Whole genome sequence of denitrifying bacterium Stutzerimonas stutzeri strain NGHE31, collected from an eutrophic wetland in Sunamganj, Bangladesh, following the 2017 flash floods

Here, we report the whole genome sequence of Stutzerimonas stutzeri strain NGHE31, isolated from Dekhar Haor, following the 2017 flash flood that resulted in mass die-offs of local wildlife. The predicted genome size is 4,434,670 bp, with 63.97% GC content, 4,035 coding sequences, 3 rRNAs, and 50 tRNAs.

Complete genome sequence of plasmid-bearing aerotolerant Campylobacter jejuni strain S2-20 isolated from retail chicken meat

Complete genome sequencing of aerotolerant Campylobacter jejuni strain S2-20 revealed the presence of a chromosome of 1,695,449 bp and a plasmid of 49,741 bp that contains predicted antimicrobial resistance and type IV secretion system genes. The chromosome harbored several putative oxidative stress genes with potential roles in aerotolerance.

The genome sequence of Tenthredo notha Klug, 1814, a sawfly

We present a genome assembly from an individual female Tenthredo notha (Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 253 megabases in span. Most of the assembly (99.91%) is scaffolded into 20 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 19.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 10,235 protein coding genes.

From tradition to innovation: conventional and deep learning frameworks in genome annotation

Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain

We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

The genome sequence of the devil's coach horse beetle, Ocypus olens (Müller, 1764)

We present a genome assembly from an individual female Ocypus olens (the devil's coach horse; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 1,084 megabases in span. The majority (98.81%) of the assembly is scaffolded into 20 chromosomal pseudomolecules, with the X sex chromosome assembled.

Complete genome sequence of Vibrio sp. strain AH4, a close relative of Vibrio metoecus isolated from Nile tilapia (Oreochromis niloticus)

Here, I report the complete genome sequence of Vibrio sp. strain AH4, which had been isolated from moribund farmed Nile tilapia (Oreochromis niloticus). Assessment of the genome sequence of this strain revealed the presence of two linear chromosomes 2,894,109 bp and 1,082,372 bp.

Complete genome sequence of Parabacteroides distasonis strain GP102, isolated from the cecum of a morbid pregnant laboratory guinea pig (Cavia porcellus)

Parabacteroides distasonis is an anaerobic bacterium with ambivalent health effects. P. distasonis strain GP102 was isolated from the cecum content of a morbid pregnant laboratory guinea pig (Cavia porcellus). The genome consists of one circular 5.39-Mbp chromosome with a G + C content of 44.79%.

Use of a Candida albicans SC5314 PacBio HiFi reads dataset to close gaps in the reference genome assembly, reveal a subtelomeric gene family, and produce accurate phased allelic sequences

Candida albicans SC5314 is the most-often used strain for molecular manipulation of the species. The SC5314 reference genome sequence is the result of considerable effort from many scientists and has advanced research into fungal biology and pathogenesis. Although the resource is highly developed and presented in a phased diploid format, the sequence includes gaps and does not extend to the telomeres on its eight chromosome pairs. Accurate SC5314 genome assembly is complicated by the presence of extensive repeated sequences and considerable allelic length variation at some loci. Advances in genome sequencing technology provide the tools to obtain highly accurate long-read data that span even the most-difficult-to-assemble genome regions. Here, we describe derivation of a PacBio HiFi data set and creation of a collapsed haploid telomere-to-telomere assembly of the SC5314 genome (ASM3268872v1) that revealed previously unknown features of the strain. ASM3268872v1 subtelomeric distances were up to 19 kb larger than in the reference genome and revealed a family of highly conserved DNA helicase-encoding genes at 10 of the 16 chromosome ends. We also describe alignments of individual HiFi reads to deduce accurate diploid sequences for the most notoriously difficult-to-assemble C. albicans genes: the agglutinin-like sequence (ALS) gene family. We provide a tutorial that demonstrates how the HiFi reads can be visualized to explore any region of interest. Availability of the HiFi reads data set and the ASM3268872v1 comparative guide assembly will streamline research efforts because accurate diploid sequences can be derived using simple in silico methods rather than time-consuming laboratory-bench approaches.

