JBrowse 2: a modular genome browser with views of synteny and structural variation

The genome sequence of the European mole, Talpa europaea Linnaeus, 1758

We present a genome assembly from a female Talpa europaea (European mole; Chordata; Mammalia; Eulipotyphla; Talpidae). The assembly contains two haplotypes with total lengths of 2,060.98 megabases and 2,056.47 megabases. Most of haplotype 1 (98.6%) is scaffolded into 17 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 16.93 kilobases in length.

The genome sequence of an orbweaving spider, Gibbaranea gibbosa (Walckenaer, 1802)

We present a genome assembly from a specimen of Gibbaranea gibbosa (orbweaving spider; Arthropoda; Arachnida; Araneae; Araneidae). The genome sequence has a total length of 2,816.88 megabases. Most of the assembly (98.61%) is scaffolded into 13 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.1 kilobases in length.

The genome sequence of the Common Sheetweb Spider Linyphia triangularis (Clerck, 1757)

We present a genome assembly from a male Linyphia triangularis (Common Sheetweb Spider Arthropoda; Arachnida; Araneae; Linyphiidae). The genome sequence has a total length of 1,349.10 megabases. Most of the assembly (95.36%) is scaffolded into 13 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 15.31 kilobases in length.

The genome sequence of the lesser earwig, Labia minor (Linnaeus, 1758)

We present a genome assembly from an individual male Labia minor (the lesser earwig; Arthropoda; Insecta; Dermaptera; Spongiphoridae). The genome sequence spans 604.50 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. Two mitochondrial scaffolds were also assembled.

The genome sequence of the black-headed gull, Chroicocephalus ridibundus (Linnaeus, 1766)

We present a genome assembly from an individual male Chroicocephalus ridibundus (the black-headed gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence spans 1,417.60 megabases. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.82 kilobases in length. The genome has been annotated on Ensembl, which reports 15,628 protein coding genes.

The genome sequence of the Rock-rose Pot Beetle, Cryptocephalus primarius Harold, 1872

We present a genome assembly from a male specimen of Cryptocephalus primarius (Rock-rose Pot Beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 370.99 megabases. Most of the assembly (87.88%) is scaffolded into 21 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.97 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,661 protein-coding genes.

The genome sequence of the Marsh Click-beetle, Actenicerus siaelandicus (Müller, O.F., 1764)

We present a genome assembly from a female specimen of Actenicerus siaelandicus (Marsh Click Beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The genome sequence has a total length of 854.91 megabases. Most of the assembly (95.23%) is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.17 kilobases in length.

The genome sequence of the false flower beetle, Anaspis frontalis (Linnaeus, 1758)

We present a genome assembly from a specimen of Anaspis frontalis (the false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The assembly contains two haplotypes with total lengths of 808.55 megabases and 802.05 megabases. Most of haplotype 1 (95.81%) is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.

The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789)

We present a genome assembly from a male specimen of Ceriagrion tenellum (Small Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence has a total length of 2,077.00 megabases. Most of the assembly (99.28%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.

The genome sequence of a soldier beetle, Malthinus seriepunctatus Kiesenwetter, 1851

We present a genome assembly from a specimen of Malthinus seriepunctatus (a soldier beetle; Arthropoda; Insecta; Coleoptera; Cantharidae). The genome sequence has a total length of 338.81 megabases. Most of the assembly (99.73%) is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 20.41 kilobases in length.

The genome sequence of the false flower beetle, Anaspis regimbarti Schilsky, 1895

We present a genome assembly from a specimen of Anaspis regimbarti (the false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The genome sequence has a total length of 457.61 megabases. Most of the assembly (99.89%) is scaffolded into 8 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length.

The genome sequence of the Antarctic lanternfish, Electrona antarctica (Günther, 1878)

We present a genome assembly from an individual female Electrona antarctica (the Antarctic lanternfish; Chordata; Actinopterigii; Myctophiformes; Myctophidae). The genome sequence has a total length of 1,427.40 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.02 kilobases in length.

The genome sequence of the butterfly blenny, Blennius ocellaris Linnaeus, 1758

We present a genome assembly from a specimen of Blennius ocellaris (the butterfly blenny; Chordata; Actinopteri; Blenniiformes; Blenniidae). The genome sequence spans 728.70 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.

The genome sequence of the Twenty-plume Moth, Alucita hexadactyla Linnaeus, 1758

We present a genome assembly from a specimen of Alucita hexadactyla (Twenty-plume Moth; Arthropoda; Insecta; Lepidoptera; Alucitidae). The genome sequence has a total length of 878.53 megabases. Most of the assembly (99.74%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length.

