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

The genome sequence of the silvery leafcutter bee, Megachile leachella Curtis, 1828

We present a genome assembly from an individual female Megachile leachella (the silvery leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 573.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.04 kilobases in length.

The genome sequence of a braconid wasp, Aleiodes testaceus (Telenga, 1941)

We present a genome assembly from an individual female Aleiodes testaceus (braconid wasp; Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence spans 110.70 megabases. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,520 protein-coding genes.

The genome sequence of the particolored bat, Vespertilio murinus Linnaeus, 1758

We present a genome assembly from an individual male Vespertilio murinus (the particolored bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1,925.6 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.96 kilobases in length.

The genome sequence of a jewel beetle, Agrilus biguttatus (Fabricius, 1776)

We present a genome assembly from an individual female Agrilus biguttatus (jewel beetle; Arthropoda; Insecta; Coleoptera; Buprestidae). The genome sequence spans 368.10 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 17.41 kilobases in length.

The genome sequence of the Dark Crimson Underwing moth, Catocala sponsa Linnaeus, 1767

We present a genome assembly from an individual female Catocala sponsa (the Dark Crimson Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence spans 803.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,493 protein-coding genes.

The genome sequence of the Northern Bottlenose Whale, Hyperoodon ampullatus (Forster, 1770)

We present a genome assembly from an individual female Hyperoodon ampullatus (the Northern Bottlenose Whale; Chordata; Mammalia; Artiodactyla; Ziphiidae). The genome sequence spans 2,828.70 megabases. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length.

The genome sequence of the harvestman spider, Odiellus spinosus (Bosc, 1792)

We present a genome assembly from an individual female Odiellus spinosus (harvestman spider; Arthropoda; Arachnida; Opiliones; Phalangiidae). The genome sequence spans 443.70 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.07 kilobases in length.

The Genome Explorer genome browser

Are two adjacent genes in the same operon? What are the order and spacing between several transcription factor binding sites? Genome browsers are software data visualization and exploration tools that enable biologists to answer questions such as these. In this paper, we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale. By downloading the data for the entire genome to the user's web browser and dynamically generating visualizations locally, we enable fine control of zoom and pan functions and real-time redrawing of the visualization, resulting in smoother and more intuitive exploration of a genome than is possible with other browsers. Further, genome features are presented together, in-line, using familiar graphical depictions. In contrast, many other browsers depict genome features using data tracks, which have low information density and can visually obscure the relative positions of features. Genome Explorer diagrams have a high information density that provides larger amounts of genome context and sequence information to be presented in a given-sized monitor than for tracks-based browsers. Genome Explorer provides optional data tracks for the analysis of large-scale data sets and a unique comparative mode that aligns genomes at orthologous genes with synchronized zooming.

IMPORTANCE

Genome browsers provide graphical depictions of genome information to speed the uptake of complex genome data by scientists. They provide search operations to help scientists find information and zoom operations to enable scientists to view genome features at different resolutions. We introduce the Genome Explorer browser, which provides extremely fast zooming and panning of genome visualizations and displays with high information density.

The genome sequence of the jumping weevil, Orchestes rusci (Herbst, 1795)

We present a genome assembly from an individual female Orchestes rusci (the jumping weevil; Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence spans 624.00 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.73 kilobases in length.

The genome sequence of the European harvest mouse, Micromys minutus (Pallas, 1771)

We present a genome assembly from an individual female Micromys minutus (the European harvest mouse; Chordata; Mammalia; Rodentia; Muridae). The genome sequence spans 2,651.80 megabases. Most of the assembly is scaffolded into 34 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.24 kilobases in length.

The genome sequence of the moss carder bee, Bombus muscorum (Linnaeus, 1758)

We present a genome assembly from an individual female Bombus muscorum (the moss carder bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence spans 317.70 megabases. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,668 protein-coding genes.

The genome sequence of a hydroid, Candelabrum cocksii (Cocks, 1854)

We present a genome assembly from an individual Candelabrum cocksii (hydroid; Cnidaria; Hydrozoa; Anthoathecata; Candelabridae). The genome sequence is 232.9 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.55 kilobases in length.

The genome sequence of a sawfly Macrophya annulata (Geoffroy, 1785)

We present a genome assembly from an individual male Macrophya annulata (sawfly; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 236.8 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 31.23 kilobases in length.

