene cyp51,a virulence-enhancing mutation in the gene VTC4, and mutations in genes linked to drug resistance. Pathogenicity tests demonstrated that C. tropicalis could induce damage to the internal organs of mice, leading to different levels of cyanosis in the abdominal cavity, white necrotic foci on the surface of internal organs, lung hemorrhage, and enlargement of the spleen and thymus.Histological sections also revealed varying degrees of hemorrhage and degenerative changes in the cells of different organs in the mice. Drug sensitivity tests showed that the fungus was highly sensitive to nystatin and ketoconazole, moderately sensitive to amphotericin B, and insensitive to antibiotics such as itraconazole, gentamicin, and penicillin. In conclusion, C. tropicalis isolated from dairy cows in the Guangxi region in this study was pathogenic and resistant to azoles such as itraconazole and fluconazole, and this study provides a theoretical basis for the further screening of novel resistance genes in C. tropicalis, as well as providing a certain reference for the drugs used for the treatment of fungal cow mastitis in this region. [ABSTRACT FROM AUTHOR]

In the long history of human relations with flowering cherry trees in Japan, 'Somei-Yoshino' occupies an exceptional position among a variety of flowering trees: it is a self-incompatible interspecific hybrid but has been enthusiastically planted by grafting throughout Japan, due most likely to its flamboyant appearance upon full bloom. Thus, 'Somei-Yoshino' gives us a rare opportunity to trace and investigate the occurrence and distribution of somatic mutations within a single plant species through analysis of the genomes of the clonally propagated trees grown under a variety of geographical and artificial environments. In the studies presented here, a total of 46 samples of 'Somei-Yoshino' trees were collected and their genomes were analysed. We identified 684 single nucleotide mutations, of which 71 were present in more than two samples. Clustering analysis of the mutations indicated that the 46 samples were classified into eight groups, four of which included 36 of the 46 samples analysed. Interestingly, all the four tree samples collected in Ueno Park of Tokyo were members of the four groups mentioned above. Based on comparative analysis of their mutations, one of the four trees growing in Ueno Park was concluded to be the closest to the original ancestor. We propose that somatic mutations may be used as tracers to establish the ancestral relationship amongst clonally propagated individuals. [ABSTRACT FROM AUTHOR]

Abstract Background Directly discharging livestock and poultry slaughter blood without proper treatment can cause severe ecological damage. Exploring the use of microorganisms to break down waste blood into smaller molecules such as peptides and amino acids, as well as investigating the possibility of transforming these small molecules into water-soluble fertilizers containing amino acids, holds significant research value in the comprehensive utilization of livestock and poultry blood. Results In this study, a single strain of Bacillus pumilus NWMCC0302, which has effectively degraded bovine blood, was isolated from abattoir blood sludge using casein agar plates and Columbia blood agar plates. The degradation test was carried out using bovine raw blood as a nitrogen source in the medium, and the results showed that the strain degraded 53.83% of bovine blood under optimal degradation conditions. The whole genome sequencing of Bacillus pumilus NWMCC0302 was conducted using the second-generation DNBSEQ platform and the third-generation PacBio platform, employing high-throughput sequencing technology. The size of the strain's entire genome was determined to be 3 868 814 bp with a G-C content of 41.63%. The total gene length accounted for 88.98% of the genome length at 3 442 341 bp and encoded 4 113 genes. The strain contained 79 tRNAs, 24 rRNAs, 7 sRNAs, and 296 repetitive sequences. The gene data obtained from sequencing were also functionally annotated using the COG, KEGG, and VFDB databases. In the COG database, 310 genes were involved in amino acid transport and metabolism, including 10 catabolic proteins related to COGs. In the KEGG database, were 201 genes involved in amino acid metabolism pathways, including 8 genes in nitrogen metabolism pathways and 2 genes in oxidative pathways. The VFDB database contains two lysostaphin genes and one serine protease-hydrolyzed ClpP gene. Conclusions In summary, Bacillus pumilus NWMCC0302 was screened for its efficient ability to degrade bovine blood. Additionally, the genetic information of Bacillus pumilus NWMCC0302 was revealed at the genetic level, providing a feasible experimental method for applying this strain to the degradation of blood from slaughtered livestock and poultry. Moreover, it is a potential functional strain for producing amino acid-containing water-soluble fertilisers.

