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

Transcription factor binding divergence drives transcriptional and phenotypic variation in maize

Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR-Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.

Repeated loss of function at HD mating-type genes and of recombination in anther-smut fungi

Basidiomycete fungi typically have two mating-type loci controlling mating compatibility, HD and PR, residing on different chromosomes. Loss-of-function in mating compatibility has been reported at the PR genes in a few heterothallic basidiomycetes, but not for the HD genes. In Microbotryum anther-smut fungi, there have been repeated linkage events between the HD and PR loci through chromosome fusions, leading to non-recombining regions. Here, we found that two sister Microbotryum species parasitizing Dianthus plants, M. superbum and M. shykoffianum, as well as the distantly related M. scorzonerae, have their HD and PR loci on different chromosomes, but with the PR chromosome fused with a part of the ancestral HD chromosome. In addition, recombination suppression has extended stepwise, generating evolutionary strata. In all three species, the HD genes lost their function in mating compatibility, natural diploid strains being often homozygous at the HD locus. Strains could be homozygous for a disrupted HD2 gene, that was hardly expressed during mating. Mating tests confirmed that a single genetic factor controlled mating compatibility and that haploid strains with identical HD alleles could mate and produce hyphae. This study shows that a unifactorial mating-type determinism can evolve, repeatedly, from a bifactorial system, by different mechanisms.

The genome sequence of the Heath Bumblebee, Bombus jonellus (Kirby, 1802)

We present a genome assembly from a female specimen of Bombus jonellus (Heath Bumblebee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 357.90 megabases. Most of the assembly (78.06%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 24.83 kilobases.

The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences

We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.

DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst in Arabidopsis thaliana

Transposable elements (TEs) are major drivers of plant genome plasticity, but the immediate molecular consequences of new TE insertions remain poorly understood. In this study, we generated a wild-type Arabidopsis thaliana population with novel insertions of ONSEN retrotransposon to investigate early epigenomic and transcriptomic changes using whole-genome and cDNA nanopore sequencing. We found that novel ONSEN insertions were distributed non-randomly, with a strong preference for genic regions, particularly in chromatin enriched for H2A.Z, H3K27me3, and H3K4me2. Most full-length ONSEN insertions within genes were rapidly recognized and spliced out as new introns (intronization), thereby mitigating potential deleterious effects on transcript isoforms. In some cases, ONSEN insertions provided alternative transcription start or termination sites, generating novel transcript isoforms. Genome-wide methylation analysis revealed that new ONSEN copies were efficiently and precisely targeted by DNA methylation. Independently on the location of the original ONSEN element, the euchromatic and heterochromatic insertions display distinct methylation signatures, reflecting the action of different epigenetic pathways. In conclusion, our results demonstrate that DNA methylation and alternative splicing are effective control mechanisms safeguarding the plant genome and transcriptome integrity after retrotransposition burst.

CRISPR-BEasy: a free web-based service for designing sgRNA tiling libraries for CRISPR-dependent base editing screens

CRISPR-dependent base editing (BE) enables the modeling and correction of genetic mutations at single-base resolution. Base editing screens, where point mutations are queried en masse, are powerful tools to systematically draw genotype-phenotype associations and characterise the function of genes and other genomic elements. However, the lack of user-friendly web-based tools for designing base editing screens can hinder broad technology adoption. Here, we introduce CRISPR-BEasy (https://crispr-beasy.cerc-genomic-medicine.ca), a free, automated web-based server that streamlines the creation of single guide (sg)RNA tiling libraries for base editing screens. Researchers can provide their genes or genomic features of interest, their base editors of choice, and target sequences to act as positive and negative controls. The server designs and annotates sgRNA libraries by integrating custom code with publicly available tools such as crisprVerse and Ensembl's Variant Effect Predictor. CRISPR-BEasy provides downloadable results, including sgRNA on/off-target scores, predicted mutational outcomes per base editor, and intuitive interactive visualizations for data quality assessment. CRISPR-BEasy also provides a separate tool that assembles sgRNA libraries into oligonucleotides for cloning following the detailed protocol documented in the searchable web server manual. Together, CRISPR-BEasy ensures the seamless design of cloning-ready sgRNA libraries, seeking to democratise access to base editing screening technologies.