Draft genome sequence of Xylella fastidiosa strain ATCC 35874 isolated from infected red oak in Washington, DC

We report here the draft genome sequence of Xylella fastidiosa strain ATCC 35874. The strain was originally isolated from infected red oak in Washington, DC, and obtained from the American Type Culture Collection. The ATCC 35874 genome contains 2,543,332 bp and has a G + C content of 51.72%.

Genome sequence of Clostridium septicum strain WW106, isolated from influent wastewater at a research center with multiple-species research animal facilities

Clostridium septicum is an anaerobic Gram-positive rod-shaped bacterial pathogen known as a lethal causative agent of progressive gas gangrene in animals and humans. We report the 3.43-Mbp genome sequence of C. septicum strain WW106, isolated from influent wastewater at a research center with multiple-species laboratory animal facilities.

Complete genome sequence of Pseudomonas phage Ep4 lysing the kiwifruit canker bacteria

Pseudomonas syringae pv. actinidiae is a pathogen of kiwifruit canker. Ep4, a bacteriophage lysing the pathogenic bacteria, was isolated from an affected plant. Sequencing and annotation have revealed 44,614-bp genome with 52 predicted open reading frames. Ep4 is closest to Pseudomonas phage YMC11/06/C171_PPU_BP, albeit with low homology.

The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794)

We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 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 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.

The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796)

We present a genome assembly from an individual female Archips crataeganus (the Brown Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,596 protein coding genes.

Multiomics analyses of two Leonurus species illuminate leonurine biosynthesis and its evolution

The Lamiaceae family is renowned for its terpenoid-based medicinal components, but Leonurus, which has traditional medicinal uses, stands out for its alkaloid-rich composition. Leonurine, the principal active compound found in Leonurus, has demonstrated promising effects in reducing blood lipids and treating strokes. However, the biosynthetic pathway of leonurine remains largely unexplored. Here, we present the chromosome-level genome sequence assemblies of Leonurus japonicus, known for its high leonurine production, and Leonurus sibiricus, characterized by very limited leonurine production. By integrating genomics, RNA sequencing, metabolomics, and enzyme activity assay data, we constructed the leonurine biosynthesis pathway and identified the arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase enzymes that catalyze key reactions in this pathway. Further analyses revealed that the UGT-SCPL gene cluster evolved by gene duplication in the ancestor of Leonurus and neofunctionalization of SCPL in L. japonicus, which contributed to the accumulation of leonurine specifically in L. japonicus. Collectively, our comprehensive study illuminates leonurine biosynthesis and its evolution in Leonurus.

Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system

A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.

Draft genome sequence of active gold mine isolate Pseudomonas iranensis strain ABS_30

Pseudomonas iranensis ABS_30, isolated from gold mining soil, exhibits metal-resistant properties valuable for heavy metal removal. We report the draft genome sequencing of the P. iranensis ABS_30 strain, which is 5.9 Mb in size.

strain TS-2, an ascomycete fungus isolated from a freshwater outflow and capable of Mn(II) oxidation

Members of the genus Periconia are commonly found as plant-associated filamentous fungi. Here, the first draft genome sequence of a new Periconia strain, TS-2, that was isolated from freshwater outflow sediment and possesses the ability to oxidize dissolved Mn(II), was obtained and has an estimated size of 40.7 Mb.

Tentaclins-A Novel Family of Phage Receptor-Binding Proteins That Can Be Hypermutated by DGR Systems

Diversity-generating retroelements (DGRs) are prokaryotic systems providing rapid modification and adaptation of target proteins. In phages, the main targets of DGRs are receptor-binding proteins that are usually parts of tail structures and the variability of such host-recognizing structures enables phage adaptation to changes on the bacterial host surface. Sometimes, more than one target gene containing a hypermutated variable repeat (VR) can be found in phage DGRs. The role of mutagenesis of two functionally different genes is unclear. In this study, several phage genomes that contain DGRs with two target genes were found in the gut virome of healthy volunteers. Bioinformatics analysis of these genes indicated that they encode proteins with different topology; however, both proteins contain the C-type lectin (C-lec) domain with a hypermutated beta-hairpin on its surface. One of the target proteins belongs to a new family of proteins with a specific topology: N-terminal C-lec domain followed by one or more immunoglobulin domains. Proteins from the new family were named tentaclins after TENTACLe + proteIN. The genes encoding such proteins were found in the genomes of prophages and phages from the gut metagenomes. We hypothesized that tentaclins are involved in binding either to bacterial receptors or intestinal/immune cells.

