Gigabyte

The lion (Panthera leo melanochaita) is one of the most iconic species and part of the big five, maintaining ecological balance and a major wildlife-based tourism attraction in South Africa. Despite its importance, it is currently threatened by rapid population decline and increasing population fragmentation. Therefore, there is a need for a high-quality genomic resource that captures the diverse genetic landscape of South African lion populations. To address this, we present a high-quality genome assembly of the lion, generated using PacBio HiFi and Omni-C sequencing technologies. The final assembly comprises 2.45 Gb, with a scaffold N50 of 148 Mb and a contig N50 of 22 Mb. Remarkably, 94.8% of the genome is anchored to 19 scaffolds, reflecting the high degree of contiguity and near-complete chromosomal level. Completeness assessment of the genome showed 98.2% BUSCO, 98.2% k-mer completeness and QV of 65.6 underscoring high accuracy and biological integrity. Genome annotation predicted 831.4 Mb (33.9%) of repetitive sequences and 21 739 protein-coding genes. This work provides high-quality genomic resource to establish a foundation for future population genomic and conservation-focused investigations of the lion populations in South Africa.

The scaly-sided merganser, Mergus squamatus, is an Endangered piscivorous duck which has been declining since the late 1900s due to habitat loss, over-hunting, and climate change. Despite being a species of global conservation concern and subject to ex- and in-situ conservation efforts, genomic research has been limited, hindering our understanding of its population genetic status and evolutionary history. In this study, we present the first fully annotated, chromosome-level genome for the scaly-sided merganser, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C sequencing. The final assembly spans 1.1 Gb across 307 scaffolds, 64 of which are anchored into 35 chromosomes, covering 99.5% of the genome. The assembly shows high contiguity (N50 = 84.3Mb) and completeness, with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 98%. Repeat sequences comprise 9.55% of the genome. Homology-based gene annotation identified [~]15,200 protein-coding genes. A complete 16,624 bp mitochondrial genome was also assembled and annotated. Synteny analysis revealed strong chromosomal conservation across the wider Anatidae family, with evidence of lineage-specific rearrangements. Pairwise Sequential Markovian Coalescence modelling indicates recent stability in the effective population size of the species, with past declines coinciding with Pleistocene glacial cycles. Our high-quality genome provides an essential resource for conservation genomic and evolutionary studies of the scaly-sided merganser, supporting ongoing efforts to manage and protect this threatened species.

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

Continuous developments in sequencing technologies have led to the generation of chromosome-scale genome assemblies across the whole tree of life, but our ability to annotate genomes has lacked behind. One major problem consists in the fact that typically not all genes are expressed at detectable levels at any given life stage or environment. Therefore, available transcriptome data needs to be complemented by gene prediction programs and protein homology evidence. However, how to optimally combine these different data types is not well understood. Here, we present a case study, where we community curated gene annotations of the Pristionchus pacificus strain RSC011. By incorporation of new Iso-seq and RNA-seq data and genome-wide screening, we identified and corrected more than 7,500 ([~]24%) gene models. While the improved gene annotation for the RSC011 strain will be useful for the P. pacificus community, our study reveals several gene annotation problems that may affect data from other species. Among these, we identified assembly errors, artificial transcript fusions resulting from overlapping genes and polycistronic RNAs, falsely called open reading frames, and error propagation based on homology data as frequent sources of gene annotation errors. Thus, our findings may be helpful in guiding future efforts to annotate genomes across different taxonomic groups.

BackgroundAlthough the biological mechanism for heterosis has been debated for a long time, heterosis is widely utilized to increase the global productivity of crops and livestock. Recently, the mechanism has been well characterized in crops and livestock with a male-heterogametic XY system due to genomic assembly advancements, especially the availability of haploid genomes. However, the biological mechanism for heterosis remains unclear in poultry possessing the female-heterogametic ZW system. ResultsHere, we assembled chromosome-level diploid and haploid genomes of the Muscovy duck. We developed an efficient and cost-effective method to assemble 12 variation graph-haploid Muscovy duck genomes from three full-sibling pairs with high quality using short-read Illumina sequences. We further characterized genetic, expression and regulatory patterns of parental alleles at multiple scales. We found that maternal haploid genomes generally had more open chromatin organization and higher accessibility, and higher levels of gene expression, while showing similar DNA methylation levels when compared to paternal haploid genomes. In contrast, the female paternal Z chromosome showed the most, and the male paternal Z chromosome presented more, relaxed chromatin organization and chromatin accessibility, and gene expression compared to the male maternal Z chromosome. Thus, the ZW system largely relies on compensation and balance to regulate gene expression on the sex Z chromosome. Moreover, we identified non-Mendelian regions covering 0.26% of the genome ([~]3.18 Mb). These regions contained lower gene density, GC content, and repeat sequence frequency, but were enriched for DNA motifs bound by transcription factors, likely leading to a compacted chromatin structure and lower chromatin accessibility. ConclusionsOur work here provides a comprehensive profile of parental alleles genetic, expression and regulatory patterns in the female-heterogametic ZW system, and might be useful for the utilization of heterosis in poultry.