The genome sequence of the Ibiza wall lizard, Podarcis pityusensis (Boscá, 1883)

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Laterata; Lacertibaenia; Lacertidae; Lacertinae; Podarcis; Podarcis pityusensis (Boscá, 1883) (NCBI:txid74359).

Chromatin loops are an ancestral hallmark of the animal regulatory genome

In bilaterian animals, gene regulation is shaped by a combination of linear and spatial regulatory information. Regulatory elements along the genome are integrated into gene regulatory landscapes through chromatin compartmentalization1,2, insulation of neighbouring genomic regions3,4 and chromatin looping that brings together distal cis-regulatory sequences5. However, the evolution of these regulatory features is unknown because the three-dimensional genome architecture of most animal lineages remains unexplored6,7. To trace the evolutionary origins of animal genome regulation, here we characterized the physical organization of the genome in non-bilaterian animals (sponges, ctenophores, placozoans and cnidarians)8,9 and their closest unicellular relatives (ichthyosporeans, filastereans and choanoflagellates)10 by combining high-resolution chromosome conformation capture11,12 with epigenomic marks and gene expression data. Our comparative analysis showed that chromatin looping is a conserved feature of genome architecture in ctenophores, placozoans and cnidarians. These sequence-determined distal contacts involve both promoter-enhancer and promoter-promoter interactions. By contrast, chromatin loops are absent in the unicellular relatives of animals. Our findings indicate that spatial genome regulation emerged early in animal evolution. This evolutionary innovation introduced regulatory complexity, ultimately facilitating the diversification of animal developmental programmes and cell type repertoires.

Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut

Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.

The genome sequence of the Vestal Cuckoo Bee, Bombus vestalis (Geoffroy, 1785)

We present a genome assembly from a haploid male specimen of Bombus vestalis (Vestal Cuckoo Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 280.01 megabases. Most of the assembly (91.96%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,600 protein-coding genes.

Developmental pathways underlying sexual differentiation in the U/V sex chromosome system of giant kelp

In many multicellular organisms, sexual development is not determined by XX/XY or ZW/ZZ systems but by U/V sex chromosomes. In U/V systems, sex determination occurs in the haploid phase, with U chromosomes in females and V chromosomes in males. Here, we explore several male, female, and partially sex-reversed male lines of giant kelp to decipher how U/V sex chromosomes and autosomes initiate male versus female development. We identify a key set of genes on the sex chromosomes involved in triggering sexual development and characterize autosomal effector genes underlying sexual differentiation. We show that male, but not female, development involves large-scale transcriptome reorganization with pervasive enrichment in regulatory genes, faster evolutionary rates, and high species-specificity of male-biased genes. Our observations imply that a female-like phenotype is the "ground state", which is complemented by the presence of a U-chromosome but overridden by a dominant male developmental program triggered by the V-chromosome.

Impact of a horizontally transferred Helitron family on genome evolution in Xenopus laevis

BACKGROUND

Within eukaryotes, most horizontal transfer of genetic material involves mobile DNA sequences and such events are called horizontal transposable element transfer (HTT). Although thousands of HTT examples have been reported, the transfer mechanisms and their impacts on host genomes remain elusive.