The genome sequence of the Sandhill Rustic moth Luperina nickerlii (Freyer, 1845) subspecies leechi Goater, 1976

We present a genome assembly from an individual female Luperina nickerlii (the Sandhill Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 662.0 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The specimen was confirmed to be a ZO female. The mitochondrial genome has also been assembled and is 15.47 kilobases in length.

The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876)

We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.

Association studies of salinity tolerance in sunflower provide robust breeding and selection strategies under climate change

Phytotoxic soil salinity is a global problem, and in the northern Great Plains and western Canada, salt accumulates on the surface of marine sediment soils with high water tables under annual crop cover, particularly near wetlands. Crop production can overcome saline-affected soils using crop species and cultivars with salinity tolerance along with changes in management practices. This research seeks to improve our understanding of sunflower (Helianthus annuus) genetic tolerance to high salinity soils. Genome-wide association was conducted using the Sunflower Association Mapping panel grown for two years in naturally occurring saline soils (2016 and 2017, near Indian Head, Saskatchewan, Canada), and six phenotypes were measured: days to bloom, height, leaf area, leaf mass, oil percentage, and yield. Plot level soil salinity was determined by grid sampling of soil followed by kriging. Three estimates of sunflower performance were calculated: (1) under low soil salinity (< 4 dS/m), (2) under high soil salinity (> 4 dS/m), and (3) plasticity (regression coefficient between phenotype and soil salinity). Fourteen loci were significant, with one instance of co-localization between a leaf area and a leaf mass locus. Some genomic regions identified as significant in this study were also significant in a recent greenhouse salinity experiment using the same panel. Also, some candidate genes underlying significant QTL have been identified in other plant species as having a role in salinity response. This research identifies alleles for cultivar improvement and for genetic studies to further elucidate salinity tolerance pathways.

The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840

We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.

The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869)

We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.

The genome sequence of Reeves' muntjac, Muntiacus reevesi (Ogilby, 1839)

We present a genome assembly from an individual female Muntiacus reevesi (the Reeves' muntjac; Chordata; Mammalia; Artiodactyla; Cervidae). The genome sequence is 2,656.2 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.35 kilobases in length.

An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution

In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.

Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior

Phoresy is an interspecies interaction that facilitates spatial dispersal by attaching to a more mobile species. Hitchhiking species have evolved specific traits for physical contact and successful phoresy, but the regulatory mechanisms involved in such traits and their evolution are largely unexplored. The nematode Caenorhabditis elegans displays a hitchhiking behavior known as nictation during its stress-induced developmental stage. Dauer-specific nictation behavior has an important role in natural C. elegans populations, which experience boom-and-bust population dynamics. In this study, we investigated the nictation behavior of 137 wild C. elegans strains sampled throughout the world. We identified species-wide natural variation in nictation and performed a genome-wide association mapping. We show that the variants in the promoter of nta-1, encoding a putative steroidogenic enzyme, underlie differences in nictation. This difference is due to the changes in nta-1 expression in glial cells, which implies that glial steroid metabolism regulates phoretic behavior. Population genetic analysis and geographic distribution patterns suggest that balancing selection maintained two nta-1 haplotypes that existed in ancestral C. elegans populations. Our findings contribute to further understanding of the molecular mechanism of species interaction and the maintenance of genetic diversity within natural populations.

The wild side of grape genomics

With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.

The genome sequence of the Banded Burying beetle, Nicrophorus investigator Zetterstedt, 1824

We present a genome assembly from a female Nicrophorus investigator (Banded Burying beetle; Arthropoda; Insecta; Coleoptera; Silphidae). The genome sequence is 202.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 23.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,046 protein coding genes.

The genome sequence of a cranefly, Tipula ( Savtshenkia) confusa van der Wulp, 1883

We present a genome assembly from an individual male Tipula confusa (cranefly; Arthropoda; Insecta; Diptera; Tipulidae). The genome sequence is 728.1 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.

The genome sequence of the chlorophyte Marvania coccoides CCAP 251/1B (Naumann) Henley, Hironaka, Guillou, M. Buchheim, J. Buchheim, M. Fawley & K. Fawley 2004

We present a genome assembly from a culture of Marvania coccoides (CCAP 251/1B) (Chlorophyta; Trebouxiophyceae; Chlorellales; Chlorellaceae). The genome sequence is 22.3 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 49.04 kilobases and 99.87 kilobases in length, respectively.

