Gigabyte

We present the genome dataset of a dipluran species, Occasjapyx japonicus, representing the first dipluran genome assembled using HiFi long-read sequencing technology. The assembled genome is approximately 439.3 Mbp in size, comparable to those of other dipluran species available in public databases. The N50 value of 15.5 Mbp exceeds that reported for other dipluran species. The assembled gene set contains 19,635 genes, a number not significantly different from those estimated in previous analyses of two other dipluran species. Functional gene annotation was conducted using predicted amino acid sequences derived from the gene set. BUSCO analysis indicated that the assembled genome contains the majority of conserved core genes. These findings suggest that the O. japonicus genome and associated data are of sufficient quality to serve as a reference genome. The dataset will be valuable for studies in comparative or evolutionary biology, particularly in understanding hexapod evolution and the emergence of insects.

Scalesia gordilloi is a critically endangered species endemic to San Cristobal Island in the Galapagos archipelago and represents one of the most unique and vulnerable lineages within the adaptive radiation of the genus Scalesia. Despite its evolutionary distinctiveness and conservation importance, no genomic resources have been available for this species. Here, we present the first high-quality reference genome of S. gordilloi, generated using Oxford Nanopore long-read sequencing. Across three PromethION R10.4.1 flow cells, we obtained 80.5 Gb of long reads (~25X coverage), which enabled a highly contiguous 3.61 Gb assembly composed of only 549 contigs and an N50 of 106.6 Mb. BUSCO completeness reached 98.6%, with assembly metrics comparable to other high-quality Asteraceae genomes. Repeat annotation revealed that 76.2% of the genome is composed of interspersed elements, dominated by LTR retrotransposons. Structural annotation resulted in 47,913 high-confidence protein-coding genes, consistent with expectations for large, repetitive Asteraceae genomes. This genome provides a critical foundation for conservation genomics, enabling assessments of genetic diversity, inbreeding, and adaptive potential in the species. It further establishes a framework for comparative genomics across the Scalesia radiation and supports future efforts to protect and restore one of the most threatened plant lineages of the Galapagos Islands.

The scientific and commercial interest in pomegranate (Punica granatum L.) cultivation has increased noticeably during the last two decades. Because of the high concentration of bioactive compounds and its promising nutraceutical properties, pomegranate has been defined as a functional food. In order to develop advanced genomic tools to improve pomegranate breeding program efficiency, we present the chromosome-scale and haplotype-resolved genome assembly of Wonderful, a pomegranate cultivar widely grown around the world. DNA isolated from diploid leaf tissues was sequenced using long read sequencing technology (PacBio and Nanopore), while DNA extracted from haploid pollen grains was sequenced using a short-reads platform (Illumina). Genomic data from 11 single haploid gamete cells were analyzed using the R package called Hapi to phase the genome. The final genome assembly size was of 372.51 Mbp anchored to eight pairs of homologous chromosomes. The present study provides an insight on the adoption of an innovative and efficient approach for the assembly of haplotype-resolved genomes, which enables a higher resolution of DNA variant detection and offers the opportunity to investigate crossover events in single gamete cells during meiosis.

Rana dybowskii is distributed across Northeast Asian and represents a valuable medical resource. A high-quality assembly of the genome has not yet been reproted. This species has 2n=24 chromosomes, but a huge genome size that estimated at 3.5 ~4.6 Gb in the previous studies. The relatively large chromosome size, exceeding hundreds of megabases, may result in difficulties of obtaining a complete chromosome level genome. Here, we constructed a chromosome-level genome assembly of R. dybowskii by integrating PacBio HiFi long-read sequencing for de novo assembly and CiFi (3C coupled with HiFi sequencing) for scaffolding. The final assembly consists of 12 chromosomes with a total of 3.95 Gb and a scaffold N50 length of 455 Mb. BUSCO assessment using the tetrapoda_odb12 database identified 94.2% complete and 0.5% fragmented orthologs, suggesting a high level of completeness of the assembly. Genomic annotation revealed that repetitive sequences comprise over 53% of the assembly, with retroelements and DNA transposons accounting for 22% and 25%, respectively. A total of 43,999 protein-coding genes were predicted with the assistance of RNA-seq reads from four tissues (muscle, eye, testis and skin). This high-quality chromosome-level reference genome provides a valuable genomic resource for advancing genetic studies of the species.