Giant kelp, Macrocystis pyrifera, occurs across northern and southern Hemisphere temperate coasts and is at high risk from ocean warming. Few giant kelp forests remain across the Southeast Australian shelf, while a handful of forests are actively being restored. Genomic resources can greatly aid in the conservation of remnant populations and enhance restoration efforts. Reference genomes are a fundamental resource as they are a prerequisite to, or enhance, many analyses used in conservation genomics. A single reference genome is available for giant kelp, assembled from a Californian haploid specimen. However, increasing evidence of genetic divergence between Northern and Southern Hemisphere populations highlights the need for regionally representative reference genomes. Here, we present two genome assemblies from the diploid vegetative tissue of Australian giant kelp specimens. We performed de novo genome assembly using long-read sequencing (PacBio HiFi and ONT R10.4 Simplex) and scaffolded the assemblies with the ONT reads, assembling 98-99% of the genomes into 35 pseudo-chromosomes. Genome sizes ranged from 528-534 Mbp, with BUSCO completeness scores of 97-98% and QV scores of 51-52. Genome annotation identified 17,565-17,800 genes in the Australian genomes. Genomic divergence between the Australian and Californian giant kelp genomes was seven-fold greater than between Australian genomes (1.5% vs 0.2%), supporting a Northern-Southern Hemisphere genetic divergence. Functional divergence was also observed between Australian and Californian genomes, reflected by differing patterns of enrichment in gene ontologies linked to energy metabolism, proteostasis and stress responses. These two new genome assemblies will serve as valuable resources for ongoing research into Southern Hemisphere giant kelp genetics, while providing the basis for genomic-guided conservation and restoration of remnant giant kelp forests in Australia.

Bactrocera zonata (Saunders) (Diptera: Tephritidae) poses a significant threat to global fruit production due to its high reproductive capacity and broad host range. This study aimed to evaluate the effects of gamma irradiation on key biological parameters of B. zonata. Six-day-old pupae were exposed to irradiation doses of 0, 30, 40, 50, 60, and 70 Gy, and subsequent developmental and reproductive traits were assessed to determine the impact of irradiation. Post-irradiation results revealed a dose-dependent trend. Higher doses ([≥]50 Gy) significantly reduced adult emergence, increased the incidence of partially emerged or deformed adults, and shortened adult longevity. Reproductive potential was significantly impaired in males irradiated at 60 and 70 Gy when mated with un-irradiated females, resulting in a marked decline in both fecundity and egg hatchability. Females irradiated at doses [≥]50 Gy failed to produce eggs when paired with either irradiated or non-irradiated males, indicating a high level of radio-sensitivity in female flies. Additionally, several traits in the F1 generation such as pupal recovery, pupal size, and adult development exhibited significant abnormalities and suggesting that the effects of irradiation may be transmitted to the next generation. Sterility was highest in males irradiated at 60 and 70 Gy, while females exhibited complete sterility at doses exceeding 40 Gy. The findings indicate that a dose of 70 Gy may be optimal for effective sterility induction in B. zonata. However, further detailed studies are required to standardize this dose, incorporating rigorous quality control measures to optimize its application in sterile insect technique (SIT) programs.

Dung beetles (Coleoptera: Scarabaeinae) are ecologically important insects, yet genomic resources for this diverse lineage remain limited. Here, we present a high-quality genome assembly for Onthophagus orpheus, an understudied species that is abundant in urban forests in the eastern United States. The assembled genome is highly contiguous and exhibits strong completeness, as assessed by Benchmarking Universal Single-Copy Ortholog (BUSCO) analyses, indicating robust representation of conserved protein-coding genes. Structural and functional annotation recovered a comprehensive gene set consistent with expectations for coleopteran genomes. This genome assembly provides an important resource for future work on the behavioral ecology and population genetics of Onthophagus orpheus, specifically, and Scarabaeinae more broadly.