Abstract Candida tropicalis (C. tropicalis) is a zoonotic pathogen that is widespread in the environment and in recent years an increasing number of dairy cows have been infected with the fungus causing mastitis in cows.In this study, 37 milk samples from the udders of cows with clinical mastitis were collected from a dairy farm in Guangxi Province, China, from which C. tropicalis was isolated and identified, and then the isolated fungi were subjected to genome frame map sequencing, genome functional analysis as well as comparative genome analysis of the sequencing results, and combined with the virulence test of the fungi and drug sensitivity test of the fungi determined in infected mice, the resistance genes and pathogenicity of the fungi were Analysis of resistance genes and pathogenicity.Our study results revealed the isolation and characterisation of C. tropicalis from diseased cows, with a genome length of approximately 14.27 Mb. Functional annotation of the genome identified 4068 genes associated with C. tropicalis. The strain exhibited a chemoresistance mutation in the gene cyp51,a virulence-enhancing mutation in the gene VTC4, and mutations in genes linked to drug resistance. Pathogenicity tests demonstrated that C. tropicalis could induce damage to the internal organs of mice, leading to different levels of cyanosis in the abdominal cavity, white necrotic foci on the surface of internal organs, lung hemorrhage, and enlargement of the spleen and thymus.Histological sections also revealed varying degrees of hemorrhage and degenerative changes in the cells of different organs in the mice. Drug sensitivity tests showed that the fungus was highly sensitive to nystatin and ketoconazole, moderately sensitive to amphotericin B, and insensitive to antibiotics such as itraconazole, gentamicin, and penicillin. In conclusion, C. tropicalis isolated from dairy cows in the Guangxi region in this study was pathogenic and resistant to azoles such as itraconazole and fluconazole, and this study provides a theoretical basis for the further screening of novel resistance genes in C. tropicalis, as well as providing a certain reference for the drugs used for the treatment of fungal cow mastitis in this region.

Lipomyces tetrasporous is an oleaginous yeast that can utilize a variety of plant-based sugars. It accumulates lipids during growth on lignocellulosic biomass hydrolysates. We present the annotated genome sequence of L. tetrasporous NRRL Y-64009 to aid in its development as a platform organism for producing lipids and lipid-based bioproducts.

Xanthomonas oryzae are destructive phytopathogens in rice production and also an important model system for studying the interaction between plants and bacterial pathogens. Here, we report the isolation and complete genome sequence of the X. oryzae strain YXol-1. Through the identification of transcription activator-like effectors and whole-genome-based phylogenetic analysis, we confirmed that YXol-1 belongs to a rarely reported type of X. oryzae pathovar named X. oryzae pv. leersiae (Xol). The present work enriches the genetic resources of Xol for studying the evolution of X. oryzae strains and can contribute to a better understanding of Xol–host interaction. [Figure: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract Identifying genomic markers for phosphate-solubilizing bacteria (PSB) is vital for advancing agricultural sustainability. This study utilizes whole-genome sequencing and comprehensive bioinformatics analysis, examining the genomes of 76 PSB strains with the aid of specialized genomic databases and analytical tools. We have identified the pqq gene cluster, particularly the pqqC gene, as a key marker for (P) solubilization capabilities. The pqqC gene encodes an enzyme that catalyzes the conversion of precursors to 2-keto-d-gluconic acid, which significantly enhances P solubilization in soil. This gene’s importance lies not only in its biochemical function but also in its prevalence and effectiveness across various PSB strains, distinguishing it from other potential markers. Our study focuses on Burkholderia cepacia 51-Y1415, known for its potent solubilization activity, and demonstrates a direct correlation between the abundance of the pqqC gene, the quantitative release of P, and the production of 2-keto-d-gluconic acid over a standard 144-h cultivation period under standardized conditions. This research not only underscores the role of the pqqC gene as a universal marker for the rapid screening and functional annotation of PSB strains but also highlights its implications for enhancing soil fertility and crop yields, thereby contributing to more sustainable agricultural practices. Our findings provide a foundation for future research aimed at developing targeted strategies to optimize phosphate solubilization, suggesting areas for further investigation such as the integration of these genomic insights into practical agricultural applications to maximize the effectiveness of PSB strains in real-world soil environments.