The genome sequence of the Large Red Tailed Bumble Bee, Bombus lapidarius (Linnaeus, 1758)

We present a genome assembly from an individual female specimen of Bombus lapidarius (Large Red Tailed Bumble Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 368.50 megabases. Most of the assembly (81.04%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.11 kilobases in length.

The genome sequence of a pallopterid fly, Toxonevra muliebris (Harris, 1780)

We present a genome assembly from an individual male specimen of Toxonevra muliebris (pallopterid fly; Arthropoda; Insecta; Diptera; Pallopteridae). The genome sequence has a total length of 491.40 megabases. Most of the assembly (99.07%) is scaffolded into 6 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.18 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,433 protein-coding genes.

The genome sequence of a flea beetle, Neocrepidodera transversa (Marsham, 1802)

We present a genome assembly from a male specimen of Neocrepidodera transversa (flea beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 671.30 megabases. Most of the assembly (93.58%) is scaffolded into 21 chromosomal pseudomolecules, including the X chromosome. The mitochondrial genome has also been assembled and is 17.02 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,840 protein-coding genes.

The genome sequence of the muscid fly Eudasyphora cyanicolor (Zetterstedt, 1845)

We present a genome assembly from an individual female specimen of Eudasyphora cyanicolor (Arthropoda; Insecta; Diptera; Muscidae). The genome sequence has a total length of 1,450.40 megabases. Most of the assembly (99.68%) is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length.

The genome sequence of a carabid beetle, Carabus problematicus Herbst, 1786

We present a genome assembly from an individual female specimen of Carabus problematicus (carabid beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence has a total length of 254.00 megabases. Most of the assembly (97.1%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.42 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,311 protein-coding genes.

The genome sequence of a leaf beetle, Galerucella nymphaeae (Linnaeus, 1758)

We present a genome assembly from an individual female specimen of Galerucella nymphaeae (leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 350.20 megabases. Most of the assembly (99.8%) is scaffolded into 16 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.95 kilobases in length.

The genome sequence of the Jersey Tiger moth, Euplagia quadripunctaria (Poda, 1761)

We present a genome assembly from an individual male specimen of Euplagia quadripunctaria (Jersey Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 668.40 megabases. Most of the assembly (99.6%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.48 kilobases in length.

FuSViz-visualization and interpretation of structural variation using cancer genomics and transcriptomics data

Structural variation (SV) is a frequent category of genetic alterations important for understanding cancer genome evolution and revealing key cancer driver events. With the development of high-throughput sequencing technologies, the ability to detect SVs of various sizes and types has improved, at both the DNA and RNA levels. However, SV calls are still prone to a considerable fraction of false positives, which necessitates visual inspection and manual curation as part of the quality control process. Identification of reliable and recurrent SVs in larger cohorts lends strength to revealing the driving roles of SVs in cancer development and to the discovery of potential diagnostic and prognostic biomarkers. Here, we present FuSViz, an application for visualization, interpretation, and prioritization of SVs. The tool provides multiple data view approaches in a user-friendly interface, allowing the investigation of prevalence and recurrence of SVs and relevant partner genes in a sample cohort. It integrates SV calls from DNA and RNA sequencing datasets to comprehensively illustrate the biological impact of SVs on the implicated genes and associated genomic regions. The functionality of FuSViz is intended for interrogation of both recurrent and private SVs, effectively assisting with pathogenicity evaluation and biomarker discovery in cancer sequencing projects.

The genome sequence of the black scavenger fly, Nemopoda nitidula (Fallén, 1820)

We present a genome assembly from an individual specimen of Nemopoda nitidula (Arthropoda; Insecta; Diptera; Sepsidae). The genome sequence has a total length of 178.40 megabases. Most of the assembly (99.2%) is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.98 kilobases in length.

The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798

We present a genome assembly from an individual female specimen of Acrobasis repandana (Warted Knot-Horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 620.40 megabases. Most of the assembly (99.78%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,522 protein-coding genes.

The genome sequence of a snakefly, Xanthostigma xanthostigma (Schummel, 1832)

We present a genome assembly from an individual male snakefly, Xanthostigma xanthostigma (Arthropoda; Insecta; Raphidioptera; Raphidiidae). The genome sequence has a total length of 623.30 megabases. Most of the assembly (99.74%) is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.75 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,251 protein-coding genes.

The genome sequence of the Stable Fly, Stomoxys calcitrans (Linnaeus, 1758)

We present a genome assembly from an individual specimen of Stomoxys calcitrans (Stable Fly; Arthropoda; Insecta; Diptera; Muscidae). The genome sequence has a total length of 1,070.90 megabases. Most of the assembly (98.96%) is scaffolded into 5 chromosomal pseudomolecules.The mitochondrial genome has also been assembled and is 17.6 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,757 protein-coding genes.