Three new species of sun orchid (Thelymitra) endemic to Aotearoa New Zealand are here described. These are T. palustris, T. scabrifolia and T. semaphora. The morphological distinctiveness of these three species has been acknowledged for decades; however, their taxonomic status has remained unresolved. Evidence from existing karyological data, recently generated DNA sequence data (LFY and ycf1) and morphological studies from historical and fresh collections are used here to support their formal description. Both, T. palustris and T. semaphora are restricted to wet habitats north of Auckland (North Island). Thelymitra scabrifolia inhabits mostly scrub, and it has a similar northern North Island distribution, but is has been found also in Manawat[a]whi / Three Kings Islands and historically in Otago (South Island). All three species are polyploids and are of conservation concern.

The Wangs garden lizard, Calotes wangi, is a widely distributed agamid species in Southern China and Northern Vietnam and exhibits pronounced colour variation and rapid body colour change. Despite increasing interest in the genomic basis of colour variation, chromosome-level genomic resources remain limited in agamid lizards. Here, we generated a chromosome-level reference genome of C. wangi using PacBio HiFi sequencing and Hi-C scaffolding. The final genome assembly was approximately 1.66 Gb in size and comprised 6 macrochromosomes and 11 microchromosomes, with a contig N50 of 110.09 Mb and 98.9% complete BUSCO genes. A total of 20,442 protein-coding genes were annotated. Comparative genomic analyses identified 297 significantly expanded gene families, with enriched functions associated with steroid metabolism, chromatin regulation, and epigenetic processes. This high-quality genome assembly provides an important genomic resource for future studies of colour variation, phenotypic plasticity, and evolutionary diversification in agamid lizards.

Gene model for the ortholog of Insulin-like peptide 3 (Ilp3) in the D. pseudoobscura Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly (GenBank Accession: GCA_000001765.2) of Drosophila pseudoobscura. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

We describe a chromosome-level, haplotype-resolved genome assembly from a male European moose (Alces alces alces). The assembly comprises two pseudo-haplotypes of 3,148 Mb and 3,112 Mb, with sex chromosomes in haplotype one, and 33 autosomes in each haplotype (68 in total). Assembly completeness is high (BUSCO 98.3% and 95.7%), with 21,496 and 20,498 annotated protein-coding genes for haplotypes one and two, respectively. This genome assembly is the most complete so far generated for European moose.

Avian malaria parasites form a highly prevalent and genetically diverse group within the haemosporidians, yet they have long been overlooked relative to their human- and rodent-infecting counterparts. Among these, parasites of the genus Haemoproteus (Haemosporida, Haemoproteidae) are widespread and prevalent blood parasites of birds, transmitted by louse flies (Hippoboscidae) and biting midges (Ceratopogonidae). Recent phylogenomic analyses place Haemoproteus parasites at the root of the haemosporidian tree, making genomic data from these taxa essential for understanding the evolutionary origins of malaria parasites. To date, only two avian Plasmodium and one avian Haemoproteus genomes have been sequenced. We present the first assembled genome of Haemoproteus majoris (lineage WW2), a common blood parasite of passerine birds. As avian erythrocytes are nucleated, parasite DNA was enriched by FACS-based sorting to discriminate and isolate the parasite from host cell nuclei prior to whole-genome amplification. The genome was assembled using Nanopore long-read sequencing and polished with Illumina short-reads, yielding 145 contigs with a total assembly size of 23.9Mb and a G+C content of 27.85%. Genome annotation identified 5501 protein-coding genes, 69 non-coding RNA genes, and 57 long terminal repeat retrotransposons (LRT-RTs), including one full-length element. This genomic resource represents a critical step towards elucidating the evolutionary history and genomic architecture of avian malaria parasites. SIGNIFICANCE STATEMENTWe present the first assembled genome of Haemoproteus majoris (lineage WW2), a prevalent and generalist avian malaria parasite. Taxonomic resolution of this genus is difficult as there are few distinct morphological differences among closely-related species. This genome provides a valuable resource for studying the evolution within the Haemoproteus genus and to elucidate the evolutionary history of malaria parasites.