Marine biodiversity documentation from the Mumbai Metropolitan Region (MMR) remains neglected despite the region having diversity of marine coastal habitats. The regions intertidal is one such habitat where species documentation remained heavily deficient due to lack of assessments and general apathy towards the habitat. This study addresses the issue of data deficiency of one of the largest taxa, Gastropoda through a decade long citizen science project, Marine Life of Mumbai. There exist large gaps in taxonomic research that have led to inconsistencies in species identification and inadequate ecosystem representation. This study addresses these issues by focusing on one of the largest taxa, the Molluscan class Gastropoda within the MMR. We present the spatial distribution of gastropod assemblages from 28 rocky, sandy and muddy intertidal sites within the Mumbai Metropolitan Region, on west coast of India. A total of 163 species were recorded from 2164 observations of marine gastropods. Among these, 29 species, 34 genera and one family Limapontiidae are new records for the region. Additionally, this study reports rediscoveries of 7 species from their type locality, with 5 species of Heterobranchs recorded after 78 years: one species from Neogastropoda, Lataxiena bombayana, after 131 years and one from Siphonariida, Siphonaria bassiensis after 31 years, from their type locality. These species are herein illustrated with detailed morphological descriptions and their local distribution on 28 sites in the Mumbai Metropolitan Region. Through this study we elucidate that the citizen science efforts and the subsequent taxonomic analysis provide an effective and low-cost method for filling data gaps from large, understudied geographical areas.

Pacific herring (Clupea pallasii) serve as a critical trophic link between plankton and many marine species targeted by fisheries. With a broad distribution throughout the North Pacific Ocean, from the Arctic to temperate latitudes, herring hold ecological, economic, and cultural importance. Despite this importance, genomic resources for this species, such as reference genome sequences, have only recently become available. To date, only one scaffold-level reference genome, representing a specimen from the Gulf of Alaska (Vancouver; 1,379 scaffolds), has been published to NCBI. Addressing this data gap, we produced a high quality 795Mb genome sequence organized into 26 chromosomes combining long read sequencing with short read sequencing of proximity ligation libraries. Our assembly is highly complete (BUSCO score of 97.7%) and contiguous (922 contigs, N50 = 7,338,470, L50 = 38; 26 scaffolds, N50 = 31,494,017; L50 = 12). Pacific herring south of the Aleutian Islands and the Alaska Peninsula are genetically differentiated from those in the Bering Sea, making a reference genome from the eastern Bering Sea an important addition to the Pacific herrings genomic toolbox.

As global reptile populations continue to decline, improving reproductive success in managed populations of listed species, such as Phrynosoma cornutum (the Texas horned lizard) has become increasingly critical for species survival. One understudied area of reproductive research in reptile species is gamete collection and storage, a crucial component for maintaining genetic diversity. In Texas, semen was collected from wild P. cornutum (n = 20) in June 2025. Semen collection was performed via electroejaculation (EEJ) under alfaxalone anesthesia. Prior to semen collection, snout-vent-lengths (SVL) and weights were recorded and testes measurements were taken using a portable ultrasound. Average sperm motility and concentration across all lizards was 83.7% and 85.7 x 106 sperm/mL, respectively. While lizards with longer SVLs had higher sperm motility, weight and testis size did not affect sperm parameters. Samples were extended in INRA96 and divided for use in cold-storage longevity or cryopreservation trials. Samples under cold-storage conditions were assessed for motility daily for 10 days. Motility was not significantly reduced until 48 hours post-collection and maintained 19% motility at day 10. For cryopreservation, samples were diluted 1:1 in INRAFreeze cryopreservation media and frozen in liquid nitrogen, then immediately thawed. Average post-thaw sperm motility was 13.9%, with the highest post-thaw motility recorded at 38.2%. This is the first report of semen storage and cryopreservation in Phrynosoma and provides valuable insight into semen storage potential in reptile species.