RESULTS

In this work, we carefully annotated three Helitron families within several Xenopus frog genomes. One of the Helitron family, Heli1Xen1, is recurrently involved in capturing and shuffling Xenopus laevis genes required in early embryonic development. Remarkably, we found that Heli1Xen1 is seemingly expressed in X. laevis and has produced multiple genomic polymorphisms within the X. laevis population. To identify the origin of Heli1Xen1, we searched its consensus sequence against available genome assemblies. We found highly similar copies in the genomes of another 13 vertebrate species from divergent vertebrate lineages, including reptiles, ray-finned fishes and amphibians. Further phylogenetic analysis provides evidence showing that Heli1Xen1 invaded these lineages via HTT quite recently, around 0.58-10.74 million years ago.

CONCLUSIONS

The frequently Heli1Xen1-involved HTT events among reptiles, fishes and amphibians could provide insights into possible vectors for transfer, such as shared viruses across lineages. Furthermore, we propose that the Heli1Xen1 sequence could be an ideal candidate for studying the mechanism and genomic impact of Helitron transposition.

The genome sequence of the harbour porpoise, Phocoena phocoena (Linnaeus, 1758)

We present a genome assembly from a female specimen of Phocoena phocoena (harbour porpoise; Chordata; Mammalia; Artiodactyla; Phocoenidae). The genome sequence has a total length of 2,512.71 megabases. Most of the assembly (94.41%) is scaffolded into 22 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.38 kilobases.

The genome sequence of the European ground squirrel, Spermophilus citellus (Linnaeus, 1766)

We present a genome assembly from a female Spermophilus citellus (European ground squirrel; Chordata; Mammalia; Rodentia; Sciuridae). The genome sequence has a total length of 3,090.03 megabases. Most of the assembly (95.47%) is scaffolded into 20 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.45 kilobases.

The genome sequence of long-finned pilot whale, Globicephala melas (Traill, 1809)

We present a genome assembly from a male specimen of Globicephala melas (long-finned pilot whale; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence has a total length of 2,651.28 megabases. Most of the assembly (89.15%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.39 kilobases. Gene annotation of this assembly on Ensembl identified 17,911 protein-coding genes.

The genome sequence of a snail-killing fly, Dichetophora obliterata (Fabricius, 1805)

We present a genome assembly from a female specimen of Dichetophora obliterata (snail-killing fly; Arthropoda; Insecta; Diptera; Sciomyzidae). The genome sequence has a total length of 1,312.79 megabases. Most of the assembly (99.78%) is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 21.36 kilobases. Gene annotation of this assembly on Ensembl identified 15,139 protein-coding genes.

The genome sequence of the short-beaked common dolphin, Delphinus delphis Linnaeus, 1758

We present a genome assembly from a male specimen of Delphinus delphis (short-beaked common dolphin; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence has a total length of 2,663.52 megabases. Most of the assembly (88.76%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.39 kilobases. Gene annotation of this assembly at Ensembl identified 17,797 protein-coding genes.

A Comprehensive Analysis of Short Specific Tissue (SST) Proteins, a New Group of Proteins from PF10950 That May Give Rise to Cyclopeptide Alkaloids

Proteins of the PF10950 family feature the DUF2775 domain of unknown function. The most studied are specific tissue (ST) proteins with tandem repeats, which are putative precursors of cyclopeptide alkaloids. Here, we study uncharacterised short ST (SST) proteins with the DUFF2775 domain by analysing 194 sequences from 120 species of 39 taxonomic families in silico. SST proteins have a signal peptide and their size and several other characteristics depend on their individual taxonomic family. Sequence analyses revealed that SST proteins contain two well-conserved regions, one resembling the ST repeat, which could constitute the core of cyclopeptide alkaloids. We studied the unique SST1 gene of Arabidopsis thaliana, which is adjacent to and co-expressed with a gene encoding a protein with a BURP domain, associated with cyclopeptide production. The empirical analysis indicated that the SST1 promoter is mainly activated in the roots, where most of the transcripts accumulate, and that the SST1 protein accumulates in the root vascular cambium. At the cellular level, SST fused to GFP appears in vesicles that co-localise with the endoplasmic reticulum and the vacuole. Thus, SSTs are a new type of PF10950 protein found in core eudicots with two conserved regions that could be involved in root biology.

