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

The genome sequence of the yellow-girdled Dasysyrphus, Dasysyrphus tricinctus (Fallén, 1817)

We present a genome assembly from an individual male Dasysyrphus tricinctus (the yellow-girdled Dasysyrphus; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence spans 1,054.90 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.39 kilobases in length.

A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application

BACKGROUND

Structural variants (SVs) such as deletions, duplications, and insertions are known to contribute to phenotypic variation but remain challenging to identify and genotype. A more complete, accessible, and assessable collection of SVs will assist efforts to study SV function in cattle and to incorporate SV genotyping into animal evaluation.

RESULTS

In this work we produced a large and deeply characterized collection of SVs in Holstein cattle using two popular SV callers (Manta and Smoove) and publicly available Illumina whole-genome sequence (WGS) read sets from 310 samples (290 male, 20 female, mean 20X coverage). Manta and Smoove identified 31 K and 68 K SVs, respectively. In total the SVs cover 5% (Manta) and 6% (Smoove) of the reference genome, in contrast to the 1% impacted by SNPs and indels. SV genotypes from each caller were confirmed to accurately recapitulate animal relationships estimated using WGS SNP genotypes from the same dataset, with Manta genotypes outperforming Smoove, and deletions outperforming duplications. To support efforts to link the SVs to phenotypic variation, overlapping and tag SNPs were identified for each SV, using genotype sets extracted from the WGS results corresponding to two bovine SNP chips (BovineSNP50 and BovineHD). 9% (Manta) and 11% (Smoove) of the SVs were found to have overlapping BovineHD panel SNPs, while 21% (Manta) and 9% (Smoove) have BovineHD panel tag SNPs. A custom interactive database ( https://svdb-dc.pslab.ca ) containing the identified sequence variants with extensive annotations, gene feature information, and BAM file content for all SVs was created to enable the evaluation and prioritization of SVs for further study. Illustrative examples involving the genes POPDC3, ORM1, G2E3, FANCI, TFB1M, FOXC2, N4BP2, GSTA3, and COPA show how this resource can be used to find well-supported genic SVs, determine SV breakpoints, design genotyping approaches, and identify processed pseudogenes masquerading as deletions.

CONCLUSIONS

The resources developed through this study can be used to explore sequence variation in Holstein cattle and to develop strategies for studying SVs of interest. The lack of overlapping and tag SNPs from commonly used SNP chips for most of the SVs suggests that other genotyping approaches will be needed (for example direct genotyping) to understand their potential contributions to phenotype. The included SV genotype assessments point to challenges in characterizing SVs, especially duplications, using short-read data and support ongoing efforts to better characterize cattle genomes through long-read sequencing. Lastly, the identification of previously known functional SVs and additional CDS-overlapping SVs supports the phenotypic relevance of this dataset.

The genome sequence of the cephid sawfly, Cephus spinipes (Panzer, 1800)

We present a genome assembly from an individual male cephid sawfly, Cephus spinipes (Arthropoda; Insecta; Hymenoptera; Cephidae). The genome sequence has a total length of 238.60 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.43 kilobases in length.

The genome sequence of the mottled worm, Allolobophora icterica (formerly Aporrectodea icterica ) (Savigny, 1826)

We present a genome assembly from an individual mottled worm, Allolobophora icterica (Annelida; Clitellata; Crassiclitellata; Lumbricidae). The genome sequence has a total length of 1,117.80 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.33 kilobases in length.

The genome sequence of the cuckoo wrasse, Labrus mixtus Linnaeus 1758

We present a genome assembly from an individual Labrus mixtus (the cuckoo wrasse; Chordata; Actinopteri; Labriformes; Labridae). The genome sequence has a total length of 740.60 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.49 kilobases in length.

Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package

BACKGROUND/OBJECTIVES

We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package.

RESULTS

We illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets.

CONCLUSIONS

The hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools.

The genome sequence of the Broom moth, Ceramica pisi Linnaeus, 1758

We present a genome assembly from an individual male Ceramica pisi (the Broom moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 732.70 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 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein-coding genes.

The genome sequence of the Brindled Ochre moth, Dasypolia templi (Thunberg, 1792)

We present a genome assembly from an individual male Brindled Ochre moth, Dasypolia templi (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 855.30 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 15.37 kilobases in length.