The genome sequence of a longhorn beetle, Rhagium mordax (Degeer, 1775)

We present a genome assembly from an individual female specimen of Rhagium mordax (longhorn beetle; Arthropoda; Insecta; Coleoptera; Cerambycidae). The genome sequence has a total length of 775.60 megabases. Most of the assembly (99.53%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.68 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,937 protein-coding genes.

Genomic Resources for the Scuttle Fly Megaselia abdita: A Model Organism for Comparative Developmental Studies in Flies

The order Diptera (true flies) holds promise as a model taxon in evolutionary developmental biology due to the inclusion of the model organism, Drosophila melanogaster, and the ability to cost-effectively rear many species in laboratories. One of them, the scuttle fly Megaselia abdita (Phoridae) has been used in evolutionary developmental biology for 30 years and is an excellent phylogenetic intermediate between fruit flies and mosquitoes but remains underdeveloped in genomic resources. Here, we present a de novo chromosome-level assembly and annotation of M. abdita and transcriptomes of 9 embryonic and 4 postembryonic stages. We also compare 9 stage-matched embryonic transcriptomes between M. abdita and D. melanogaster. Our analysis of these resources reveals extensive chromosomal synteny with D. melanogaster, 28 orphan genes with embryo-specific expression including a novel F-box LRR gene in M. abdita, and conserved and diverged features of gene expression dynamics between M. abdita and D. melanogaster. Collectively, our results provide a new reference for studying the diversification of developmental processes in flies.

The genome sequence of the Pacific oyster, Magallana gigas (Thunberg, 1793)

We present a genome assembly from an individual Magallana gigas (the Pacific oyster; Mollusca; Bivalvia; Ostreida; Ostreidae). The genome sequence is 564.0 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,775 protein-coding genes.

The genome sequence of the Grey Arches moth, Polia nebulosa Hufnagel, 1766

We present a genome assembly from an individual male specimen of Polia nebulosa (Grey Arches; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 1,011.20 megabases. Most of the primary assembly (99.27%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length.

The genome sequence of a seed weevil, Aspidapion aeneum (Fabricius, 1775)

We present a genome assembly from a specimen of Aspidapion aeneum (seed weevil; Arthropoda; Insecta; Coleoptera; Apionidae). The genome sequence has a total length of 1,286.20 megabases. Most of the assembly (98.78%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.49 kilobases in length.

Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region

Amaranthus palmeri (Palmer amaranth), Amaranthus retroflexus (redroot pigweed), and Amaranthus hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as "pigweeds," these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. The development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweeds. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified an approximately 2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed that two genes, RESTORER OF FERTILITY 1 (RF1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), within the male-specific region were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target-site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.

Developing pangenomes for large and complex plant genomes and their representation formats

BACKGROUND

The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations.

AIM

This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species' genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction. This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity.

The genome sequence of Greek sea-spurrey, Spergularia bocconei (Scheele) Graebn. (Caryophyllaceae)

We present a genome assembly from a specimen of Spergularia bocconei (Greek sea-spurrey; Streptophyta; Magnoliopsida; Caryophyllales; Caryophyllaceae). The genome sequence has a total length of 466.20 megabases. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules suggesting the individual is an allotetraploid (2 n = 4 x = 36). The mitochondrial and plastid genome assemblies have lengths of 327.07 kilobases and 152.41 kilobases, respectively.

Photosynthesis in Synechocystis sp. PCC 6803 is not optimally regulated under very high CO2

One strategy for CO2 mitigation is using photosynthetic microorganisms to sequester CO2 under high concentrations, such as in flue gases. While elevated CO2 levels generally promote growth, excessively high levels inhibit growth through uncertain mechanisms. This study investigated the physiology of the cyanobacterium Synechocystis sp. PCC 6803 under very high CO2 concentrations and yet stable pH around 7.5. The growth rate of the wild type (WT) at 200 µmol photons m-2 s-1 and a gas phase containing 30% CO2 was 2.7-fold lower compared to 4% CO2. Using a CRISPR interference mutant library, we identified genes that, when repressed, either enhanced or impaired growth under 30% or 4% CO2. Repression of genes involved in light harvesting (cpc and apc), photochemical electron transfer (cytM, psbJ, and petE), and several genes with little or unknown functions promoted growth under 30% CO2, while repression of key regulators of photosynthesis (pmgA) and CO2 capture and fixation (ccmR, cp12, and yfr1) increased growth inhibition under 30% CO2. Experiments confirmed that WT cells were more susceptible to light inhibition under 30% than under 4% CO2 and that a light-harvesting-impaired ΔcpcG mutant showed improved growth under 30% CO2 compared to the WT. These findings suggest that enhanced fitness under very high CO2 involves modifications in light harvesting, electron transfer, and carbon metabolism, and that the native regulatory machinery is insufficient, and in some cases obstructive, for optimal growth under 30% CO2. This genetic profiling provides potential targets for engineering cyanobacteria with improved photosynthetic efficiency and stress resilience for biotechnological applications. KEY POINTS: • Synechocystis growth was inhibited under very high CO2. • Inhibition of growth under very high CO2 was light dependent. • Repression of photosynthesis genes improved growth under very high CO2.