Horizontal Transfer of Bacterial Operons into Eukaryote Genomes

In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.

Bioinformatic, structural, and biochemical analysis leads to the discovery of novel isonitrilases and decodes their substrate selectivity

Bacterial species, such as Mycobacterium tuberculosis, utilize isonitrile-containing peptides (INPs) for trace metal trafficking, e.g., copper or zinc. Despite their importance, very few INP structures have been characterized to date. Reported INPs consist of a peptide backbone and β-isonitrile amide moieties. While the peptide backbone can be annotated using an adenylation domain predictor of non-ribosomal peptide synthetase (NRPS), determining the alkyl chain of β-isonitrile amide moieties remains challenging via conventional analytical techniques. In this study, we focus on non-heme iron and 2-oxoglutarate (Fe/2OG) dependent isonitrilases that exhibit inherent selectivity toward the alkyl chain length of the substrate, thus enabling the structural elucidation of INPs. Based on two known isonitrilase structures, we identified eight residue positions that control substrate selectivity. Using a custom Python program that we developed, BioSynthNexus, over 350 Fe/2OG isonitrilase genes were identified. One of these enzymes was engineered through mutations at eight selected positions, effectively modifying its substrate preference to favor either a shorter or a longer alkyl chain. Furthermore, by examining several annotated isonitrilases at eight selected positions, substrate preferences of several isonitrilases were predicted and validated through biochemical assays. Together, these findings allow for effective identification of isonitrilases and INPs, and establish a predictive framework for determining the preferred alkyl chain of β-isonitrile amide moieties.

The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars

Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated 'Asm2sv', identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.

High rate of mutation and efficient removal by selection of structural variants from natural populations of Caenorhabditis elegans

The importance of genomic structural variants (SVs) is well-appreciated, but much less is known about their mutational properties than of single nucleotide variants (SNVs) and short indels. The reason is simple: the longer the mutation, the less likely it will be covered by a single sequencing read, thus the harder it is to map unambiguously to a unique genomic location. Here we report SV mutation rate estimates from six mutation accumulation (MA) lines from two strains of C. elegans (N2 and PB306) using long-read (PacBio) sequencing. The inferred SV mutation rate ~1/10 the SNV rate and ~1/4 the short indel rate. We identified 40 mutations, and removed 52 false positives (FP) by manual inspection of each SV call. Excluding one atypical line (5 mutations, 35 FPs), the signal (inferred mutant) to noise (FP) ratio is approximately 2:1. False negative rates were determined by simulating variants in the reference genome, and observing 'recall'. Recall rate ranges from >90% for short indels and declines as SV length increases. Small deletions have nearly the same recall rate as small insertions (~100bp), but deletions have higher recall rates than insertions as size increases. The reported SV mutation rate is likely an underestimate. A quarter of identified SV mutations occur in SV hotspots that harbor pre-existing low complexity repeat variation. By comparison of the spectrum of spontaneous SVs to wild isolates, we infer that natural selection is not only efficient at removing SVs in exons, but also removes roughly half of SVs in intergenic regions.

The genome sequence of a cave beetle, Leptodirus hochenwartii F.J.Schmidt, 1832

We present a genome assembly from a male specimen of Leptodirus hochenwartii (cave beetle; Arthropoda; Insecta; Coleoptera; Leiodidae). The genome sequence has a total length of 492.36 megabases. Most of the assembly (98.03%) is scaffolded into 14 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.01 kilobases in length.

The genome sequence of the Four-spotted Footman moth, Lithosia quadra (Linnaeus, 1758)

We present a genome assembly from a male Lithosia quadra (Four-spotted Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 456.27 megabases. Most of the assembly (99.91%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.

The genome sequence of the Straw-barred Pearl moth, Pyrausta despicata Scopoli, 1763

We present a genome assembly from a male specimen of Pyrausta despicata (Straw-barred Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 481.83 megabases. Most of the assembly (99.61%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.