Abstract African swine fever (ASF) is an acute and fatal hemorrhagic disease in domestic pigs and wild boars caused by African swine fever virus (ASFV) that currently threatens the pig industry worldwide. Since the 2018 ASF outbreak in China, ASFV has evolved and caused diverse clinical manifestations, such as chronic and asymptomatic infections. Therefore, it is important to understand the molecular mechanisms underlying ASFV attenuation in the field. Here, we isolated three ASFVs from one diseased and two asymptomatic pigs by using primary porcine alveolar macrophages (PAMs) from both domestic pigs and Bama minipigs. The three ASFVs exhibited similar phenotypes in cell culture, including cytopathic effects (CPEs), hemadsorptions (HADs), viral protein expressions and growth curves. Genome sequencing revealed that all three ASFVs were genotype II strains. Genomic comparisons suggested that the disruption of the viral genes MGF360 and MGF110, rather than EP402R and EP153R, is likely involved in the potential attenuation of ASFV via the upregulation of innate immune responses.

SUMMARY: Genetic screens are powerful tools for biological research and are one of the reasons for the success of the thale cress Arabidopsis thaliana as a research model. Here, we describe the whole‐genome sequencing of 871 Arabidopsis lines from the Homozygous EMS Mutant (HEM) collection as a novel resource for forward and reverse genetics. With an average 576 high‐confidence mutations per HEM line, over three independent mutations altering protein sequences are found on average per gene in the collection. Pilot reverse genetics experiments on reproductive, developmental, immune and physiological traits confirmed the efficacy of the tool for identifying both null, knockdown and gain‐of‐function alleles. The possibility of conducting subtle repeated phenotyping and the immediate availability of the mutations will empower forward genetic approaches. The sequence resource is searchable with the ATHEM web interface (https://lipm‐browsers.toulouse.inra.fr/pub/ATHEM/), and the biological material is distributed by the Versailles Arabidopsis Stock Center. Significance Statement: Genetic screenings in plants have been constrained by sample size and phenotyping capacity including in model organisms. Here, we report a fully‐sequenced collection of 871 Arabidopsis homozygous EMS mutants which significantly expands the capacity of our community of plant geneticists to conduct forward or reverse screens and rapidly access to the causal genetic changes. [ABSTRACT FROM AUTHOR]

This work aimed to isolate and characterize a novel chitin‐degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY‐4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus Paenibacillus, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA–DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of Paenibacillus woosongensis B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy‐metal toxicity and 359 carbohydrate‐active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies. [ABSTRACT FROM AUTHOR]

Bacillus thuringiensis (Bt) is a Gram-positive, spore-forming, and ubiquitous bacterium harboring plasmids encoding a variety of proteins with insecticidal activity, but also with activity against nematodes. The aim of this work was to perform the genome sequencing and analysis of a native Bt strain showing bipyramidal parasporal crystals and designated V-CO3.3, which was isolated from the dust of a grain storehouse in Córdoba (Spain). Its genome comprised 99 high-quality assembled contigs accounting for a total size of 5.2 Mb and 35.1% G + C. Phylogenetic analyses suggested that this strain should be renamed as Bacillus cereus s.s. biovar Thuringiensis. Gene annotation revealed a total of 5495 genes, among which, 1 was identified as encoding a Cry5Ba homolog protein with well-documented toxicity against nematodes. These results suggest that this Bt strain has interesting potential for nematode biocontrol. Dataset: The BioSample data have been submitted under accession number SAMN41014059. The whole-genome sequences have been submitted to the NCBI with BioProject number PRJNA1102171. The assembled genome sequences are available under accession number JBCGZW000000000. The (Illumina) raw reads have been submitted to Sequence Read Archives (SRA) under accession number SRR28927673. The V-CO-3.3 strain has been stored in the Spanish Type Culture Collection (CECT) at the University of Valencia (Spain) under accession number CECT 31068. Dataset License: CC-BY-NC [ABSTRACT FROM AUTHOR]

Chili pepper (Capsicum spp.) is an economically important crop in Indonesia. The popularity of extremely spicy cuisines has surged in recent years, making Capsicum frutescens L. the preferred cultivar for such purpose. To enhance breeding efforts for C. frutescens, we investigated traditional cultivars that possess desirable traits. In this study, we focused on Saha Mpida, a traditional cultivar from Bima in Sumbawa Island, known for its high pungency and small fruit size. Utilizing the genome sequence of Saha Mpida, we conducted a comparative analysis and identified two accessions from Brazil and one accession from Bolivia as its closest genetic relatives. The phenotypic descriptions further validated the resemblance between Saha Mpida and its genetic relatives. By analyzing DNA sequence variation in key genes involved in capsaicin biosynthesis, we uncovered numerous missense mutations. However, we did not identify any disruptive mutations that could obstruct capsaicin biosynthesis. Further investigations, especially on gene expression level and enzyme activities, are necessary to identify the specific genes responsible for the elevated capsaicin content in Saha Mpida. Unveiling the genetic determinants underlying this unique trait will facilitate marker-assisted breeding approaches and contribute to the development of improved C. frutescens cultivars with enhanced pungency, fruit quality, and adaptability to diverse agro-climatic conditions. In addition, the publicly available genome sequence data will enrich the data pool of genomic diversity of Capsicum spp. worldwide. [ABSTRACT FROM AUTHOR]

