Gigabyte

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.

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.

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.

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.

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.

Abstract The gayal (Bos frontalis) is an endangered semi-domesticated bovine species renowned for its high-quality beef. However, its semi-feral lifestyle, ongoing habitat fragmentation, and extensive genetic introgression from sympatric local cattle have led to dramatic population decline and severe erosion of purebred genetic integrity, posing substantial challenges to its conservation and utilization. To address the urgent demand for rapid, non-invasive, and field-compatible germplasm identification, we developed an integrated artificial intelligence (AI) framework that predicts genomic admixture composition from external morphological images. We constructed a comprehensive dataset comprising 6,245 morphological images and matched genomic sequences from 52 gayals maintained at the Yunnan Provincial Gayal Conservation Farms. Following a preliminary evaluation of nine deep learning models, five were incorporated into a anatomical segment-based multi-modal pipeline, among which Inception_V3 delivered the optimal overall performance. To enhance simultaneous extraction of local fine-grained features and global structural information, we further designed an innovative HybridInceptionViT model by integrating the multi-scale Inception module with the Vision Transformer (ViT) framework. This hybrid model significantly outperformed the baseline Inception_V3, boosting the accuracy of phenotype-derived prediction against genomic admixture estimate from 69.69% to 87.87% (absolute error <15%). This study establishes a practical, low-cost "phenotype-to-genotype" tool for rapid on-site gayal germplasm screening, offering a scalable strategy for the conservation and breeding management of endangered livestock, and holds broad application prospects for agricultural and livestock production systems.

Background: Chromosome-level genome assemblies are increasingly enabling tests of chromosome evolution, conserved synteny, and sex chromosome conservation across diverse animal lineages, including spiders. Results: Here, we present a chromosome-level genome assembly for the African hermit spider, Nephilingis cruentata, a species with extreme female-biased sexual size dimorphism and a cytogenetically inferred XX2 sex chromosome system. The final Hi-C-assisted assembly spans 1.72 Gbp, with 99.5% of bases assigned to 13 pseudochromosomes, a scaffold N50 of 131.6 Mbp, and a BUSCO completeness score of 98.8%. We annotated 20,021 protein-coding genes, and repetitive elements accounted for 42.7% of the genome. Sex-specific whole-genome resequencing identified Chr02 and Chr07 as candidate X chromosomes based on reduced male coverage, consistent with the expected XX2 system. Using comparative whole-genome alignments across existing chromosome-scale spider assemblies, we also show that sex-linked chromosomes retain broad homologous identity across sampled spider lineages but exhibit lower synteny conservation and greater chromosome-length divergence than autosomes. Conclusions: These results suggest that spider sex chromosomes are conserved in homologous identity but more labile in structure, providing a comparative framework for studying sex chromosome conservation and divergence across Araneae.

Spatial transcriptomics keeps measurement of gene expression while preserving spatial context, yet traditional analysis methods face challenges in computational efficiency, biological interpretability, and autonomous discovery. This project presents a framework solving these issues through three parts: (1) an ensemble clustering system achieving 66.7% improvement over baseline average and 23.9% over best single method with silhouette score of 0.540 and statistical significance (p = 0.0032, Cohens d = 1.82); (2) a knowledge-based clustering framework that annotates 88.6% of cells across 8 ovarian cell types using 428 marker genes; and (3) a GPT-4o-mini-powered autonomous agent that generated 3 biological hypotheses with validations.

Mosquitoes in the Toxorhynchites genus (Theobald, 1901) are specialized predators of container-breeding mosquito larvae, including major Aedes disease vectors. Despite their biological control potential, species boundaries and phylogenetic relationships remain poorly understood. Utilizing country-wide sampling across Panama, we evaluated the taxonomic status and diversity of local Toxorhynchites species. We collected 147 specimens from artificial and natural containers, yielding 97 cytochrome c oxidase subunit I barcodes from 101 sequenced individuals. A Panama-only Neighbor-Joining analysis revealed four distinct, well-supported clusters (I - IV) exhibiting high mean inter-cluster genetic divergence (4.8 - 20.2%), alongside morphological and ecological segregation. A subsequent global Neighbor-Joining analysis incorporating BOLD and GenBank sequences recovered Toxorhynchites as a strongly supported monophyletic group (99.0% bootstrap support) and revealed deep phylogenetic divergence separating Old World Toxorhynchites (Toxorhynchites) (Clades A and B) from New World Toxorhynchites (Lynchiella) (Clades C - G) lineages. Panamanian Clusters I and II formed two distinct groupings within Clade G, nesting as sisters to Subclade G1 characterized by severe taxonomic discordance involving sequences labeled as Tx. moctezuma, Tx. theobaldi, and Tx. rutilus. Cluster III nested within Tx. hypoptes (1.5% divergence) in Clade E, whereas Cluster IV associated with Tx. haemorrhoidalis s.l. (>5.0% divergence) in Clade C. The high degree of taxonomic uncertainty or cryptic diversity uncovered within Clades C, D, and G underscores an urgent need for formal taxonomic revision to accurately delimit species boundaries. Due to its widespread peri-urban distribution, Cluster I (within the Tx. moctezuma s.l. complex) shows the greatest promise for mass-rearing and Aedes biocontrol applications in Panama.