The genome sequence of Red Underwing, Catocala nupta Linnaeus, 1767

We present a genome assembly from an individual female specimen of Catocala nupta (Red Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 930.40 megabases. Most of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,889 protein-coding genes.

The genome sequence of Dolichopus griseipennis Stannius, 1831

We present a genome assembly from an individual male Dolichopus griseipennis (Arthropoda; Insecta; Diptera; Dolichopodidae). The genome sequence has a total length of 897.50 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 16.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,532 protein-coding genes.

Auditory Neuropathy Caused by a Structural Variation in the OTOF Gene, Identified Using Oxford Nanopore Adaptive Sampling

BACKGROUND/OBJECTIVES

The OTOF gene is reported to be the causative gene for non-syndromic recessive sensorineural hearing loss and auditory neuropathy spectrum disorder. About 300 variants have been reported, but there have been no reports to date on copy gain variants.

METHODS

We identified a copy gain variant in the OTOF gene through short-read next-generation sequencing analysis from one patient with auditory neuropathy. We also performed long-read next-generation sequencing analysis using the Oxford Nanopore Technologies adaptive sampling procedure.

RESULTS

The four-year-old male carried a duplication of chr2: 26,477,852 to 26,483,106 (a 5254-base duplication including exon 14 to exon 18 of the OTOF gene NM_001287489) and a c.5385C>A single nucleotide variant. We also confirmed that these two variants were located in the trans configuration based on haplotype phasing results using the long-read next-generation sequencing data.

CONCLUSIONS

This is the first report of an auditory neuropathy patient with a large duplication variant in the OTOF gene. The identified variants were novel, but based on the clinical phenotype of the patient, these variants seem to be the genetic cause of this patient's phenotype. Oxford Nanopore Technologies adaptive sampling is a powerful tool for the analysis of structural variants (particularly for determining the breakpoint and direction) and haplotype phasing.

The genome sequence of the common sole, Solea solea (Linnaeus, 1758)

We present a genome assembly from an individual female Solea solea (Linnaeus, 1758) (the common sole; Chordata; Actinopteri; Pleuronectiformes; Soleidae). The genome sequence spans 643.80 megabases. Most of the assembly (97.81%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.03 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,646 protein-coding genes.

The genome sequence of the Ruddy Darter, Sympetrum sanguineum (Müller, 1764)

We present a genome assembly from a male specimen of Sympetrum sanguineum (Ruddy Darter; Arthropoda; Insecta; Odonata; Libellulidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,500.53 megabases and 1,304.05 megabases. Most of haplotype 1 is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome, while haplotype 2 is scaffolded into 12 autosomes.

The genome sequence of the tawny cockroach, Ectobius (Ectobius) pallidus (Olivier, 1789)

We present a genome assembly from a specimen of Ectobius pallidus (tawny cockroach; Arthropoda; Insecta; Blattodea; Ectobiidae). The assembly contains two haplotypes with total lengths of 2,087.55 megabases and 2,124.67 megabases, respectively. Most of haplotype 1 (98.55%) is scaffolded into 11 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.75 kilobases in length.

SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research

Soybean is a globally important crop for food, feed, oil, and nitrogen fixation. A variety of multi-omics studies have been carried out, generating datasets ranging from genotype to phenotype. In order to efficiently utilize these data for basic and applied research, a soybean multi-omics database with extensive data coverage and comprehensive data analysis tools was established. The Soybean Omics Database (SoyOD) integrates important new datasets with existing public datasets to form the most comprehensive collection of soybean multi-omics information. Compared to existing soybean databases, SoyOD incorporates an extensive collection of novel data derived from the deep-sequencing of 984 germplasms, 162 novel transcriptomic datasets from seeds at different developmental stages, 53 phenotypic datasets, and more than 2500 phenotypic images. In addition, SoyOD integrates existing data resources, including 59 assembled genomes, genetic variation data from 3904 soybean accessions, 225 sets of phenotypic data, and 1097 transcriptomic sequences covering 507 different tissues and treatment conditions. Moreover, SoyOD can be used to mine candidate genes for important agronomic traits, as shown in a case study on plant height. Additionally, powerful analytical and easy-to-use toolkits enable users to easily access the available multi-omics datasets, and to rapidly search genotypic and phenotypic data in a particular germplasm. The novelty, comprehensiveness, and user-friendly features of SoyOD make it a valuable resource for soybean molecular breeding and biological research. SoyOD is publicly accessible at https://bis.zju.edu.cn/soyod.