Identifying genomic markers for phosphate-solubilizing bacteria (PSB) is vital for advancing agricultural sustainability. This study utilizes whole-genome sequencing and comprehensive bioinformatics analysis, examining the genomes of 76 PSB strains with the aid of specialized genomic databases and analytical tools. We have identified the pqq gene cluster, particularly the pqqC gene, as a key marker for (P) solubilization capabilities. The pqqC gene encodes an enzyme that catalyzes the conversion of precursors to 2-keto-d-gluconic acid, which significantly enhances P solubilization in soil. This gene's importance lies not only in its biochemical function but also in its prevalence and effectiveness across various PSB strains, distinguishing it from other potential markers. Our study focuses on Burkholderia cepacia 51-Y1415, known for its potent solubilization activity, and demonstrates a direct correlation between the abundance of the pqqC gene, the quantitative release of P, and the production of 2-keto-d-gluconic acid over a standard 144-h cultivation period under standardized conditions. This research not only underscores the role of the pqqC gene as a universal marker for the rapid screening and functional annotation of PSB strains but also highlights its implications for enhancing soil fertility and crop yields, thereby contributing to more sustainable agricultural practices. Our findings provide a foundation for future research aimed at developing targeted strategies to optimize phosphate solubilization, suggesting areas for further investigation such as the integration of these genomic insights into practical agricultural applications to maximize the effectiveness of PSB strains in real-world soil environments. [ABSTRACT FROM AUTHOR]

African swine fever (ASF) is an acute and fatal hemorrhagic disease in domestic pigs and wild boars caused by African swine fever virus (ASFV) that currently threatens the pig industry worldwide. Since the 2018 ASF outbreak in China, ASFV has evolved and caused diverse clinical manifestations, such as chronic and asymptomatic infections. Therefore, it is important to understand the molecular mechanisms underlying ASFV attenuation in the field. Here, we isolated three ASFVs from one diseased and two asymptomatic pigs by using primary porcine alveolar macrophages (PAMs) from both domestic pigs and Bama minipigs. The three ASFVs exhibited similar phenotypes in cell culture, including cytopathic effects (CPEs), hemadsorptions (HADs), viral protein expressions and growth curves. Genome sequencing revealed that all three ASFVs were genotype II strains. Genomic comparisons suggested that the disruption of the viral genes MGF360 and MGF110, rather than EP402R and EP153R, is likely involved in the potential attenuation of ASFV via the upregulation of innate immune responses. [ABSTRACT FROM AUTHOR]

Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome for a Hoplonemertea species is crucial. Such data will be highly useful for future investigations toward a better understanding of molecular ecology, venom evolution, and regeneration not only in Nemertea but also in other marine invertebrate phyla. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well suited for laboratory experimentation. The genome has an assembly size of 157.9 Mb. Hi-C scaffolding yielded chromosome-level scaffolds, with a scaffold N50 of 10.0 Mb and a score of 95.1% for complete BUSCO genes found as a single copy. Annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50. [ABSTRACT FROM AUTHOR]