Here we report a newly developed method utilizing long-range PCR and long-read Pacific Biosciences HiFi sequencing that successfully obtained two full-length and annotated mitochondrial genomes from Culex quinquefasciatus Say, 1823 and Culex tarsalis Coquillett, 1896, both from Maricopa County, Arizona, USA. Given the substantial burden of West Nile virus in Maricopa County over the past decade, and that these vectors are primarily responsible for spillover to human populations in the county, it is critical to better understand their distribution over time and space. This study begins to approach this need by contributing a novel approach that has resulted in the first West Nile virus vector mitochondrial genomes from Arizona. Our circular Cx. quinquefasciatus mitogenome is 15,587 bp in length, making it the first USA-based mitogenome sequenced through the AT-rich control region. The Cx. tarsalis mitochondrial genome is 16,416 bp long, longer than recently published California-based CTarK1 and Texas-based PQ585801 mitogenomes. The increased length of the Cx. tarsalis mitogenome is a result of a 905 bp insertion in the AT-rich control region, not present in the species publicly available mitogenomes. A maximum likelihood-based phylogenetic reconstruction supports the species designation of these newly-sequenced mitogenomes. The newly developed methodology offers a unique approach to study medically-important vector species around the globe, providing a solution to study populations through pooled vector pathogen surveillance programs.

Genetically informed conservation is critically important to ensure that interventions benefit the population of interest. In corals, preserving genetic diversity and accurate species identification are crucial for the sexual propagation. While various methods exist for species identification and measuring intraspecific variation, obtaining and analysing molecular data that enables rapid yet informed decisions on broodstock choice and progeny quality assurance remains challenging. Here we present a novel approach towards resource effective intraspecific genetic profiling by targeting extended genomic regions around ultra-conserved elements (UCEs). By sorting loci by parsimony informativeness and using a locus window size as small as 5000 bp upstream and downstream of the UCE, we identified a subset of 500 UCE-associated loci that can accurately resolve phylogenetic relationships among species and assess intraspecific variation with accuracy comparable to a whole-genome dataset, while. This method was validated using existing population genomic data from six species of staghorn coral (Acropora hyacinthus, Acropora tersa, Acropora pectinata, Acropora sp. "VI-3", Acropora kenti and Acropora cf. spathulata). The phylogeny produced by the UCE subset is congruent with the phylogeny based on complete data. With the moderate number and length of target genomic region sizes providing a balance between resolution and sequencing effort, this study provides a proof-of-concept approach towards developing fast, scalable, and cost-effective workflows using a real-time long-read sequencers such as Oxford Nanopore Technologies. The methodology has the broad potential to be applied to support genetic assessment across taxa where taxonomic uncertainty is common, improving confidence in experimental frameworks and conservation decisions.

Catenulids are free-living flatworms, common in eutrophic freshwaters such as ponds, ditches, or peatbogs, with most of the diversity described from tropical regions to date. Although the majority of the species have been described from warmer climates, most molecular studies have been done on specimens from temperate zones in Europe. We addressed this gap by sampling for exotic species in localities available in a temperate climate. In this study, we investigated catenulid diversity in the greenhouses at the University of Warsaw Botanic Garden and recorded two species known only from tropical areas (Stenostomum paraguayense and Suomina evelinae) and one exotic species recorded previously from a greenhouse in Poland (Stenostomum corderoi). Additionally, in the latter species, we provide evidence for environmentally induced coloration of sensory pits, which has not been reported thus far. We placed the collected species on a phylogeny using barcoding of 18S, 28S, and COI genes and retrieved paraphyly of the family Catenulidae, with S. evelinae forming a sister group to the genus Paracatenula, and hence we propose a revision of its systematic position. In total, we recorded six species, including three with a wide cosmopolitan distribution (C. turgida, S. grande and S. tuberculosum), and provided sequences for five of them, three of which had no previous molecular records (S. paraguayense, S. evelinae and S. corderoi). Thus, we confirm that greenhouses represent an important source of exotic species for taxonomic work on microscopic invertebrates.

Summary: Agentic AI platforms enable the engineering of autonomous workflows but are not designed for experimentation and hypothesis testing. ASAREE (Analytical Sandbox for Agentic AI Research, Engineering, and Experimentation), is an open-source platform to address this gap. ASAREE creates agents, connects to MCP servers and tools, and designs factorial experiments through a visual interface or Python SDK. It records a full provenance trace for every run and routes all model calls through a provider-agnostic bridge that supports local deployments, ensuring data privacy. As a use-case, we use ASAREE to evaluate key design choices in a mutli-agent machine learning pipeline. Across a 2 x 2 x 2 factorial design, more advanced models, greater reasoning effort, and critic agent use significantly increased compute time, token use, cost, and feature count without improving predictive performance. The lowest-cost baseline, Claude Sonnet 5 with medium effort and no critic, achieved the highest mean PR AUC while Claude Opus 5 with extra high effort and a critic agent cost 15.5x more (USD) and ran 13.1x longer while performing worse on average. These findings highlight ASAREE as a robust framework for evaluating agentic system performance and resource efficiency.

The global expansion of Black Soldier Fly (BSF), Hermetia illucens (L.), production systems for organic waste management has increased the need to better understand its reproductive biology in order to optimize mass-rearing programs. In this study, we macroscopically characterized chronological morphological changes in the internal genitalia of adult H. illucens reared on a sustainable alternative larval diet based on coffee pulp and corn bran. Morphological assessments and dissections were conducted on female and male reproductive tracts at 3, 6, and 9 days after adult emergence. Overall, the general organization of both reproductive systems was consistent with previous descriptions. A notable observation was the presence of a tripartite fertilization chamber in females, composed of three distinct compartments apparently associated with the three spermathecae. The functional significance of this anatomical organization remains to be determined. Females showed progressively advanced ovarian development and reached the clearest morphological indicators of reproductive maturity at 9 days, while males showed the greatest testicular distention and opacity at the same age. Compared with maturation times reported in previous studies using conventional larval diets, these observations suggest a later pattern of reproductive maturation under the coffee pulp-based diet. The observed differences may be associated with the nutritional composition and carbohydrate-to-protein balance of the larval diet. These results provide chronological and iconographic information that may contribute to the optimization of laboratory rearing protocols and the use of coffee by-products in H. illucens bioconversion systems.

The field of genomics has enabled extraordinary progress in horticultural crop research. However, there is still a need for cost-effective, high-resolution technologies flexible to the diversity found in emerging crops. To this end, we introduce CannSelect, a high-quality genotyping platform for Cannabis sativa. Designed for use in diversity analyses and trait mapping, probe targets were selected from four genotyped diversity panels and a curated gene list. This platform has been used to effectively map day-neutrality in a segregating population to the Autoflower1 locus with average capture efficiencies of 88.5%. With broad genome coverage, demonstrated target specificity, and reproducibility, CannSelect is expected to perform well across the diversity of C. sativa. We describe the methodology used to design CannSelect v1.0 and performance metrics for testing capture efficiency and target alignment in diverse genome assemblies. The CannSelect platform represents a robust and scalable, genome-wide genotyping tool for C. sativa researchers and breeders.

We present a genome assembly of Aiptasia strain F003, a broadly used laboratory strain of the sea anemone and coral model organism Exaiptasia diaphana (Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Aiptasiidae; Exaiptasia). The genome assembly spans 237.34 Mb across 12,480 contigs with a contig N50 of 76.47 kb (12,423 scaffolds with a scaffold N50 of 77.93 kb), including a single-contig mitochondrial genome with a length of 19.79 kb. The assembly is highly complete with a BUSCO completeness of 96.50% based on the metazoa dataset, including 94.80% single-copy, 1.70% duplicated, 1.70% fragmented, and 1.80% missing BUSCO genes. Genome annotation identified 29,589 protein-coding genes (including 2 pseudogenes) and a repeat content of 32.89%. The genome of the female Aiptasia strain F003 enhances the utility of a key cnidarian model organism by enabling comparisons among Aiptasia strains in studies of symbiosis, microbiomes, and thermal stress. It thereby strengthens the value of Aiptasia as a model for investigating the mechanisms underlying coral holobiont function, response, and resilience to environmental change.

Italian ryegrass (Lolium multiflorum) is a key temperate forage species underpinning livestock production in Europe. Genomic resources remain limited by its large (2.2 Gb), repetitive, and highly heterozygous genome. Here, we present a high-quality chromosome-scale genome assembly of the Swiss L. multiflorum ecotype Tremona, collected in 2008 in Ticino, Switzerland, and subsequently incorporated into recurrent breeding cycles in the Swiss breeding program. To address systematic assembly artefacts caused by unresolved haplotypes in our initial PacBio HiFi assembly, we developed ParaLies, a post-assembly tool that identifies and removes artefactual duplications based on sequence divergence while preserving true paralogous gene copies. ParaLies reduced the duplicated BUSCO rate from 16.91% to 6.72% without loss of bona fide genomic content. The resulting assembly has a contig N50 of 15.69 Mb and captures 94% of the expected 2.2-Gb genome size. We further analyzed whole-genome resequencing data from Tremona, additional Swiss ecotypes, and publicly available North American germplasm. Tremona was genetically homogeneous, with no evidence of pronounced recent bottlenecks or substantial within-population structure, and was genetically distinct from the other Swiss ecotypes analyzed. Together, the Tremona genome and ParaLies provide valuable resources for L. multiflorum genomics and breeding and demonstrate a scalable approach for reducing haplotype-induced redundancy in highly heterozygous genomes.

Khang Dan 18 (KD18) is an Oryza sativa L. subsp. indica rice cultivar widely cultivated in northern Vietnam and used as an experimental and breeding background in Vietnamese rice research. Although KD18 has previously been represented in low-depth population resequencing datasets, a contiguous and annotated cultivar-specific genome has not been available. Here, we report a chromosome-scale genome assembly of KD18 generated using Oxford Nanopore long-read and Illumina short-read sequencing. The 395.3-Mb assembly comprises 12 chromosome-scale pseudomolecules containing approximately 95% of the assembled sequence and 99.6% of the predicted protein-coding genes. The assembly showed 97.2% BUSCO completeness, an average Merqury quality value of 46 and a long terminal repeat assembly index of 13.21. A total of 56,546 protein-coding genes representing 71,237 transcripts were predicted, with 99% BUSCO and 98.68% OMArk completeness. These statistics are similar to those of other high-quality genome assemblies that were recently published for different Asian rice cultivars, therefore providing a cultivar-specific genomic resource for research involving KD18 and KD18-derived materials.

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

Genetic gains for yield and yield-contributing traits are low or stagnant in sorghum especially under low soil moisture environments which have contributed to a yield gap of 3.0 in Africa. Exploring the extent of variation for yield-determining traits in sorghum will effective variety design to boost production in drought-stressed environments. Therefore, the objective of this study was to determine genetic variability, heritability and genetic gains for agronomic and physiological traits in sorghum under varying drought stress conditions to guide cultivar and trait selection for breeding. The study was conducted as a three-way factorial treatment structure involving a genetically diverse panel of two hundred and twenty-five (225) sorghum genotypes which were grown under three drought conditions [i.e., non-stressed (NS), pre-anthesis drought stress (PrADS), and post-anthesis drought stress (PoADS)] and two environments (e.g., field and glasshouse environments) using a 15 x 15 alpha lattice design in two replicates. Data were collected on agronomic and physiological traits, namely: days to anthesis (DA), days to maturity (DM), plant height (PH), stay-green (SG), seed weight (TKW), biomass yield (BM), harvest Index (HI), grain yield (GY), leaf area (LA), leaf chlorophyll content (SPAD) and stomatal conductance (SC) and subjected to various statistical analyses. Combined analysis of variance showed highly significant (P < 0.001) genotype, drought condition and environment, and their interactions for most traits under assessment. Genotypic coefficient of variation (GCV) was lower than phenotypic coefficient of variation (PCV) for all traits. Heritability in the broad-sense (H2) was moderate for GY (40%) under PrADS condition, but high under NS (60%) and PoADS (65%) conditions. Similarly, high genetic advance was recorded for traits with high heritability. GY positively and significantly correlated with HI under NS (r = 0.88), PrADS (r = 0.62) and PoADS (r = 0.61). Other agronomic and physiological traits poorly correlated with GY. The following genotypes were selected based on high grain yield and suitable agronomic and physiological traits under NS conditions; DAN YARA (5.7 t/ha and SC = 335.5) and JARWA (GY = 5.6 t/ha, SC = 326.3); under PrADS CSRO1 (GY = 2.9 t/ha, SC = 275.2) and ICNSL2014-021-1 (GY = 2.7 t/ha, SC = 268.2) and under PoADS conditions DANYAR BANA (GY = 4.2 t/ha, SC = 237.2) and DAN YARA (3.9 t/ha. SC = 330.0). The selected genotypes with the desirable traits are useful genetic resources for breeding high-performing sorghum hybrids to boost sorghum productivity in drought-prone areas in Africa.