The genome sequence of an anthomyiid fly, Pegoplata infirma (Meigen, 1826) (Diptera, Anthomyiidae)

We present a genome assembly from an individual male Pegoplata infirma (anthomyiid fly; Arthropoda; Insecta; Diptera; Anthomyiidae). The genome sequence is 1384.4 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 16.15 kilobases in length.

The genome sequence of the European pine marten, Martes martes (Linnaeus, 1758)

We present a genome assembly from an individual male Martes martes (the European pine marten; Chordata; Mammalia; Carnivora; Mustelidae). The genome sequence is 2,484.6 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.57 kilobases in length.

The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758

We present a genome assembly from an individual male Agonopterix heracliana (the Common Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 539.1 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 15.36 kilobases in length.

The genome sequence of the Coccidian parasite, Eimeria praecox (Apicomplexa: Eucoccidiorida)

We present a genome assembly from sporozoites from a clonal line of Eimeria praecox (the Coccidian parasite; Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 64.3 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The organelle genomes have also been assembled and the mitochondrial genome is 6.23 kilobases in length, while the apicoplast genome is 28.83 kilobases long.

The genome sequence of a cased caddisfly, Molanna angustata Curtis, 1834

We present a genome assembly from an individual male Molanna angustata (cased caddisfly; Arthropoda; Insecta; Trichoptera; Molannidae). The genome sequence is 994.9 megabases in span. Most of the assembly is scaffolded into 27 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 14.92 kilobases in length.

The genome sequence of the tree-moss, Climacium dendroides (Hedw.) F.Weber & D.Mohr (Climaciaceae)

We present a genome assembly from an individual Climacium dendroides gametophyte (the tree-moss; Bryophyta; Bryopsida; Leucodontales; Climaciaceae). The genome sequence is 413.1 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 104.86 kilobases and 124.96 kilobases in length, respectively.

The genome sequence of a cased caddisfly, Mystacides longicornis (Linnaeus, 1758)

We present a genome assembly from an individual male Mystacides longicornis (cased caddisfly; Arthropoda; Insecta; Trichoptera; Leptoceridae). The genome sequence is 665.1 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.75 kilobases in length.

The genome sequence of the grey gurnard, Eutrigla gurnardus (Linnaeus, 1758)

We present a genome assembly from an individual Eutrigla gurnardus (the grey gurnard; Chordata; Actinopteri; Scorpaeniformes; Triglidae). The genome sequence is 680.5 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.51 kilobases in length.

Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli

Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g., in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e., they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with the acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection, in which the expression of flhDC was altered by an insertion sequence element. These results suggest a fitness trade-off between acid tolerance and motility.IMPORTANCEEscherichia coli is extremely acid-resistant, which is crucial for survival in the gastrointestinal tract of vertebrates. Recently, we systematically studied the response of E. coli to mild and severe acidic conditions using Ribo-Seq and RNA-Seq. We found that motility genes are induced at pH 5.8 but not at pH 4.4, indicating stress-dependent synthesis of flagellar components. In this study, we demonstrate that motility-activating mutations upstream of flhDC, encoding the master regulator of flagella genes, reduce the ability of E. coli to survive periods of acid shock. Furthermore, we show an inverse correlation between motility and acid survival using a chromosomal isopropyl β-D-thio-galactopyranoside (IPTG)-inducible flhDC promoter and by sampling differentially motile subpopulations from swim agar plates. These results reveal a previously undiscovered trade-off between motility and acid tolerance and suggest a differentiation of E. coli into motile and acid-tolerant subpopulations, driven by the integration of insertion sequence elements.

Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation

Regulatory elements are important constituents of plant genomes that have shaped ancient and modern crops. Their identification, function, and diversity in crop genomes however are poorly characterized, thus limiting our ability to harness their power for further agricultural advances using induced or natural variation. Here, we use DNA affinity purification-sequencing (DAP-seq) to map transcription factor (TF) binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production, providing empirical binding site annotation for 5.3% of the maize genome. TF binding site comparison in B73 and Mo17 inbreds reveals widespread differences, driven largely by structural variation, that correlate with gene expression changes. TF binding site presence-absence variation helps clarify complex QTL such as vgt1, an important determinant of maize flowering time, and DICE, a distal enhancer involved in herbivore resistance. Modification of TF binding regions via CRISPR-Cas9 mediated editing alters target gene expression and phenotype. Our functional catalog of maize TF binding events enables collective and comparative TF binding analysis, and highlights its value for agricultural improvement.