Simple Summary: Outbreaks of chicken anemia virus (CAV) had occurred in specific-pathogen-free (SPF) chicken flocks. Removing seropositive chickens and adjacent seronegative chickens from the SPF facility and disinfecting housing with chemical agents did not halt outbreaks. Incidences decreased with an increase in chicks hatched from CAV-seropositive hens as maternal antibodies protected these chicks from CAV infection. We isolated eggs from CAV-seropositive hens through artificial insemination using CAV-free semen from roosters. The eggs were transferred to a new SPF facility and used to produce CAV-free progeny. To date, the colony raised at the new facility has been CAV-free for longer than two years. A specific-pathogen-free (SPF) chicken colony was maintained with successive groups a month apart in age. The absence of specific pathogens, including chicken anemia virus (CAV), was confirmed through periodic serological tests for each group. However, some groups became CAV seropositive. The procedures of removing seropositive and the adjacent seronegative chickens followed with chemically disinfecting the housing did not halt CAV outbreaks. The full genome sequence of the CAV strain that appeared was closely related to low-virulence isolates in China. The outbreaks of CAV decreased with an increase in the seropositive chicken population, indicating that the progeny is protected from CAV infection by maternal anti-CAV antibodies. The persistence of CAV in erythroid and lymphoid tissues or reproductive tissues from CAV seropositive chickens was examined in chickens of various ages using polymerase chain reaction (PCR). Since a low persistence of CAV was observed in the colony, we isolated eggs from CAV seropositive hens through artificial insemination using semen collected from roosters and confirmed as CAV-free by PCR. Fertilized eggs were transferred to a new SPF facility and used for generating CAV-free progeny. To date, chickens reared in the new facility have been CAV-free for longer than two years. Redirection of eggs from seropositive hens was an effective means of eliminating CAV from chickens. [ABSTRACT FROM AUTHOR]

Pythium species are distributed globally, with certain members playing significant roles as plant and animal pathogens. Pythium cedri Chen 4 has been identified as a pathogenic isolate responsible for causing root rot on Cedrus deodara. Here, a comprehensive genome-wide sequence of P. cedri strain Chen 4 utilizing the Illumina NovaSeq sequencing platform and a Pacific Biosciences Sequel sequencing platform is presented. The genome of P. cedri strain Chen 4 was assembled into 150 contigs containing a combined size of 41.25 Mb, N50 value of 1,717,859 bp and N90 value of 431,829 bp. Genome annotation revealed 14,077 protein-encoding genes and 364 of the 1016 predicted proteins were putative effectors. The present work enriches the genetic resources of P. cedri for studying its evolution and can contribute to a better understanding of P. cedri–host interaction.

In March 2024, the emergence of highly pathogenic avian influenza (HPAI) A (H5N1) infections in dairy cattle was detected in the United Sates for the first time. We genetically characterize HPAI viruses from dairy cattle showing an abrupt drop in milk production, as well as from two cats, six wild birds, and one skunk. They share nearly identical genome sequences, forming a new genotype B3.13 within the 2.3.4.4b clade. B3.13 viruses underwent two reassortment events since 2023 and exhibit critical mutations in HA, M1, and NS genes but lack critical mutations in PB2 and PB1 genes, which enhance virulence or adaptation to mammals. The PB2 E627 K mutation in a human case associated with cattle underscores the potential for rapid evolution post infection, highlighting the need for continued surveillance to monitor public health threats.

We present a genome assembly from an individual male ichneumonid wasp, Pimpla contemplator (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence has a total length of 270.30 megabases. Most of the assembly (92.24%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.79 kilobases in length.

We present a genome assembly from an individual male Mythimna pallens (the Common Wainscot moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 719.10 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,343 protein-coding genes.

We present a genome assembly from an individual female Falcaria lacertinaria (the Scalloped Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 300.20 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.07 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,709 protein-coding genes.

We present a genome assembly from a tetraploid specimen of the confused eyebright, Euphrasia confusa (Streptophyta; Magnoliopsida; Lamiales; Orobanchaceae). The genome sequence has a total length of 976.50 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2n = 4x = 44). There are two mitochondrial genome scaffolds with lengths of 329.69 and 112.33 kilobases, and the plastid genome is 144.97 kilobases long.

We present a genome assembly from a female specimen of Gastrophysa polygoni (knotweed leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 369.80 megabases. Most of the assembly (99.89%) is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.11 kilobases in length.

We present a genome assembly from a specimen of Coprinellus micaceus (the glistening inkcap; Basidiomycota; Agaricomycetes; Agaricales; Psathyrellaceae). The genome sequence is 52.0 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 54.99 kilobases in length.

We present a genome assembly from an individual male Myotis mystacinus (whiskered bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence has a total length of 2,081.20 megabases. Most of the assembly (97.52%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.93 kilobases in length.

We present a genome assembly from a juvenile female Lagenorhynchus albirostris (the white-beaked dolphin; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence has a total length of 2,544.80 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length.

We present a genome assembly from a specimen of small nettle, Urtica urens (Streptophyta; Magnoliopsida; Rosales; Urticaceae). The genome sequence has a total length of 339.60 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 335.02 kilobases and 147.51 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 18,378 protein-coding genes.