The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906)

We present a genome assembly from an individual female Pale November moth, Epirrita christyi (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 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 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.

The genome sequence of the ruby bryozoan, Bugula neritina (Linnaeus, 1758)

We present a genome assembly from a specimen of Bugula neritina (the ruby bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence has total length of 216.00 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,264 protein-coding genes.

The genome sequence of an Entiminae weevil, Polydrusus pterygomalis Boheman, 1840

We present a genome assembly from an individual female Entiminae weevil, Polydrusus pterygomalis (Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence has a total length of 1,051.50 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 20.95 kilobases in length.

The genome sequence of the European conger eel, Conger conger (Linnaeus, 1758)

We present a genome assembly from an individual Conger conger (the European conger eel; Chordata; Actinopteri; Anguilliformes; Congridae). The genome sequence spans 1,136.40 megabases. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.

Diversification and conservation of DNA binding specificities of SPL family of transcription factors

SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors in Arabidopsis thaliana, providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins. Comparative analysis between the paralogs AtSPL9 and AtSPL15 revealed differences in their binding motifs, suggesting divergent regulatory functions. Additionally, we expanded our investigation to homologs of AtSPL9/15 in Zea mays (ZmSBP8/30) and Triticum aestivum (TaSPL7/13), identifying conserved and unique DNA-binding patterns across species. These findings provide key resources for understanding the molecular mechanisms of SPL transcription factors in regulating plant development and evolution across different species.

The genome sequence of the marsh cinquefoil, Comarum palustre L., also known as Potentilla palustris (L.) Scop. (Rosaceae)

We present a genome assembly from an individual Comarum palustre (the marsh cinquefoil; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence has a total length of 528.90 megabases. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2 n = 6 x = 42). The mitochondrial and plastid genome assemblies have lengths of 362.32 kilobases and 154.29 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 37,459 protein-coding genes.

The genome sequence of the Dogs-Mercury Flea Beetle, Hermaeophaga mercurialis (Fabricius, 1792)

We present a genome assembly from an individual Dogs-Mercury Flea Beetle, Hermaeophaga mercurialis (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a length of 479.40 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,633 protein-coding genes.

The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839)

We present a genome assembly of a female Silver-barred Sober moth Aproaerema taeniolella (Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a length of 636.60 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 15.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,274 protein-coding genes.

The genome sequence of the thistle gall fly, Urophora cardui (Linnaeus 1758)

We present a genome assembly from an individual female thistle gall fly, Urophora cardui (Arthropoda; Insecta; Diptera; Tephritidae). The genome sequence has a total length of 837.80 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.37 kilobases in length.

The genome sequence of an ichneumonid wasp, Hyposoter dolosus (Gravenhorst, 1829)

We present a genome assembly from an individual male Hyposoter dolosus (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence spans 222.70 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.89 kilobases in length.

The genome sequence of the Scarce Cardinal Beetle, Schizotus pectinicornis (Linnaeus, 1758)

We present a genome assembly from an individual female Schizotus pectinicornis (the Scarce Cardinal Beetle; Arthropoda; Insecta; Coleoptera; Pyrochroidae). The genome sequence spans 181.10 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 16.59 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,605 protein-coding genes.

The genome sequence of the Eurasian minnow, Phoxinus phoxinus (Linnaeus, 1758)

We present a genome assembly from an individual female Phoxinus phoxinus (the Eurasian minnow; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The genome sequence spans 950.50 megabases. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.36 kilobases in length.

Cell cycle arrest combined with CDK1 inhibition suppresses genome-wide mutations by activating alternative DNA repair genes during genome editing