Grapevine (Vitis vinifera) is one of the worlds most economically important fruit crops and a model species for perennial fruit tree genetics and genomics. The extensive genetic diversity found in cultivated and wild Vitis species provides a valuable resource for studies of domestication, adaptation, trait evolution, and breeding. This article presents a standardized whole-genome variant dataset comprising 547 grapevine accessions maintained in the INRAE Bordeaux grapevine germplasm collection, including 397 domesticated V. vinifera cultivars and 150 wild Vitis accessions. Whole-genome sequencing data were generated at a target sequencing depth of approximately 20x, and sequence variants were identified using a standardized Genome Analysis Toolkit (GATK) workflow against the reference genome PN40024v4 (40X). Variant discovery was carried out simultaneously across the complete sample set to ensure consistent genotype calling. All accessions were sequenced using the same technology and processed using the same reference genome, sequence alignment, variant-calling, and filtering workflow to produce a standardized variant dataset comprising ca. 9.1M SNPs and 0.77M INDELs. The resulting VCF files provide a harmonized genomic resource that can be readily reused for studies of grapevine genetics, germplasm characterization, population genomics, comparative genomics, genome-wide association studies, and the development and benchmarking of bioinformatic methods. SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@490449org.highwire.dtl.DTLVardef@1b884fborg.highwire.dtl.DTLVardef@12280bforg.highwire.dtl.DTLVardef@32bcceorg.highwire.dtl.DTLVardef@1099221_HPS_FORMAT_FIGEXP M_TBL C_TBL VALUE OF THE DATAO_LIThis dataset provides whole-genome raw sequencing for 118 wild Vitis accessions originating from North America and Asia and a sequencing-derived variant data for these accessions and 429 Vitis vinifera cultivars and wild accessions from the INRAE Bordeaux germplasm collection, previously published by Dong et al. 2023[1]. The dataset captures genetic variation across a total of 547 grapevine accessions, including domesticated and wild grapevine germplasm using a common variant-calling pipeline, facilitating direct comparisons among accessions. C_LIO_LIThe inclusion of wild Vitis species together with cultivated grapevine accessions provides a resource for studies of grapevine diversity, domestication, phylogenetic relationships, and comparative genomics. The dataset enables the investigation of genetic variation across multiple Vitis species using a standardized set of genomic variants. C_LIO_LIThe variant call format (VCF) file can be reused for population genetics, phylogenetic analyses, genetic diversity assessments, introgression analyses, and the identification of genomic regions of interest. The dataset is compatible with widely used bioinformatics software and can be integrated with other publicly available grapevine genomic resources. C_LIO_LIThis dataset constitutes a genomic resource for grapevine breeding and conservation research. Researchers can use these data to identify genetic diversity in wild relatives, compare allelic variation between cultivated and wild germplasm, investigate candidate loci associated with traits of interest, and support the management and characterization of grapevine germplasm collections. C_LI

The preparation of multi panel figures remains a labor intensive step in scientific publication. Albeit there are specific tools available to solve this problem, they are often highly specialized, difficult to install, or time consuming to learn. Griphus is a standalone graphical application designed for rapid composition and experimentation with multi panel figures, developed by and for zoological taxonomists. Functions specifically designed for multi panel composition include automatic figure numbering and placement, aspect ratio operations, spacers, layout rotation, layout suggestions, and automatic generation of figure legends, including scale bar descriptions. The software can perform both spatial interpretation of images on the canvas and work with a simple, editable layout formula. It also enables instant multi panel composition, with numbered images and automatic contrast selection for the numbers, obtained simply by loading images. User defined parameters such as target printable dimensions, resolution, spacing, and color mode are preserved throughout the work. The program produces coordinated outputs consisting of the final composite figure, a readable file describing the layout structure, and a .gri file storing images, transformations, and parameters for exact regeneration. Griphus is intended as a complementary tool to professional image software, providing a simple and efficient environment for constructing high quality multi panel figures.

Nematodes of the superfamily Thelastomatoidea are found in the digestive system of various arthropods, feeding on their host microbiome. They are sometimes considered to be ecologically intermediate forms between free-living rhabditids and parasitic Spirurina, while phylogenetically they are nested within the latter. In addition to new morphological data on the male morphology, this manuscript presents the first nuclear genome assembly of a thelastomatid species, Cranifera cranifera, using long-read sequencing approach, making a total of three nuclear genomes available for superfamilyThelastomatoidea. The C. cranifera nuclear genome assembly presented here is 246 Mb long, consists of 7563 contigs, has an N50 of 43 kb and includes 94% of the BUSCO nematoda_odb12 genes. The mitochondrial genome is 24646 bases long, includes a complete set of protein coding, rRNA and tRNA genes, and a repetitive region 9731 bases long, which includes multiple copies of tRNA-Asn(gtt) and tRNA-Lys(ttt). The nuclear assembly also contained two sequence variants of the 28S rRNA gene, highlighting the presence of intragenomic variation within rRNA operon. The newly generated assemblies (nuclear and organelle) will add to a growing body of genomic resources for underrepresented and understudied animal parasitic nematodes from the Clade 3, enabling comprehensive studies in their phylogeny and trait evolution in the future.