We present a genome assembly from an individual female Periphyllus acericola (the sycamore periphyllus aphid; Arthropoda; Insecta; Hemiptera; Aphididae). The genome sequence has a total length of 405.30 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 33.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,463 protein-coding genes.

We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.

We present a genome assembly from an individual female solidierfly, Stratiomys singularior (Arthropoda; Insecta; Diptera; Stratiomyidae). The genome sequence has a total length of 715.20 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,614 protein-coding genes.

We present a genome assembly from an individual Sardina pilchardus (the sardine; Chordata; Actinopteri; Clupeiformes; Clupeidae). The genome sequence spans 869.40 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.57 kilobases in length.

We present a genome assembly from an individual Bromus sterilis (the barren brome; Streptophyta; Magnoliopsida; Poales; Poaceae). The genome sequence has a total length of 2,677.90 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 523.28 kilobases and 136.96 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 29,147 protein-coding genes.

We present a genome assembly from an individual male Tenthredo scrophulariae (Figwort Sawfly; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence has a total length of 233.10 megabases. Most of the assembly (99.96%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 26.26 kilobases in length.

We present a genome assembly from an individual Medicago arabica (the spotted medick; Tracheophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence is 515.5 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 324.47 kilobases and 125.07 kilobases in length, respectively. Gene annotation of this assembly on Ensembl identified 24,619 protein-coding genes.

ABSTRACT Avian leukosis is a significant viral disease affecting chicken populations globally, including Bangladesh, resulting in high mortality and morbidity rates and causing substantial economic losses in the commercial poultry industry. This study aimed to detect avian leukosis virus (ALV) during recent outbreaks in Bangladesh, utilising a molecular‐based approach. A total of 14 liver samples were collected from the suspected layer flocks in Bangladesh. The diagnosis of ALV infection in chickens was confirmed through necropsy, histopathological examinations, reverse transcription‐polymerase chain reaction (RT‐PCR), and sequence analysis. Gross observations revealed severe liver enlargement with scattered white nodules on the surface in the infected chickens. Histopathological observations showed the infiltration of huge mononuclear inflammatory cells in the periportal area of liver and microvesicular fatty degeneration and necrosis of some hepatocytes. RT‐PCR results identified three samples positive for the env gene of ALV. Sequence analysis of the env genes demonstrated high homology among the identified strains (97%–98%) and with reference strains (92%–96%) at the nucleotide level. The phylogenetic tree revealed close relatedness of the three identified strains to reference strains from India, USA, and China. Mutational analysis indicated several mutations throughout the envelope glycoprotein of the identified strains. Protein structure analysis showed minor changes in the hydrophobic region of the envelope protein of the identified strains. In conclusion, this study, the first detailed investigation in Bangladesh, contributes to understanding ALV epidemiology, highlights genetic diversity, and emphasises the necessity for further investigations and the implementation of effective control measures in the affected regions.

We present a genome assembly from an individual female Tinea pellionella (the Case-bearing Clothes moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 245.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 25.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,811 protein coding genes.

We present a genome assembly from a specimen of Black Medic, Medicago lupulina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 575.40 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 294.12 kilobases and 123.99 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,424 protein-coding genes.

We present a genome assembly from an individual female woodlouse fly, Melanophora roralis (Arthropoda; Insecta; Diptera; Rhinophoridae). The genome sequence has a total length of 565.10 megabases. Most of the assembly (98.9%) is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 19.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,321 protein-coding genes.

We present a genome assembly from a specimen of Draba incana (Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence has a total length of 667.80 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2n = 32). The mitochondrial and plastid genome assemblies have lengths of 283.08 kilobases and 153.57 kilobases, respectively.

We present a genome assembly from an individual female Tachina grossa (the giant tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence spans 936.90 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.82 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,428 protein-coding genes.

We present a genome assembly from an individual female Golden-tabbed robberfly, Eutolmus rufibarbis (Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 285.90 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.22 kilobases in length.

We present a genome assembly from an individual male Clangula hyemalis (the Long-tailed duck; Chordata; Aves; Anseriformes; Anatidae). The genome sequence spans 1,206.10 megabases. Most of the assembly is scaffolded into 41 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.63 kilobases in length.

We present a genome assembly from an individual of Inga oerstediana (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 970.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 1,166.81 and 175.18 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 33,334 protein-coding genes.

We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.

We present a genome assembly from an individual male Asteroscopus sphinx (the Sprawler moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 857.30 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome and a putative B chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length.