Cells regularly repair numerous mutations. However, the effect of CRISPR/Cas9-induced dsDNA breaks on the repair processes of naturally occurring genome-wide mutations is unclear. In this study, we used TSCE5 cells with the heterozygous thymidine kinase genotype (TK+/-) to examine these effects. We strategically inserted the target sites for guide RNA (gRNA)/Cas9 and I-SceI into the functional allele and designed the experiment such that deletions of > 81 bp or base substitutions within exon five disrupted the TK gene, resulting in a TK-/- genotype. TSCE5 cells in the resting state exhibited 16 genome-wide mutations that affected cellular functions. After gRNA/Cas9 editing, these cells produced 859 mutations, including 67 high-impact variants that severely affected cellular functions under standard culture conditions. Mutation profile analysis indicated a significant accumulation of C to A substitutions, underscoring the widespread induction of characteristic mutations by gRNA/Cas9. In contrast, gRNA/Cas9-edited cells under conditions of S∼G2/M arrest and cyclin-dependent kinase 1 inhibition showed only five mutations. Transcriptomic analysis revealed the downregulation of DNA replication genes and upregulation of alternative DNA repair genes, such as zinc finger protein 384 (ZNF384) and dual specificity phosphatase, under S∼G2/M conditions. Additionally, activation of nucleotide and base excision repair gene, including O-6-methylguanine-DNA methyltransferase and xeroderma pigmentosum complementation group C, was observed. This study highlights the profound impact of CRISPR/Cas9 editing on genome-wide mutation processes and underscores the emergence of novel DNA repair pathways. Finally, our findings provide significant insights into the maintenance of genome integrity during genome editing.

Asteraceae genome database: a comprehensive platform for Asteraceae genomics

Asteraceae, the largest family of angiosperms, has attracted widespread attention for its exceptional medicinal, horticultural, and ornamental value. However, researches on Asteraceae plants face challenges due to their intricate genetic background. With the continuous advancement of sequencing technology, a vast number of genomes and genetic resources from Asteraceae species have been accumulated. This has spurred a demand for comprehensive genomic analysis within this diverse plant group. To meet this need, we developed the Asteraceae Genomics Database (AGD; http://cbcb.cdutcm.edu.cn/AGD/). The AGD serves as a centralized and systematic resource, empowering researchers in various fields such as gene annotation, gene family analysis, evolutionary biology, and genetic breeding. AGD not only encompasses high-quality genomic sequences, and organelle genome data, but also provides a wide range of analytical tools, including BLAST, JBrowse, SSR Finder, HmmSearch, Heatmap, Primer3, PlantiSMASH, and CRISPRCasFinder. These tools enable users to conveniently query, analyze, and compare genomic information across various Asteraceae species. The establishment of AGD holds great significance in advancing Asteraceae genomics, promoting genetic breeding, and safeguarding biodiversity by providing researchers with a comprehensive and user-friendly genomics resource platform.

splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq

Motivation

Analysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. To the best of our knowledge, there is currently no integrative open-source software dedicated to this task.

Results

Here, we introduce splicekit, a Python package that provides and integrates a set of existing and novel splicing analysis tools for conducting splicing analysis.

Availability and implementation

The software splicekit is open-source and available at Github (https://github.com/bedapub/splicekit) and via the Python Package Index.

The genome sequence of an ichneumonid wasp, Ophion ventricosus Gravenhorst, 1829

We present a genome assembly from an individual female Ophion ventricosus (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence spans 436.80 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.71 kilobases in length.

An efficient in vivo-inducible CRISPR interference system for group A Streptococcus genetic analysis and pathogenesis studies

While genome-wide transposon mutagenesis screens have identified numerous essential genes in the significant human pathogen Streptococcus pyogenes (group A Streptococcus or GAS), many of their functions remain elusive. This knowledge gap is attributed in part to the limited molecular toolbox for controlling GAS gene expression and the bacterium's poor genetic transformability. CRISPR interference (CRISPRi), using catalytically inactive GAS Cas9 (dCas9), is a powerful approach to specifically repress gene expression in both bacteria and eukaryotes, but ironically, it has never been harnessed for controlled gene expression in GAS. In this study, we present a highly transformable and fully virulent serotype M1T1 GAS strain and introduce a doxycycline-inducible CRISPRi system for efficient repression of bacterial gene expression. We demonstrate highly efficient, oligo-based single guide RNA cloning directly to GAS, enabling the construction of a gene knockdown strain in just 2 days, in contrast to the several weeks typically required. The system is shown to be titratable and functional both in vitro and in vivo using a murine model of GAS infection. Furthermore, we provide direct in vivo evidence that the expression of the conserved cell division gene ftsZ is essential for GAS virulence, highlighting its promise as a target for emerging FtsZ inhibitors. Finally, we introduce SpyBrowse (https://veeninglab.com/SpyBrowse), a comprehensive and user-friendly online resource for visually inspecting and exploring GAS genetic features. The tools and methodologies described in this work are poised to facilitate fundamental research in GAS, contribute to vaccine development, and aid in the discovery of antibiotic targets.