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.

Bigtools: a high-performance BigWig and BigBed library in Rust

MOTIVATION

The BigWig and BigBed file formats were originally designed for the visualization of next-generation sequencing data through a genome browser. Due to their versatility, these formats have long since become ubiquitous for the storage of processed sequencing data and regularly serve as the basis for downstream data analysis. As the number and size of sequencing experiments continues to accelerate, there is an increasing demand to efficiently generate and query BigWig and BigBed files in a scalable and robust manner, and to efficiently integrate these functionalities into data analysis environments and third-party applications.

RESULTS

Here, we present Bigtools, a feature-complete, high-performance, and integrable software library for generating and querying both BigWig and BigBed files. Bigtools is written in the Rust programming language and includes a flexible suite of command line tools as well as bindings to Python.

AVAILABILITY AND IMPLEMENTATION

Bigtools is cross-platform and released under the MIT license. It is distributed on Crates.io, Bioconda, and the Python Package Index, and the source code is available at https://github.com/jackh726/bigtools.

The genome sequence of the silver stretch spider, Tetragnatha montana (Simon, 1874) (Araneae: Tetragnathidae)

We present a genome assembly from an individual female Tetragnatha montana (the silver stretch spider; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 784.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length.

The genome sequence of the Marbled Minor moth, Oligia strigilis (Linnaeus, 1758)

We present a genome assembly from an individual male Oligia strigilis (Marbled Minor; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 626.1 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 15.35 kilobases in length.

The genome sequence of the cut surfclam, Spisula subtruncata (da Costa, 1778)

We present a genome assembly from a specimen of Spisula subtruncata (the cut surfclam; Mollusca; Bivalvia; Venerida; Mactridae). The genome sequence is 930.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.64 kilobases in length.

The genome sequence of the Muslin Footman moth, Nudaria mundana (Linnaeus, 1761)

We present a genome assembly from an individual male Nudaria mundana (the Muslin Footman moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 643.9 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 17.14 kilobases in length.

The genome sequence of the German scorpionfly, Panorpa germanica Linnaeus, 1758

We present a genome assembly from an individual male Panorpa germanica (the German scorpionfly; Arthropoda; Insecta; Mecoptera; Panorpidae). The genome sequence is 464.2 megabases in span. Most of the assembly is scaffolded into 21 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 Ruddy Streak moth, Tachystola acroxantha (Meyrick, 1885)

We present a genome assembly from a female Tachystola acroxantha (the Ruddy Streak; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 388.1 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 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,656 protein coding genes.

The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis & Schiffermüller) 1775

We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. 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 17.64 kilobases in length.

WormBase 2024: status and transitioning to Alliance infrastructure

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.

The Arabidopsis Information Resource in 2024

Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a "gold standard" functional annotation set that reflects the current state of knowledge about the Arabidopsis genome. At the same time, the resource serves as a nexus for community-based collaborations aimed at improving data quality, access, and reuse. For the past decade, our work has been made possible by subscriptions from our global user base. This update covers our ongoing biocuration work, some of our modernization efforts that contribute to the first major infrastructure overhaul since 2011, the introduction of JBrowse2, and the resource's role in community activities such as organizing the structural reannotation of the genome. For gene function assessment, we used gene ontology annotations as a metric to evaluate: (1) what is currently known about Arabidopsis gene function and (2) the set of "unknown" genes. Currently, 74% of the proteome has been annotated to at least one gene ontology term. Of those loci, half have experimental support for at least one of the following aspects: molecular function, biological process, or cellular component. Our work sheds light on the genes for which we have not yet identified any published experimental data and have no functional annotation. Drawing attention to these unknown genes highlights knowledge gaps and potential sources of novel discoveries.

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome

Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .

The genome sequence of the chaffinch, Fringilla coelebs Linnaeus, 1758

We present a genome assembly from an individual male Fringilla coelebs (the chaffinch; Chordata; Aves; Passeriformes; Fringillidae). The genome sequence is 1,209.2 megabases in span. Most of the assembly is scaffolded into 40 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.8 kilobases in length.

The genome sequence of the lesser stag beetle, Dorcus parallelipipedus (Linnaeus, 1758)

We present a genome assembly from an individual male Dorcus parallelipipedus (the lesser stag beetle; Arthropoda; Insecta; Coleoptera; Lucanidae). The genome sequence is 470.9 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 18.19 kilobases in length.