Characterizing genomic properties such as genome size, ploidy level, heterozygosity, and repetitive DNA proportion and composition without relying on genome assembly is crucial for profiling the genomes of non-model species. Little is known about the nuclear genome of the large neotropical orchid genus Epidendrum. This study compares genome profiles of Epidendrum anisatum and Epidendrum marmoratum, using flow cytometry and k-mer analysis approaches, as well as bioinformatics ploidy level estimation and repeatome characterization. Multiple depths of coverage, k values, and k-mer-based tools for genome size estimation were explored and contrasted with cytometry genome size estimations. Cytometry and k-mer analyses yielded a consistently higher genome size for E. anisatum (mean 1C genome size = 2.59 Gb) than E. marmoratum (mean 1C genome size = 1.13 Gb), which represents a 2.3-fold genome size difference. Both species were identified as diploid with no evidence of strict partial endoreplication. The most important aspects to be taken into account to improve genome size estimation were heterozygosity, depth of coverage, and the maximum k-mer coverage. The genomes of both species were found to be highly repetitive (63-73%) and heavily dominated by Ty3-gypsy retrotransposons, particularly those of the Ogre family. Additionally, the genome of E. anisatum was characterized by the presence of a 172 bp satellite (AniS1), which represented 11% of the genome size. Together, both Ty3-gypsy transposons and AniS1 shape the genome size difference between the two genomes. This study provides the first genome profiling for species in the genus Epidendrum, but also highlights the importance of using flow cytometry, cytogenetic approaches and bioinformatics techniques in combination for genome profiling.

The potential usage of genomic open data can help us to understand patterns in biodiversity. They can also be helpful for identifying morphologically similar species. An example of taxon in which this can be useful is Nematomorpha, one of the less studied animal phyla, for which data has started to be available recently and where species identification can be hard. In this study, I planned initially to evaluate the usage of mitochondrial data for population analyses using an RNA sequencing (RNA-seq) dataset labelled as belonging to Chordodes fukuii. After surprising results using extracted sequences from the barcoding gene cytochrome c oxidase subunit I (COXI), I evaluated species delimitation using a mix of a previously released double-digest restriction-site-associated DNA sequencing (ddRADseq) SRA dataset plus the RNA-seq one. PCA, R analyses through "adegenet" and ADMIXTURE confirmed the presence of two species in the RNA-seq dataset, which should be labelled as C. formosanus and C. japonensis; however, some individuals labelled as C. japonensis according to COXI clustered with C. formosanuss specimens or had some C. formosanus ancestry when more data was used, indicating potential introgression or incomplete lineage sorting. The study shows how previously released data can be used for evaluating species delimitation, potential previous demographic events and potential needs in DNA barcoding and genomics for avoiding future misidentification of morphologically similar species.

BackgroundNicotiana benthamiana has been found to exhibit grafting capability with phylogenetically distant plant species by accomplishing cell-cell adhesion as the first step in graft establishment. Morphological and physiological studies combined with time-course transcriptome analysis revealed that this grafting triggered various biological processes. Thus, further elucidation of accumulated datasets is required to describe the processes during grafting. ResultsIn this study, we performed a Bayesian network analysis to identify crucial gene modules in the transcriptome of Nicotiana benthamiana interfamily grafting. Our bioinformatics analyses of the transcriptome included threshold-based clustering, functional annotation, Bayesian network analysis, module analysis, and hub gene identification. We defined six distinct temporal gene expression patterns in the transcriptome data. Gene ontology enrichment was performed for each expression pattern, and results were summarized as Gene ontology supercluster treemaps. Bayesian gene networks were constructed using the SiGN-BN HC + BS program along with 120 N. benthamiana transcriptome data covering the whole life cycle. Gene modules were identified using two module detection algorithms: Molecular Complex Detection (MCODE) and GLay. Gene modules were characterized by identifying Gene Ontologies and hub genes as the most interconnected nodes in the gene network using the Cytohubba plugin. ConclusionThis study provides further knowledge and enhances our understanding of the molecular mechanisms underlying interfamily grafting.