IMPORTANCE

While group A Streptococcus (GAS) remains a predominant cause of bacterial infections worldwide, there are limited genetic tools available to study its basic cell biology. Here, we bridge this gap by creating a highly transformable, fully virulent M1T1 GAS strain. In addition, we established a tight and titratable doxycycline-inducible system and developed CRISPR interference (CRISPRi) for controlled gene expression in GAS. We show that CRISPRi is functional in vivo in a mouse infection model. Additionally, we present SpyBrowse, an intuitive and accessible genome browser (https://veeninglab.com/SpyBrowse). Overall, this work overcomes significant technical challenges of working with GAS and, together with SpyBrowse, represents a valuable resource for researchers in the GAS field.

The genome sequence of a green lacewing, Nineta flava (Scopoli, 1763)

We present a genome assembly from an individual Nineta flava (green lacewing; Arthropoda; Insecta; Neuroptera; Chrysopidae). The genome sequence spans 732.30 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.

The genome sequence of an ichneumonid wasp, Cylloceria caligata (Gravenhorst, 1829)

We present a genome assembly from an individual male Cylloceria caligata (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence spans 596.20 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 33.21 kilobases in length.

The genome sequence of a cuckoo wasp, Hedychridium roseum (Rossi, 1790)

We present a genome assembly from an individual female Hedychridium roseum (cuckoo wasp; Arthropoda; Insecta; Hymenoptera; Chrysididae). The genome sequence has a total length of 174.70 megabases. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.84 kilobases in length.

The genome sequence of a tephritid fruit fly, Merzomyia westermanni Meigen 1826

We present a genome assembly from an individual Merzomyia westermanni (a tephritid fruit fly; Arthropoda; Insecta; Diptera; Tephritidae). The genome sequence spans 986.20 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,765 protein-coding genes.

The genome sequence of an ichneumonid wasp, Rhimphoctona ( Xylophylax) megacephalus (Gravenhorst, 1829)

We present a genome assembly from an individual female Rhimphoctona megacephalus (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence spans 406.00 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.53 kilobases in length.

The genome sequence of the Purple Clay moth, Diarsia brunnea (Denis & Schiffermüller) 1775

We present a genome assembly from an individual male Diarsia brunnea (the Purple Clay moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 586.80 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 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,730 protein-coding genes.

The genome sequence of a ground beetle, Clivina fossor (Linnaeus, 1758)

We present a genome assembly from an individual female Clivina fossor (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence spans 612.60 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 16.48 kilobases in length.

The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808)

We present a genome assembly from an individual female Essex Skipper butterfly, Thymelicus lineola (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence spans 511.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.

The genome sequence of the Hawthorn Fruit Fly, Anomoia purmunda (Harris, 1780)

We present a genome assembly from a female Hawthorn Fruit Fly, Anomoia purmunda (Arthropoda; Insecta; Diptera; Tephritidae). The genome sequence has a length of 798.30 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 16.48 kilobases in length.

The genome sequence of the yellow mealworm beetle, Tenebrio molitor Linnaeus, 1758

We present a genome assembly from a male yellow mealworm Tenebrio molitor larva (Arthropoda; Insecta; Coleoptera; Tenebrionidae). The genome sequence has a total length of 277.00 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 15.78 kilobases in length.

The genome sequence of the Small Scabious Mining Bee, Andrena marginata Fabricius, 1776

We present a genome assembly from an individual female Andrena marginata (the Small Scabious Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence spans 373.60 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.16 kilobases in length.

The genome sequence of a braconid wasp, Dinocampus coccinellae (Schrank, 1802)

We present a genome assembly from an individual female Dinocampus coccinellae (a braconid wasp; Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence spans 110.40 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.88 kilobases in length.

The genome sequence of a braconid wasp, Aleiodes leptofemur van Achterberg & Shaw, 2016

We present a genome assembly from an individual male Aleiodes leptofemur (braconid wasp; Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence spans 271.20 megabases. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 32.28 kilobases in length.

The genome sequence of a robberfly Leptogaster cylindrica (De Geer, 1776)

We present a genome assembly from an individual female Leptogaster cylindrica (robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence spans 196.60 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,816 protein-coding genes.