Animal venoms are a rich source of bioactive molecules, yet their diversity remains incompletely characterized in many species. Here we present the first long-read transcriptomic analysis of venom glands from Philippine tarantulas (Theraphosidae), a highly endemic but understudied group. Using Oxford Nanopore sequencing, we reconstructed near full-length venom gland transcriptomes across multiple species and identified extensive repertoires of toxin-encoding peptides. Venom glands were enriched in cysteine-rich inhibitor cystine knot (ICK) peptides, which dominated the toxin landscape and are known modulators of ion channels. Cross-species comparative analyses revealed a distinct transcriptional signature separating venom from non-venom tissues, driven by coordinated expression of toxin-associated and regulatory gene families. Phylogenomic reconstruction based on orthologous peptides recovered expected taxonomic relationships while revealing potential lineage-specific diversification and potential cryptic taxa. Despite a conserved core set of toxin families, substantial variation in toxin composition was observed among species, consistent with rapid evolution driven by gene duplication and functional divergence. Analysis of highly expressed ICK peptides showed a conserved cysteine framework alongside marked sequence variability in inter-cysteine regions, supporting a model in which structural stability is maintained while functional diversification proceeds. Together, these findings establish the first long-read transcriptomic resource for Philippine theraphosid spiders, reveal a conserved molecular signature underlying venom gland specialization, and provide new insights into the diversification of ICK toxin repertoires that may facilitate future evolutionary and functional studies, including the discovery and characterization of bioactive venom peptides.

The black bean aphid, Aphis fabae is a crop pest and vector of insect-transmitted pathogens, comprising closely related sub-species with overlapping host ranges. In other Aphis species, over-expression of specific detoxification genes has been linked to insecticide tolerance. We present two chromosome-scale assemblies for a clonal A. fabae line, representing two phased haplotypes, generated using HiFi and Hi-C sequencing technologies. A comprehensive genome annotation, built with PacBio Iso-Seq data, was used to investigate genes underlying insecticide tolerance. Both genomes are comprised of four chromosomal blocks (haplotype 1: 427 Mb; haplotype 2: 396 Mb) with high BUSCO completeness (98.7%). Comparative genomics revealed an expansion of UDP-glycosyltransferases, whose expression is linked to insecticide detoxification in other Aphis species. These high-quality references provide a foundation for studying A. fabae sub-species and a genomic resource for investigating insecticide tolerance across the Aphis genus. Author summaryHere we have provided a comprehensive assembly and annotation for further study into the Black bean aphid, Aphis fabae, using up to date long-range sequencing technologies. The final assemblies for both haplotypes are chromosome length and consist of 4 main chromosome blocks, consistent with the literature. The A. fabae genome was found to contain an increase in copy number of UDP-glycosyltransferases, which have previously been linked to insecticide resistance. The work here will be a resource to those studying insecticide tolerance in crop pests, as well as the differences between A. fabae sub-species.

Advances and accessibility to next-generation technology provide opportunities to sequence non-model organisms. Despite this increase in whole-genome sequencing data, annotation and the production of reference genomes remain limited. Reference genomes are a critical tool for a variety of studies in evolutionary biology, functional genomics, and conservation genetics. Tiger beetles (Cicindelidae) are a diverse and globally distributed family of beetles that serve as bioindicator taxa and flagship species for insect conservation. Here, we report highly complete, contiguous, and annotated genome assemblies representing draft reference genomes for three species of tiger beetle spanning the phylogeny. These draft reference genomes are for Audouins night-stalking tiger beetle, Omus audouini; the montane giant tiger beetle, Amblycheila baroni; and the western red-bellied tiger beetle, Cicindelidia sedecimpunctata. Article SummaryTiger beetles are a charismatic group with [~]3000 species distributed globally. Despite their popularity among insect enthusiasts and their role as bioindicators of ecosystem health, the group currently lacks a reference genome. This article outlines genome assembly and annotation for three tiger beetle species that span evolutionary relationships within the lineage. Quality control analyses show that the assemblies are reference quality and demonstrate high contiguity, completeness, and accuracy. The resulting draft genome annotations will be a valuable resource for scientific endeavors and allow for continued research on tiger beetles and their allies.

The European leaf-toed gecko (Euleptes europaea) is a small, nocturnal gecko endemic to the western Mediterranean. As a phylogenetically distinctive member of the Gondwanan family Sphaerodactylidae, it represents an important species for studying Mediterranean island biogeography, adaptation, and reptile genome evolution. The species also occupies a key position for investigating the evolution of sex chromosomes, as geckos exhibit remarkable diversity and frequent transitions in sex-determination systems. We present a chromosome-level genome assembly of Euleptes europaea generated as part of the Vertebrate Genomes Project. The 1.8 Gb assembly has a scaffold N50 of 102.3 Mb (contig N50 27 Mb), with 21 chromosome-scale scaffolds corresponding to the known karyotype (2n = 42). The primary assembly has a BUSCO completeness of 97.80% (95.60% as single-copy), a k-mer completeness of 96.00%, and a k-mer quality value (QV) of 61.20. Repetitive elements account for 53.20% of the genome and genome annotation identified 18,633 protein-coding genes. This high-quality reference genome will facilitate studies of genome evolution, island adaptation, and sex chromosome evolution across geckos and other reptiles.

Accurate species identification is fundamental for understanding insect pest diversity and developing effective management strategies. Wheat aphids are among the most destructive insect pests worldwide, yet comprehensive molecular confirmation of species diversity in Bangladesh has been lacking. This study employed an integrative taxonomic approach combining DNA barcoding and morphological characterization to identify wheat aphid species collected from major wheat-growing regions of Bangladesh. Aphid specimens were sampled from 11 locations across four districts during the 2024-2025 wheat growing season. A partial fragment of the mitochondrial cytochrome C oxidase subunit I (COI) gene was amplified and sequenced, followed by BLAST analysis, phylogenetic reconstruction using the Maximum Likelihood method, genetic distance estimation, and detailed morphometric analyses. COI sequence analysis identified five wheat aphid species: Sitobion avenae, Rhopalosiphum padi, R. maidis, R. rufiabdominalis, and Hysteroneura setariae. Sitobion avenae was the predominant species, occurring across all surveyed regions. BLAST similarity ranged from 99.68% to 100%, confirming reliable species-level identification. Phylogenetic analysis grouped all specimens into five well-supported species-specific clades with strong bootstrap support (97-100%), corroborating molecular identification. Pairwise genetic distance analysis revealed very low intraspecific divergence (0.0-0.18%) and clear interspecific divergence (4.9-11.9%), indicating strong genetic discrimination among species. Morphological and morphometric analyses further distinguished the five species, with significant interspecific differences (P < 0.0001) observed for body length, antennal length, tubercle width, cauda length, and cornicle length. The concordance between molecular and morphological evidence demonstrates the robustness of the integrative taxonomic framework. This study provides the first comprehensive molecular and morphological characterization of wheat aphid species in Bangladesh, establishing a reliable baseline for biodiversity assessment, pest surveillance, insecticide resistance monitoring, and the development of evidence-based integrated pest management strategies to support sustainable wheat production amid changing agroecological conditions.

Wildlife biobanking depends on consistent, reproducible cell culture outcomes, yet no standardised framework exists for assessing culture quality across taxa or for integrating quality metrics into institutional collections management systems. Here, we present the Cell Viability and Utility Index (CVUI), a scored pipeline framework validated in a pilot study of 154 culture rounds from 46 species held in the Ian Potter Australian Wildlife Biobank at Museums Victoria Research Institute. The CVUI was adapted from the Wildlife Sperm Index (Jacobs et al., 2026) and assigns weighted scores encompassing four sequential culture stages -- establishment, first passage, expansion, and cryobanking -- with a continuous viability modifier applied at the cryobanking stage. Survival analysis identified individual animal identity as the primary source of variance in culture establishment, whereas taxon was the primary predictor of first-passage success. Beyond first passage, failure rates were too low to reliably assess either effect, with critical attrition concentrated at the earliest pipeline stages. These findings informed the differential weighting of CVUI components and have direct implications for workflow prioritisation and banking strategy. Monitoring can now be targeted at establishment and first passage, the stages where intervention has the greatest impact, with taxon-specific attention warranted at first passage and individual-level attention at establishment, while the robustness of the late-stage protocol means that banking yield is largely determined before a culture reaches P1. Integration of CVUI scores into collections management platforms such as Axiell EMu (Electronic Museum) would transform passive record-keeping into active decision support, enabling real-time quality tracking, early flagging of at-risk cultures, and longitudinal benchmarking of biobank performance across species, collectors, and tissue types. This framework provides a foundation for optimising wildlife fibroblast biobanking protocols, developing taxon-specific culture standards, and expanding standardised quality assessment across wildlife biobanks nationally and internationally.

Gene model for the ortholog of Density regulated protein (DENR) in the Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly (GenBank Accession: GCA_000001765.2) of Drosophila pseudoobscura. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Gene model for the ortholog of raptor in the D. eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of Drosophila eugracilis. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.