The genome sequence of a beetle, Pycnomerus fuliginosus Erichson, 1842

We present a genome assembly from a female Pycnomerus fuliginosus (beetle; Arthropoda; Insecta; Coleoptera; Zopheridae). The genome sequence has a total length of 359.22 megabases. Most of the assembly (95.81%) is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,547 protein-coding genes.

The genome sequence of the Common Pochard, Aythya ferina (Linnaeus, 1758)

We present a genome assembly from a female specimen of Aythya ferina (Common Pochard; Chordata; Aves; Anseriformes; Anatidae). The assembly contains two haplotypes with total lengths of 1,252.30 megabases and 1,103.59 megabases. Most of haplotype 1 (92.13%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.6 kilobases.

The genome sequence of the Maple Pug moth, Eupithecia inturbata (Hübner, 1817)

We present a genome assembly from a female Eupithecia inturbata (Maple Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 427.76 megabases. Most of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.33 kilobases. Gene annotation of this assembly on Ensembl identified 12,386 protein-coding genes.

The genome sequence of the True Lover's Knot moth, Lycophotia porphyrea (Denis & Schiffermüller), 1775

We present a genome assembly from an individual male Lycophotia porphyrea (the True Lover's Knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 542.40 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 15.39 kilobases in length. Gene annotation of this assembly at Ensembl identified 17,907 protein-coding genes.

The genome sequence of a bark-dwelling beetle, Silvanus unidentatus (Olivier, 1790)

We present a genome assembly from a specimen of Silvanus unidentatus (bark-dwelling beetle; Arthropoda; Insecta; Coleoptera; Silvanidae). The genome sequence has a total length of 187.15 megabases. Most of the assembly (84.24%) is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,364 protein-coding genes.

The genome sequence of an ichneumonid wasp, Polytribax perspicillator (Gravenhorst, 1807)

We present a genome assembly from a male Polytribax perspicillator (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence has a total length of 314.21 megabases. Most of the assembly (99.94%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.68 kilobases in length.

Saccharomyces Genome Database: advances in genome annotation, expanded biochemical pathways, and other key enhancements

Budding yeast (Saccharomyces cerevisiae) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and proteins. The Saccharomyces Genome Database (SGD) is a scientific resource that provides information about the genome and biology of S. cerevisiae. For more than 30 years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation for budding yeast along with search and analysis tools to explore these data. Here, we describe recent updates at SGD, including the 2 most recent reference genome annotation updates, expanded biochemical pathway representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface. These activities are part of our continuing effort to promote insights gained from yeast to enable the discovery of functional relationships between sequence and gene products in fungi and higher eukaryotes.

SpudDB: a database for accessing potato genomic data

Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1-3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit the identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists, and breeders to continue to improve this key food crop.

The genome sequence of a chironomid fly, Chironomus tentans Fabricius, 1805

We present a genome assembly from a specimen of Chironomus tentans (chironomid fly; Arthropoda; Insecta; Diptera; Chironomidae). The genome sequence has a total length of 185.47 megabases. Most of the assembly (99.7%) is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.09 kilobases. Gene annotation of this assembly on Ensembl identified 12,575 protein-coding genes.

The genome sequence of the European smelt, Osmerus eperlanus (Linnaeus, 1758)

We present a genome assembly from a specimen of Osmerus eperlanus (European smelt; Chordata; Actinopteri; Osmeriformes; Osmeridae). The genome sequence has a total length of 508.70 megabases. Most of the assembly (95.79%) is scaffolded into 28 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.61 kilobases.

The genome sequence of the common crane, Grus grus (Linnaeus, 1758)

We present a genome assembly from a male specimen of Grus grus (common crane; Chordata; Aves; Gruiformes; Gruidae). The assembly contains two haplotypes with total lengths of 1,352.26 megabases and 1,291.08 megabases. Most of haplotype 1 (91.85%) is scaffolded into 40 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 18.9 kilobases in length.