The genome sequence of the blonde ray, Raja brachyura Lafont, 1871

We present a genome assembly from an individual female Raja brachyura (Blonde Ray; Chordata; Chondrichthyes; Rajiformes; Rajidae). The genome sequence spans 2,700.50 megabases. Most of the assembly is scaffolded into 49 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,252 protein-coding genes.

The genome sequence of a leaf beetle, Chrysolina haemoptera (Linnaeus, 1758)

We present a genome assembly from a female leaf beetle, Chrysolina haemoptera (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The total length of the genome sequence is 718.30 megabases. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.87 kilobases long. Gene annotation of this assembly on Ensembl identified 12,298 protein-coding genes.

The genome sequence of the sand star, Astropecten irregularis (Pennant, 1777)

We present a genome assembly from an individual Astropecten irregularis (the sand star; Echinodermata; Asteroidea; Paxillosida; Astropectinidae). The genome sequence spans 475.80 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.34 kilobases in length.

The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis & Schiffermüller), 1775

We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,087 protein-coding genes.

The genome sequence of the Cotton Bollworm moth, Helicoverpa armigera (Hübner, 1808)

We present a genome assembly from an adult female Cotton Bollworm moth, Helicoverpa armigera (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 362.20 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 15.36 kilobases in length.

The genome sequence of a segmented worm, Terebella lapidaria Linnaeus, 1767

We present a genome assembly from an individual Terebella lapidaria (segmented worm; Annelida; Polychaeta; Terebellida; Terebellidae). The genome sequence spans 765.20 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.97 kilobases in length.

The genome sequence of an ichneumonid wasp, Rhorus exstirpatorius (Gravenhorst, 1829)

We present a genome assembly from an individual male Rhorus exstirpatorius (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence spans 420.30 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.77 kilobases in length.

Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae)

Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousand genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior differ between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute to our understanding of the molecular bases underlying the progression of polyembryony. However, only the genome sequence of the US strain generated by the short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structures from those in the US strain. This was accomplished through functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected in amino acid sequences of vasa that play a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detailed genomic regions responsible for the ecological and physiological characteristics of C. floridanum.

Genome-wide analysis and visualization of copy number with CNVpytor in igv.js

SUMMARY

Copy number variation (CNV) and alteration (CNA) analysis is a crucial component in many genomic studies and its applications span from basic research to clinic diagnostics and personalized medicine. CNVpytor is a tool featuring a read depth-based caller and combined read depth and B-allele frequency (BAF) based 2D caller to find CNVs and CNAs. The tool stores processed intermediate data and CNV/CNA calls in a compact HDF5 file-pytor file. Here, we describe a new track in igv.js that utilizes pytor and whole genome variant files as input for on-the-fly read depth and BAF visualization, CNV/CNA calling and analysis. Embedding into HTML pages and Jupiter Notebooks enables convenient remote data access and visualization simplifying interpretation and analysis of omics data.

AVAILABILITY AND IMPLEMENTATION

The CNVpytor track is integrated with igv.js and available at https://github.com/igvteam/igv.js. The documentation is available at https://github.com/igvteam/igv.js/wiki/cnvpytor. Usage can be tested in the IGV-Web app at https://igv.org/app and also on https://github.com/abyzovlab/CNVpytor.

PanVA: Pangenomic Variant Analysis

Genomics researchers increasingly use multiple reference genomes to comprehensively explore genetic variants underlying differences in detectable characteristics between organisms. Pangenomes allow for an efficient data representation of multiple related genomes and their associated metadata. However, current visual analysis approaches for exploring these complex genotype-phenotype relationships are often based on single reference approaches or lack adequate support for interpreting the variants in the genomic context with heterogeneous (meta)data. This design study introduces PanVA, a visual analytics design for pangenomic variant analysis developed with the active participation of genomics researchers. The design uniquely combines tailored visual representations with interactions such as sorting, grouping, and aggregation, allowing users to navigate and explore different perspectives on complex genotype-phenotype relations. Through evaluation in the context of plants and pathogen research, we show that PanVA helps researchers explore variants in genes and generate hypotheses about their role in phenotypic variation.

OysterDB: A Genome Database for Ostreidae

The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters ( http://oysterdb.com.cn/ ).