The genome sequence of a sawfly, Athalia cordata Serville, 1823

We present a genome assembly from a female specimen of Athalia cordata (sawfly; Arthropoda; Insecta; Hymenoptera; Athaliidae). The genome sequence has a total length of 169.00 megabases. Most of the assembly (99.98%) is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.47 kilobases in length.

The genome sequence of a cranefly, Diogma glabrata (Meigen, 1818)

We present a genome assembly from a specimen of Diogma glabrata (cranefly; Arthropoda; Insecta; Diptera; Cylindrotomidae). The genome sequence has a total length of 1,328.70 megabases. Most of the assembly (90.7%) is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.5 kilobases in length.

The genome sequence of the red fox, Vulpes vulpes (Linnaeus, 1758)

We present a genome assembly from an individual female Vulpes vulpes (red fox; Chordata, Mammalia, Carnivora, Canidae). The assembly comprises two haplotypes, with total lengths of 2,411.71 megabases and 2,398.53 megabases, respectively. For both haplotypes, 97.8% of haplotype 1 and 97.97% of haplotype 2 are scaffolded into 17 chromosomal pseudomolecules. Additionally, the mitochondrial genome has been assembled, with a total length of 16.68 kilobases.

The genome sequence of a beetle, Brachypterus glaber (Newman, 1834)

We present a genome assembly from an individual female specimen of Brachypterus glaber (beetle; Arthropoda; Insecta; Coleoptera; Kateretidae). The genome sequence has a total length of 648.30 megabases. Most of the assembly (95.55%) is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,733 protein-coding genes.

The genome sequence of the European Corn Borer, Ostrinia nubilalis Hübner, 1796

We present a genome assembly from an individual female specimen of Ostrinia nubilalis (European Corn Borer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 495.50 megabases. Most of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,780 protein-coding genes.

Conservation of symmetry breaking at the level of chromatin accessibility between fly species with unrelated anterior determinants

Establishing the anterior-posterior body axis is a fundamental process during embryogenesis, and the fruit fly, Drosophila melanogaster, provides one of the best-known case studies of this process. In Drosophila, localized mRNA of bicoid serves as anterior determinant (AD). Bicoid engages in a concentration-dependent competition with nucleosomes and initiates symmetry-breaking along the AP axis by promoting chromatin accessibility at the loci of transcription factor (TF) genes that are expressed in the anterior of the embryo. However, ADs of other fly species are unrelated and structurally distinct, and little is known about how they function. We addressed this question in the moth fly, Clogmia albipunctata, in which a maternally expressed transcript isoform of the pair-rule segmentation gene odd-paired is localized in the anterior egg and has been co-opted as AD. We provide a de novo assembly and annotation of the Clogmia genome and describe how knockdown of zelda and maternal odd-paired transcript affect chromatin accessibility and expression of TF-encoding loci. The results of these experiments suggest direct roles of Cal-Zld in opening and closing chromatin during nuclear cleavage cycles and show that Clogmia's maternal odd-paired activity promotes chromatin accessibility and anterior expression during the early phase of zygotic genome activation at Clogmia's homeobrain and sloppy-paired loci. We conclude that unrelated dipteran ADs initiate anterior-posterior axis-specification at the level of enhancer accessibility and that homeobrain and sloppy-paired homologs may serve a more widely conserved role in the initiation of anterior pattern formation given their early anterior expression and function in head development in other insects.

The genome sequence of a leafhopper, Allygus modestus Scott, 1876

We present a genome assembly from an individual male specimen of Allygus modestus (leafhopper; Arthropoda; Insecta; Hemiptera; Cicadellidae). The genome sequence has a total length of 1,819.90 megabases. Most of the assembly (99.86%) is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.69 kilobases in length.

The genome sequence of a sawfly, Abia candens Konow, 1887

We present a genome assembly from an individual male specimen of Abia candens (sawfly; Arthropoda; Insecta; Hymenoptera; Cimbicidae). The genome sequence has a total length of 261.00 megabases. Most of the assembly (82.7%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.72 kilobases in length.