CsMPDB 1.0: An interactive web application for visualizing and exploring the microRNAs and phasiRNAs of tea plant (Camellia sinensis var. sinensis 'Shuchazao')

The microRNAs and phasiRNAs of plant are small non-coding RNAs with important functions through regulating gene expression at the post-transcriptional level. However, identifying miRNAs, phasiRNAs and their target genes from numerous sequencing raw data requires multiple software and command-line operations, which are time-consuming and labor-intensive for non-model plants. Therefore, we present CsMPDB (miRNAs and phasiRNAs database of Camellia sinensis), an interactive web application with multiple analysis modules developed to visualize and explore miRNA and phasiRNA in tea plants based on 259 sRNA-seq samples and 24 degradome-seq samples in NCBI. The source code for the CsMPDB was written in R/shiny. It is compatible, extendable, and portable to be easily set up on different operating systems, and can be accessed at http://myshiny.cpolar.io/CsMPDB. This application plays an important role in accelerating the functional study of sRNAs in the transcriptional regulation of tea plants, and has important reference value for the development of sRNA databases of other species.

The BioGenome Portal: a web-based platform for biodiversity genomics data management

Biodiversity genomics projects are underway with the aim of sequencing the genomes of all eukaryotic species on Earth. Here we describe the BioGenome Portal, a web-based application to facilitate organization and access to the data produced by biodiversity genomics projects. The portal integrates user-generated data with data deposited in public repositories. The portal generates sequence status reports that can be eventually ingested by designated metadata tracking systems, facilitating the coordination task of these systems. The portal is open-source and fully customizable. It can be deployed at any site with minimum effort, contributing to the democratization of biodiversity genomics projects. We illustrate the features of the BioGenome Portal through a number of specific instances. One such instance is being used as the reference portal for the Catalan Initiative for the Earth Biogenome Project, a regional project aiming to sequencing the genomes of the species of the Catalan linguistic area.

Chromatin State Maps of Blood Pressure-Relevant Renal Segments Reveal Potential Regulatory Role for SNPs

BACKGROUND

Hypertension or elevated blood pressure (BP) is a worldwide clinical challenge and the leading primary risk factor for kidney dysfunctions, heart failure, and cerebrovascular disease. The kidney is a central regulator of BP by maintaining sodium-water balance. Multiple genome-wide association studies revealed that BP is a heritable quantitative trait, modulated by several genetic, epigenetic, and environmental factors. The SNPs identified in genome-wide association studies predominantly (>95%) reside within noncoding genomic regions, making it difficult to understand how they regulate BP. Given the central role of the kidney in regulating BP, we hypothesized that chromatin-accessible regions in renal tissue would be enriched for BP-associated single nucleotide polymorphisms.

METHODS

We manually dissected 2 important kidney segments that maintain the sodium-water balance: proximal tubules and medullary thick ascending limbs from the human and rat kidneys. To delineate their chromatin and transcriptomic profiles, we performed the assay for transposase-accessible chromatin and RNA sequencing, respectively.

RESULTS

The chromatin accessibility maps revealed the shared and unique cis-regulatory elements that modulate the chromatin accessibility in proximal tubule and medullary thick ascending limbs of humans and rats. We developed a visualization tool to compare the cross-species epigenomic maps to identify potential regulatory targets for hypertension pathogenesis. We also identified a significant enrichment of BP-associated single nucleotide polymorphisms (1064 for human proximal tubule and 1172 for human medullary thick ascending limbs) within accessible chromatin regions of both segments, including rs1173771 and rs1421811 at the NPR3 locus and rs1800470 at the TGFb1 locus.

CONCLUSIONS

Collectively, this study lays a foundation for interrogating how intergenic single nucleotide polymorphisms may regulate polygenic traits such as BP.

Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping

Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing [Oxford Nanopore Technologies (ONT)] bridge this resolution gap and offer enhanced performance for cytogenetic applications. Additionally, both methods can capture epigenetic information as they profile native, individual DNA molecules. We compared the effectiveness of the two methods in characterizing the structural, copy number and epigenetic landscape of a clear cell renal cell carcinoma tumor. Both methods provided comparable results for basic karyotyping and CNVs, but differed in their ability to detect SVs of different sizes and types. ONT outperformed OGM in detecting small SVs, while OGM excelled in detecting larger SVs, including translocations. Differences were also observed among various ONT SV callers. Additionally, both methods provided insights into the tumor's methylome and hydroxymethylome. While ONT was superior in methylation calling, hydroxymethylation reports can be further optimized. Our findings underscore the importance of carefully selecting the most appropriate platform based on specific research questions.

The genome sequence of a long-legged fly, Scellus notatus (Fabricius, 1781)

We present a genome assembly from a female Scellus notatus (long-legged fly; Arthropoda; Insecta; Diptera; Dolichopodidae). The genome sequence has a total length of 446.83 megabases. Most of the assembly (99.72%) is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.7 kilobases in length.

The genome sequence of a mirid bug, Stenodema calcarata (Fallen, 1807)

We present a genome assembly from a specimen of Stenodema calcarata (mirid bug; Arthropoda; Insecta; Hemiptera; Miridae). The genome sequence has a total length of 575.35 megabases. Most of the assembly (98.42%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.31 kilobases in length.

The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767)

We present a genome assembly from a male specimen of Plagodis dolabraria (Scorched Wing; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 939.07 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.97 kilobases in length.

A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758

We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.

The genome sequence of the Dotted Footman moth, Pelosia muscerda (Hufnagel, 1767)

We present a genome assembly from a male Pelosia muscerda (Dotted Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 500.49 megabases. Most of the assembly (99.98%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.42 kilobases in length.

The genome sequence of the Tropical Bluetail Damselfly, Ischnura senegalensis (Rambur, 1842)

We present a genome assembly from a specimen of Ischnura senegalensis (Tropical Bluetail; Arthropoda; Insecta; Odonata; Coenagrionidae). The assembly contains two haplotypes with total lengths of 1,599.82 megabases and 1,602.78 megabases. Most of haplotype 1 (96.41%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome, which haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 18.11 kilobases in length.

The genome sequence of the click beetle, Ampedus sanguinolentus sanguinolentus (Schrank, 1776)

We present a genome assembly from a female specimen of Ampedus sanguinolentus sanguinolentus (click beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The assembly contains two haplotypes with total lengths of 1,574.76 megabases and 1,572.87 megabases. Most of haplotype 1 (97.13%) is scaffolded into 10 chromosomal pseudomolecules, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 15.99 kilobases in length.

The genome sequence of the amphioxus, Branchiostoma lanceolatum (Pallas, 1774)

We present a genome assembly from a specimen of Branchiostoma lanceolatum (Amphioxus; Chordata; Leptocardii; Amphioxiformes; Branchiostomatidae). The assembly contains two haplotypes with total lengths of 468.40 megabases and 465.81 megabases, respectively. Most of haplotype 1 (99.34%) is scaffolded into 19 chromosomal pseudomolecules. Haplotype 2 is a scaffold level assembly. The mitochondrial genome has also been assembled and is 15.14 kilobases in length.

The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767)

We present a genome assembly from a female Epinotia brunnichana (Large Birch Bell, Large Birch Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 943.10 megabases. Most of the assembly (99.68%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,003 protein-coding genes.

The genome sequence of the Coppice Mining Bee, Andrena helvola (Linnaeus, 1758)

We present a genome assembly from a female Andrena helvola (Coppice Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence has a total length of 442.47 megabases. Most of the assembly (91.93%) is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.61 kilobases in length.