The genome sequence of the European flat oyster, Ostrea edulis (Linnaeus, 1758)

We present a genome assembly from an individual Ostrea edulis (the European flat oyster; Mollusca; Bivalvia; Ostreida; Ostreidae). The genome sequence is 894.8 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.35 kilobases in length.

Genome Sequence Resource of Cladosporium velox Strain C4 Causing Cotton Boll Disease in Xinjiang, China

Cladosporium spp., as one of the largest and most heterogeneous genera of hyphomycetes, are widely distributed worldwide. This genus is usually adaptable to a wide variety of extreme environments. However, only 11 genomes of Cladosporium genus have been publicly released. From 2017, we found for the first time that Cladosporium velox could cause cotton boll disease and lead to stiffness and cracking boll in Xinjiang, China. Herein, we provide a high-quality reference genome for the C. velox strain C4 isolated from cotton boll in Xinjiang, China. The genome size and encoding gene number of the C. velox strain C4 and C. cucumerinum strain CCNX2, which was recently released and caused the cucumber scab, showed minor differences. This resource will contribute to future research that aims to elucidate the genetic basis of C. velox pathogenicity and could expand our knowledge of Cladosporium spp. genomic characteristics that will be valuable for the development of Cladosporium disease control measures.

Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446T (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

The genome sequence of the light-bulb sea squirt, Clavelina lepadiformis (Müller, 1776)

We present a genome assembly from an individual Clavelina lepadiformis (the light-bulb sea squirt; Chordata; Ascidiacea; Aplousobranchia; Clavelinidae). The genome sequence is 210.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.48 kilobases in length.

The genome sequence of a ground beetle, Pterostichus niger (Schaller, 1783)

We present a genome assembly from an individual male Pterostichus niger (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 674.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.16 kilobases in length.

The genome sequence of the Gelatinous Scale Worm, Alentia gelatinosa (Sars, 1835)

We present a genome assembly from an individual Alentia gelatinosa (Gelatinous Scale Worm); Annelida; Polychaeta; Phyllodocida; Polynoidae). The genome sequence is 1,237.5 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.37 kilobases in length.

The genome sequence of an ichneumonid wasp, Heteropelma amictum (Fabricius, 1775)

We present a genome assembly from an individual female Heteropelma amictum (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 226.4 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.65 kilobases in length.

The genome sequence of the common buff snailkiller, Tetanocera ferruginea (Fallén, 1820)

We present a genome assembly from an individual male Tetanocera ferruginea (the common buff snailkiller; Arthropoda; Insecta; Diptera; Sciomyzidae). The genome sequence is 790.4 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.07 kilobases in length.

The genome sequence of the Chestnut, Conistra vaccinii (Linnaeus, 1761)

We present a genome assembly from an individual male Conistra vaccinii (the Chestnut; Arthropoda; None; Lepidoptera; Noctuidae). The genome sequence is 720.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,109 protein coding genes.

Complete genome sequences of Ruminococcus torques strains JCM 36208 and JCM 36209, isolated from the feces of a healthy Japanese male

Here, we report the complete genome sequences of two Ruminococcus torques strains (JCM 36208 and JCM 36209) that were newly isolated from the feces of a healthy Japanese male. Both genomes consist of a single circular chromosome with a length of ~2.8 Mbp and a G+C content of 41.8%.

The complete genome sequence of Pantoea agglomerans NBBC-01, isolated from rot potato tubers

The Gram-negative bacterium Pantoea agglomerans has been isolated from various habitats including disease plants. Here, we present the genome of P. agglomerans strain NBBC-01 obtained from rotten potatoes that were infected by Ditylenchus desstructor. The genome information will prove advantageous in elucidating its ecological role.

Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

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.

Genome sequence of the virulent Aeromonas salmonicida atypical strain T30 isolated from sablefish with furunculosis

Aeromonas salmonicida, a Gram-negative bacterium, causes the disease furunculosis in multiple fish species. We present the complete genome sequence of the atypical A. salmonicida strain T30, which was isolated from furunculosis in sablefish in Manchester, WA, USA. Analyzing this genome will help to identify the bacterium's role in marine aquaculture.

De novo assembly of Roseomonas mucosa isolated from patients with atopic dermatitis

Roseomonas mucosa is associated with the normal skin microflora. Here, we present de novo sequence assemblies from R. mucosa isolates obtained from the skin lesions of three atopic dermatitis patients.

Whole-genome sequence of Staphylococcus epidermidis strain AH3, isolated from Nile tilapia (Oreochromis niloticus)

The whole-genome sequence of Staphylococcus epidermidis strain AH3 isolated from moribund farmed Nile tilapia (Oreochromis niloticus) was performed using a combination of the Illumina and Pacific Biosciences (PacBio) sequencing platforms. The genome sequence is composed of a single chromosome of 2,464,380 bp with a GC content of 32.2% and 2,220 predicted protein-coding genes.

The genome sequence of the Wasp Spider, Argiope bruennichi (Scopoli, 1772)

We present a genome assembly from an individual female Argiope bruennichi (the Wasp Spider; Arthropoda; Arachnida; Araneae; Araneidae). The genome sequence is 1,778.4 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.06 kilobases in length.

Physics-Based Signal Analysis of Genome Sequences: An Overview of GenomeBits

A comprehensive overview of the recent physics-inspired genome analysis tool, GenomeBits, is presented. This is based on traditional signal processing methods such as discrete Fourier transform (DFT). GenomeBits can be used to extract underlying genomics features from the distribution of nucleotides, and can be further used to analyze the mutation patterns in viral genomes. Examples of the main GenomeBits findings outlining the intrinsic signal organization of genomics sequences for different SARS-CoV-2 variants along the pandemic years 2020-2022 and Monkeypox cases in 2021 are presented to show the usefulness of GenomeBits. GenomeBits results for DFT of SARS-CoV-2 genomes in different geographical regions are discussed, together with the GenomeBits analysis of complete genome sequences for the first coronavirus variants reported: Alpha, Beta, Gamma, Epsilon and Eta. Interesting features of the Delta and Omicron variants in the form of a unique 'order-disorder' transition are uncovered from these samples, as well as from their cumulative distribution function and scatter plots. This class of transitions might reveal the cumulative outcome of mutations on the spike protein. A salient feature of GenomeBits is the mapping of the nucleotide bases (A,T,C,G) into an alternating spin-like numerical sequence via a series having binary (0,1) indicators for each A,T,C,G. This leads to the derivation of a set of statistical distribution curves. Furthermore, the quantum-based extension of the GenomeBits model to an analogous probability measure is shown to identify properties of genome sequences as wavefunctions via a superposition of states. An association of the integral of the GenomeBits coding and a binding-like energy can, in principle, also be established. The relevance of these different results in bioinformatics is analyzed.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles moucheti, Evans, 1925

We present a genome assembly from an individual male Anopheles moucheti (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 271 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length.

The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761)

We present a genome assembly from an individual female Ochropleura plecta (the Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 643.9 megabases in span. 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 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,016 protein coding genes.

The genome sequence of a darkling beetle, Lagria hirta (Linnaeus, 1758)

We present a genome assembly from an individual male Lagria hirta (darkling beetle; Arthropoda; Insecta; Coleoptera; Tenebrionidae). The genome sequence is 336.8 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,850protein coding genes.