BackgroundMicrosporidia sp. MB is an intracellular parasite of anopheline mosquitoes identified across the African continent. Microsporidia sp. MB infections appear to have no significant effect on host fitness and vertically transmit, whilst infected individuals have exhibited significantly reduced levels of Plasmodium falciparum transmission. These combined characteristics make Microsporidia sp. MB a promising candidate for use in malaria control. A comprehensive genome would greatly facilitate investigation into the evolution and biological pathways underlying important phenotypes, such as the mechanism of malarial inhibition. ResultsIn this study, we present the de novo assembly of the first complete genome of Microsporidia sp. MB SOUVK7. Multi-platform sequencing was performed on ovary samples of laboratory established Anopheles coluzzii collected from Burkina Faso. The SOUVK7 genome has a total size of 9.16Mb, encodes 2,435 genes and is organised into 13 chromosomes with telomeres identified at all flanks. Telomeric repeats exhibit a 4-mer motif due to a glutamine deletion previously unobserved in Microsporidia. Ploidy analysis of Illumina reads predicts MB as tetraploid, whilst analysis of CpG methylation and retroelements highlights loci in all chromosomes with characteristics consistent with regional centromeres. Orthology analysis identifies several key genes in pathways associated to telomeric and centromeric maintenance, along with methylation and host invasion machinery. A loss of several components of the infection machinery is observed in Microsporidia sp. MB and the wider Enterocytozoonida, consistent with a general trend towards genome size reduction in the clade. ConclusionThis study provides the first complete, telomere to telomere assembly of Microsporidia sp. MB, offering new insight into the genomic architecture of Microsporidia sp. MB and the broader Mrazekiidae family.

We present new distributional records of Argiope spiders in India, based on more than 10,000 digital images of the genus from the region curated by iNaturalist (www.inaturalist.org). Notable range expansions to India are documented for three species: A. chloreides Chrysanthus, 1961, A. mangal Koh, 1991, and A. sector (Forssk[a]l, 1776). Second, previously unrecorded field characters, updated distributional data, and a re-examination of published descriptions of type material, support the resurrection of A. undulata Thorell, 1887 as a valid species, long treated as a synonym of A. pulchella Thorell, 1881. Finally, we report the first in situ photographic records of live specimens of the rarely documented A. caesarea Thorell, 1897 and A. macrochoera Thorell, 1891. These varied findings for a small and conspicuous taxon highlight the value of online community-science platforms for documenting the arachnofauna of a biodiverse region, as well as illustrate the need for continued taxonomic review, even within well-known genera.

Cnidarians are important models for the studying the evolution of animal development, regeneration, cell type differentiation, and allorecognition. The marine hydrozoan Podocoryna americana is related to the well-established model species Hydractinia symbiolongicarpus. Although both species possess a sessile polyp stage, P. americana differs in that it also has a free-swimming medusa (jellyfish) stage in its life cycle. We used a combination of PacBio CLR long-read and Illumina Hi-C short-read genome sequencing to produce a chromosome-level genome assembly for P. americana. The final assembly is 327 Mbp in total length with 17 chromosome-scale scaffolds representing 98% of the assembly. Comprehensive functional annotation with BRAKER3 generated a total of 19,085 predicted protein-coding genes in this assembly, covering 91.2% of the metazoan BUCSO gene set. Comparison of the P. americana genome to other chromosome-level cnidarian genome assemblies revealed a high degree of macrosynteny conservation, and ortholog identification and gene family evolution analysis identified 522 expanded and 1,026 contracted gene families in P. americana. This high-quality, chromosome-level genome assembly of P. americana will be an invaluable resource for researchers studying the evolution of development, regeneration, and allorecognition in cnidarians and other metazoans.

This protocol generates gregarious and solitarious density-dependent phenotypes in multiple Schistocerca species under controlled environmental conditions. It describes cage setup, feeding, animal handling, and sterile dissection workflows to isolate nervous, chemosensory, gut, fat body, and female reproductive tissues from nymphs and adults. It emphasizes rapid tissue stabilization and RNase-control practices for downstream single-tissue DNA and RNA analyses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/705994v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@119ec2forg.highwire.dtl.DTLVardef@e115b7org.highwire.dtl.DTLVardef@158ad1dorg.highwire.dtl.DTLVardef@cd54d7_HPS_FORMAT_FIGEXP M_FIG C_FIG

The Neprilysin-like 15 (Nepl15) transcript in Drosophila melanogaster displays sex and organ specific phenotypes and only has one known transcript in the fly database (FlyBase.org). Given that the Nepl15 gene is differentially expressed in a tissue-specific and sex-specific manner, we sought to identify if there were additional Nepl15 transcripts available in Oregon-R strain flies which had not been reported in the fly database by performing sequencing-based approaches. We have identified presence of different codons in the transcript different than what had been reported in FlyBase. Further experimentation is needed to determine the full effect of these changes on fly physiology.

Gene Model for Insulin-like peptide 4 (Ilp4) in the D. simulans DsimGB2 assembly (GCA_000754195.3). The characterization of this ortholog was carried out as part of a larger, ongoing dataset designed to explore the evolution of the insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila, utilizing the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences.