Gigabyte

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.

The Woolly bottlebrush (Greyia radlkoferi) is an indigenous South African plant known for its ornamental appeal and potential medicinal uses. It naturally grows on rocky hillsides and grasslands and highly resilient to drought, temperature fluctuations, and nutrient-poor soils. Its flavonoid-rich compounds with anti-tyrosinase activity support its traditional use to treat skin pigmentation disorders in humans. Despite its outstanding ecological and biochemical characteristics, no reference genome is available for Greyia radlkoferi. Therefore, this study aimed to generate the first draft genome of the Greyia Radlkofleri using PacBio Sequel IIe HiFi long read sequencing. A total of 56.07 Gb HiFi data was generated, providing a total genome coverage of 270X. The assembled genome size was 206Mb, with the longest scaffold being 13.9 Mb. The assembly statistics yielded a scaffold and contig N50 of 10.1 Mb, and an L50 of 9, and with an overall GC content of 34.9 %. The genome scope profile set at kmer = 17 indicated that the genome is triploid. The genome annotation predicted 17,804 protein-coding genes and 17,804 transcripts with an average gene length of 3,116.03 bp. This is the first draft genome of its kind for the Greyia genus and provides a foundation for future studies aimed at elucidating the genetic basis of its environmental resilience and the biosynthetic pathways underlying its medicinal properties.

Gene model for the ortholog of raptor in the May 2011 (Agencourt Dere_CAF1/DereCAF1) Genome Assembly (GenBank Accession: GCA_000005135.1) of Drosophila erecta. 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 Lst8 (Lst8) in the May 2011 (WUGSC dyak_caf1/DyakCAF1) Genome Assembly (GenBank Accession: GCA_000005975.1) of Drosophila yakuba. 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.

Banana (Musa spp.) is a vital staple food and cash crop cultivated in over 140 countries, providing nourishment and livelihoods to more than 400 million people worldwide. In this context, Bhimkol (Musa balbisiana, BB genome), a diploid banana variety native to Northeast India holds significant nutritional and commercial value. Its high iron and nutrient content have already been commercially validated through products like Bhimvita and Bhimshakti, which utilize fresh fruit pulp as nutrient-rich food for infants. However, Bhimkol fruits typically contain 100-150 seeds, an undesirable trait for product development. The manual removal of these seeds significantly increases production time and labour costs. Furthermore, because bananas are recalcitrant to traditional breeding, there is a constant need for rapid in vitro transformation protocols. To address these challenges, as a proof of concept, our research aims to knockout the INNER NO OUTER (INO) gene, which is responsible for ovule development. Using CRISPR/Cas12a technology, we established an efficient and reproducible in vitro regeneration and transformation system using Embryogenic Cell Suspensions (ECS). The resulting CRISPR-edited plantlets exhibited various mutations, including insertions and deletions (INDELs) within the targeted INO gene. These INDELs resulted in frameshift mutations that triggered premature stop codons. While these genetic changes are expected to render the banana seedless, phenotypic verification is currently underway to confirm the absence of seeds in mature fruit. Significance StatementDespite its superior nutritional profile, the commercial viability of the Bhimkol banana (Musa balbisiana) is restricted due to abundance of seeds (100-150 per fruit). This study employs CRISPR/Cas12a-mediated knockout the INNER NO OUTER (INO) gene in Bhimkol and expected to develop seedless fruits. The resulting plantlets exhibit targeted indels that trigger frameshift mutations, effectively disrupting ovule developmental INO gene.

Gene model for the ortholog of raptor in the D. grimshawi May 2011 (Agencourt dgri_caf1/DgriCAF1) Genome Assembly (GenBank Accession: GCA_000005155.1) of Drosophila grimshawi. 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 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.

1The measurement of visual fields in arachnology has a long-standing history. Given the wide variety of eye positions, orientation and structure, the topic is fundamental for studies of taxonomy, evolution, ecology and behavior. The existing methods for measuring visual fields deploy ophthalmoscopic measurements, which require custom microscopes, anatomical structures like the reflective tapetum, which may not always be present, or the capacity to detect photoreceptor autofluorescence. Here we present the ctSpyderFields python package: a tool for geometrically predicting the visual fields of arachnids from digital images of the lens and retina. The tool uses images coming from computed tomography (CT) scans of specimens, but could be applied to other 3D microscopy techniques, to virtually project the boundaries of the retina through the geometrically predicted nodal point of the lens, deriving a rough per-eye visual field both in cartesian and spherical coordinates. The extracted data can then be used to calculate likely visual field overlap between eyes and angular spans, which can be compared within or between species. We also provide a use case, reporting the visual field data extracted from a museum specimen of Philaeus crysops. We propose that the tool will allow a wider comparative analysis of visual fields across spider species, unlocking the potential for a deeper understanding of visual ecology and evolution.

Gene model for the ortholog of tango (tgo) in the Sep. 2015 (UC Berkeley ASM127793v1/DbusGB1) Genome Assembly (GenBank Accession: GCA_001277935.1) of Drosophila busckii. 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.

Holcosus orcesi, the Orces Blue Whiptail, is a Critically Endangered lizard endemic to the upper Jubones River basin in southern Ecuador. Restricted to a narrow elevational range within semi-arid Andean shrublands, it represents one of the few montane members of a predominantly lowland lineage. Here we present the first high-quality reference genome for H. orcesi, generated using Oxford Nanopore Technologies long-read sequencing. The assembly spans 1.68 Gb across only 91 contigs, with an N50 of 76.2 Mb and a BUSCO completeness of 96.8%, making it among the most contiguous and complete squamate genomes to date. Structural annotation predicted 25,682 genes, of which 85% showed homology to known proteins and 45% were assigned Gene Ontology terms. Repetitive elements accounted for 46.3% of the genome, with LINEs representing the predominant class. This genome provides a foundational resource for future evolutionary, comparative and conservation-genomic research of H. orcesi and other mountain reptiles, enabling studies of population genomics, local adaptation, and genomic erosion in isolated populations. By expanding the genomic representation of tropical montane reptiles, this work helps address longstanding phylogenetic and geographic gaps in global biodiversity genomics and provides a foundation for evidence-based conservation of H. orcesi and related taxa.

Carpobrotus chilensis (Chilean sea fig) is a coastal succulent of uncertain origin that has naturalized along the California coast, where it co-occurs and hybridizes with the invasive species, Carpobrotus edulis. Despite their ecological importance and widely supported hybridization, genomic resources for this genus remain scarce. Here, we present a draft genome assembly of C. chilensis generated from PacBio HiFi long reads. The assembled nuclear genome spans 981.7 Mb across 178 contigs. The contig N50 was 73.0 Mb, and BUSCO completeness was 96.3%. K-mer and SNP-based analyses indicate extremely low heterozygosity (3.4 x 10-), reduced genetic diversity in this population. The genome is highly repetitive, with 81.67% of the sequences composed of transposable elements, predominantly long terminal repeat (LTR) retrotransposons. Gene prediction identified 21,744 protein-coding genes, with BUSCO completeness of 95.8%. Comparative analysis with C. edulis identified 8,783 single-copy orthologous gene pairs, with a median synonymous substitution rate (dS) of 0.019, indicating low sequence divergence between the two species. This genome assembly provides a foundational resource for investigating the genomic basis of hybridization and invasion in Carpobrotus.

Gene model for the ortholog of Density regulated protein (DENR) in the Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of D. 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.

The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.

The slipper lobster (Thenus australiensis) is rapidly emerging as a high-potential species for commercial aquaculture. Because females exhibit superior growth characteristics due to less frequent moulting after sexual maturity, developing monosex breeding strategies is highly desirable for industry profitability. However, the lack of genomic resources and early sex-identification tools has hindered this development. Here, we report the first draft male genome assembly for T. australiensis, generated using a combination of whole-genome shotgun sequencing, DArT-seq, and multi-tissue transcriptomics. The curated assembly spans 0.913 Gbp with high functional completeness (93.0% BUSCO), providing a robust repertoire of 30,100 protein-coding genes. Through k-mer subtraction and population-level DArT-seq genotyping, we provide definitive evidence that T. australiensis utilizes an XX/XY sex-determination system. Crucially, by identifying male-specific structural variations within a neo-Y locus, we developed a diagnostic PCR assay targeting a male-exclusive sequence. This 171 bp marker achieved 100% accuracy in phenotypic sex identification across wild-caught populations. Ultimately, these foundational genomic resources, combined with a highly reliable molecular sexing tool, provide the critical framework necessary for early sex sorting, broodstock management, and the commercial advancement of monosex slipper lobster farming.

BackgroudWuzhishan (WZS) pigs are native to Hainan Province of China, and serve as both important agricultural resources and biomedical models. Although the published WZS pig genome (T2T-pig1.0) even achieving telomere-to telomere (T2T) completeness, substantial genetic diversity still exists within the same pig breed, another WZS pig genome named WZS-T2T was assembled in this study. ResultsMultiple sequencing data were used to assemble genome, and finally yielded a [~]2.68 Gb telomere-to-telomere genome, with N50 length [~]142.87 Mb, and annotated protein coding genes of 23,100. Compared to T2T-pig1.0, QV and BUSCO value was higher, and the Y chromosome (ChrY) length was longer in WZS-T2T than that of T2T-pig1.0. ChrY of two WZS pigs shared 11 genes, including sex differentiation-related genes of SHOX, PRKX, and DDX3X, and SRY; however, energy metabolism gene SLC25A4 and the macrophage-related receptor gene CSF2RA of ChrY were specific to WZS-T2T. An inversion SV on chromosome 10 with length [~]33.86 Mb was identified between two WZS pigs, and three proofs were proposed for proving the accuracy sequence orientation of WZS-T2T.The genetic diversity was consistent with LD decay speed in population different analysis. WZS pigs exhibited higher genetic diversity than other four pig populations (Tunchang pigs, Yuxi black pigs, Large White pig, and Duroc pigs) examined in this study, and presented slower LD decay compared to other four breeds. ConclusionsTherefore, WZS-T2T provided a higher-quality assembly, and potential advantages of both agricultural production and biomedical targets for WZS pigs.

For over four decades, the bivalve Anomalocardia flexuosa has been recorded in Hong Kong coastal waters. However, the known native distribution of this heavily exploited commercial species is restricted to the Atlantic coast of South America, raising questions about the biogeographical validity of the Hong Kong populations. By employing an integrative taxonomic approach combining morphological re-evaluations and molecular phylogenetic analysis of the COI gene, we confirm that the species in Shui Hau, Hong Kong, China, has been historically misidentified. The population belongs to Cryptonema producta (syn. Anomalocardia producta).

Here, we present a comprehensive multiomics analysis of anthocyanin biosynthesis in Rubus armeniacus, known for its dark fruits. A phased genome sequence of the tetraploid blackberry was generated, achieving an N50 of 34 Mb with an assembly size of 1.2 Gbp based on Oxford Nanopore Technology sequencing (ONT). The BUSCO score for the total assembly shows a high completeness of 99.1%. The assembly was separated into 4 pseudohaplophases, with the pseudohaplophase A representing the R. armeniacus genome in 7 chromosome scale contigs, with an N50 of 46 Mbp and 98.8% conserved BUSCO genes. A total of 118,183 protein coding genes were annotated within the genome assembly and all relevant genes encoding enzymes and transcriptional regulators of the anthocyanin biosynthesis pathway were identified within each pseudohaplophase. To further understand the underlying cause of dark pigmentation, the gene expression was analysed during different stages of berry development revealing a strong induction of anthocyanin biosynthesis genes including the anthocyanin activating subgroup 6 MYB transcriptions during the berry ripening process. Further, a quantification of cyanidin-3-O-glucoside in methanolic berry extract, utilizing a UHPLC-HRAM-MS analysis, revealed an approximately 500-fold increase of cyanidin-3-O-glucoside from green to black fruit, indicating that dark pigmentation in R. armeniacus results from high anthocyanin accumulation. Significance statementThis study provides a multiomics analysis of the dark pigmentation of Rubus armeniacus, including a high quality phased assembly and an in-depth analysis of the anthocyanin biosynthesis pathway. A transcriptional and metabolomic analysis revealed that dark berry pigmentation is caused by a high accumulation of cyanidin-3-O-glucoside during fruit ripening.

The diversity of the brown frog genus Rana may be underestimated as the high similarity of morphological characters. A new species belonging to the genus Rana is delineated based on eight specimens obtained from the Tianma National Nature Reserve, Jinzhai County, Luan City, Anhui Province, China. The phylogenetic analysis based on three mitochondrial genes (12S, ND2, and Cyt b) and one nuclear gene (BDNF) showed that the new species formed an independent clade closely related to R. culainensis and received strong support. In addition, morphological differentiation confirmed the phylogenetic results, and both supported the validity of a new species (Rana tianmaensis sp. nov.) in the R. japonica species group. The discovery of this new species enhances peoples understanding of the biodiversity of Rana and can provide important foundational data for scientific decision-making on protected area construction, ecological conservation, and species diversity. With the inclusion of newly described species in this study, the distribution of Rana genus in China now includes 31 recognized species.

The marbled teal (Marmaronetta angustirostris) is a widely distributed but declining waterfowl species, classified as Near Threatened globally and Critically Endangered in Spain. Despite ongoing conservation actions, including ex situ management and population reinforcement programmes, the genomic consequences of long-term captivity, inbreeding, and patterns of functional genetic variation remain unknown due to the absence of a species-specific reference genome. Here, we present the first chromosome-level genome assembly for this species. The genome was generated using PacBio HiFi long reads and Omni-C data, yielding a 1.15Gb assembly with a scaffold N50 of 76.95Mb. A total of 97.16% of the assembly was anchored into 36 chromosome-scale scaffolds, including the Z and W sex chromosomes. BUSCO analysis recovered 99.2% of conserved avian genes. Gene prediction was performed using both ab initio and homology-based strategies, resulting in 16,048 protein-coding genes. This resource provides a foundation for genomewide analyses of inbreeding, demographic history, and adaptive variation, and will support evidencebased in situ and ex situ conservation strategies for this threatened species.

Two threatened new species of Podostemaceae belonging to the genus Inversodicraea, I. joulei and I. lebbiei, both from the Republic of Sierra Leone, are described and illustrated. A first record in Sierra Leone of the genus Lestestuella is also reported. Inversodicraea is the most species-rich genus of Podostemaceae in Africa and now comprises 38 species. Inversodicraea joulei is easily recognised because it has a persistent spine distally on the median rib of each fruit valve, and scattered, membranous scale-leaves with broadly rounded apices, while Inversodicraea lebbiei is distinct in having narrowly triangular robust scale-leaves which are inrolled, spreading distally, and completely covering the stem, arranged in five ranks. Inversodicraea joulei is known from a single location with three sites while I. lebbiei is known from two locations each with one site. Using the latest IUCN Red List guidance, Inversodicraea joulei is assessed as Critically Endangered and I. lebbiei is assessed as Endangered, due to threats from dam construction projects, agricultural practices and mining activities, resulting in high levels of siltation on rocks in the fast-flowing rivers where these species grow.