Isolation and characterization of Pinibacter soli sp. nov., and in silico genome mining of Pinibacter for biosynthetic gene cluster prediction

A Gram-stain-negative, aerobic, rod-shaped, non-motile and non-flagellated novel bacterial strain, designated MAH-24T, was isolated from the rhizospheric soil of a pine garden. The colonies were observed to be orange-coloured, smooth, spherical and 0.4-0.8 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAH-24T was found to be able to grow at 10-35 °C, at pH 6.0-9.0 and in the presence of 0-1.0 % NaCl (w/v). The strain was found to be positive for the catalase and oxidase tests. The strain was positive for hydrolysis of aesculin and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pinibacter and to be closely related to Pinibacter aurantiacus MAH-26T (99.2 % sequence similarity). The novel strain MAH-24T has a draft genome size of 5 918 133 bp (13 contigs), annotated with 4613 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-24T and the closest type strain P. aurantiacus MAH-26T were in the range of 85.3 and 29.9 %, respectively. In silico genome mining revealed that both novel strain MAH-24T and P. aurantiacus MAH-26T have a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 41.0 mol%. The predominant isoprenoid quinone was menaquinone-7. The major fatty acids were identified as C15:0 iso, C15:1 iso G and C17:0 iso 3OH. On the basis of dDDH, ANI, genotypic, chemotaxonomic and physiological data, strain MAH-24T represents a novel species within the genus Pinibacter, for which the name Pinibacter soli sp. nov. is proposed, with MAH-24T (=KACC 19747T=CGMCC 1.13659T) as the type strain.

The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758)

We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length.

The genome sequence of the Hornet Moth, Sesia apiformis (Clerck, 1759)

We present a genome assembly from an individual male Sesia apiformis (the Hornet Moth; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 546.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,358 protein coding genes.

The genome sequence of the Saxon Wasp, Dolichovespula saxonica (Fabricius, 1793)

We present a genome assembly from an individual male Dolichovespula saxonica (the Saxon Wasp; Arthropoda; Insecta; Hymenoptera; Vespidae). The genome sequence is 221.8 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.97 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,856 protein coding genes.

The genome sequence of Fabricius' Nomad Bee, Nomada fabriciana (Linne, 1767)

We present a genome assembly from an individual female Nomada fabriciana (Fabricius' Nomad Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence is 233.6 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 9,700 protein coding genes.

The genome sequence of the Rock Grayling, Hipparchia semele (Linnaeus, 1758)

We present a genome assembly from an individual female Hipparchia semele (the Rock Grayling; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 403.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,540 protein coding genes.

An improved Lodderomyces elongisporus NRRL YB-4239 genome assembly substantiated by its electrophoretic karyotype

Pacific Biosciences long-read sequencing was used to improve the genome assembly for Lodderomyces elongisporus strain NRRL YB-4239 (ATCC 11503). The new assembly included eight chromosomes that were substantiated by the electrophoretic karyotype. The nuclear genome was 16.1 Mb (37.2% GC) with 5,740 genes predicted.

Complete genome sequence of Butyricimonas faecihominis JCM 18676T

We report a complete genome sequence of Butyricimonas faecihominis JCM 18676T, generated by nanopore sequencing. The genome consists of a single circular chromosome of 4,851,806 bp, with a G + C content of 42.9%, and was predicted to contain 15 rRNA and 61 tRNA genes and encode for 3,946 proteins.

Genome sequence of Gordonia alkaliphila strain WW102, isolated from influent wastewater at a research center with multiple-species research animal facilities

Gordonia alkaliphila is a little known mesophilic Gram-positive rod-shaped bacterium. We report the 3.85-Mbp genome sequence of G. alkaliphila strain WW102, isolated from wastewater at a research center with multiple-species laboratory animal facilities. The genome predicted FadD32 gene clusters that are involved in the biosynthesis of mycolic acids as found in Mycobacterium tuberculosis.

Genome sequence of Enterococcus gallinarum AH4, a milk oligosaccharide-degrading strain isolated from suckling rats

We had previously isolated Enterococcus gallinarum AH4, a strain capable of degrading rat milk oligosaccharides. In this study, we determined the whole-genome sequence of AH4. This whole-genome information will expand our understanding of milk oligosaccharide-mediated symbioses between bacteria and host mammals.