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.

Widow spiders of the genus Latrodectus are important animals for biomedical, pest and conservation research. Here, we present the assembled genomes of two closely related Latrodectus species: the Australian L. hasselti and the New Zealand endemic L. katipo. The genome of L. katipo consists of 13 scaffolds likely corresponding to chromosomes (90% of the total length) and 1267 short scaffolds (10%). It has a total length of 1.5 Gbp and BUSCO of 94.9%. The genome of L. hasselti consists of 379 scaffolds and has a total length of 1.7 Gbp and a BUSCO score of 95.4%. The repeat content is very similar in both genomes with a total proportion of 37.2% for L. katipo and 39.9% for L. hasselti. Genome annotation predicted 12706 and 15111 genes for L. katipo and L. hasselti respectively. An ortholog analysis shows large overlap between orthogroups suggesting either duplication events in L. hasselti or loss of genes in L. katipo.

The worlds largest and rarest eagle, the Philippine Eagle (Pithecophaga jefferyi), also known as the monkey-eating eagle, is the national bird of the Philippines. This raptor species is endemic to the Philippine archipelago, with populations on the islands of Luzon, Leyte, Samar, and Mindanao. It is critically endangered, with an average estimated population of 392 potentially breeding pairs or 784 mature individuals. In this paper, we describe a reference genome of the Philippine Eagle (Pithecophaga jefferyi) from a female juvenile from the province of Nueva Ecija on the island of Luzon. We generated a de novo genome assembly with high contiguity and completeness, comprising 178 contigs totaling 1.345 Gbp. The genome was sequenced at a coverage of 75.2x, and Benchmarking Universal Single-Copy Orthologs (BUSCO)/Compleasm analysis yielded a BUSCO score of 99.92% (aves_odb12), corresponding to 99.7% single-copy, 0.21% duplicated, and 0.08% fragmented genes. A consensus mitogenome sequence of 19,377 bp was also generated. The genome assembly included 23,847 putative genes, and our annotation estimated that 15.78% of the genome consisted of repetitive elements. Genome heterozygosity (H) was estimated to be 0.020%, in comparison to other birds with genome heterozygosity values ranging from 0.0103% to 0.923%. Whole-genome comparisons with publicly available genomes suggest that the Philippine eagle belongs to the snake-eagle subfamily (Circaetinae) rather than the harpy-eagle subfamily (Harpiinae). Pairwise sequentially Markovian coalescent (PSMC) analysis suggests that the effective population size was around 4,000 individuals from about 100 KYA to about 1 KYA. Finally, we constructed a minimum spanning network, which revealed that our mitogenome from the northern island of Luzon occupies a peripheral position, separated from the dominant haplotype cluster found in the southern island of Mindanao by multiple mutational steps, indicating substantial mitochondrial divergence.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 genus Trichiurus is the most economically valuable fish in the family Trichiuridae, currently recognized to include 10 valid species. However, historically numerous morphologically similar congeners have been erroneously assigned as synonyms or subspecies of T. lepturus. In this study, we examined 16 hairtail specimens collected from the southern waters of Java Island, Indonesia. Integrated morphological and mitochondrial phylogenetic analyses (COX1 and 16S rRNA), compared against global Trichiurus sequences, revealed that these specimens form an independent lineage that diverged early from other congeners. Consequently, we describe this lineage as a previously undescribed cryptic species. Diagnostic characters include: first anal-fin spine below 36th-37th dorsal-fin rays; anus below 35th-36th dorsal-fin rays; anteriormost tip of supraoccipital well posterior to posterior distal margin of eye; anterior margin of the pectoral-fin spine non-serrated; fangs on both jaws with barb-like processes; upper jaw long, mean 16.6% (15.5-17.6%) of preanal length; snout short, 12.0% (10.9-13.1%) of preanal length; eye small, diameter 5.3% (4.3-5.7%) of preanal length; and absence of hyperostosis on dorsal cranium. We herein propose the name Trichiurus javaensis sp. nov., and provide a formal morphological description and diagnostic characterization of this species.

Increasing human activities along the US west coast are of concern for populations of cetaceans and particularly for a number of large whale species that are recovering from overexploitation during the era of commercial whaling. New rapid monitoring tools, such as satellite imagery analysis powered by recent advances in artificial intelligence, have potential to provide additional broad-scale and near real-time capacities for survey and monitoring. This paper investigates and demonstrates the feasibility of automatic detection of gray whales in sub-meter satellite imagery off the coast of California, USA. Observations and statistical analysis of regional imagery allowed not only an assessment of their detectability but also the development of robust signal processing and machine learning-based solutions for automated detection. To that end, a regional dataset of 221 gray whales was created using signal processing to inform a deep-learning-based detection framework, and 20 different large neural network architectures for feature extraction followed by a support vector machine algorithm for classification were evaluated for their detection performance. Neural network backbones included 19 convolutional neural networks and 1 transformer network. The best architecture generally achieved satisfying performance with an average balanced accuracy reaching up to 99.90%. It is also demonstrated that panchromatic imagery, in spite of the lesser amount of information provided, can be used to perform detection with a relatively high accuracy of 87.05%, allowing wider spatial and temporal coverage. Large-scale deployment of the best performing models over a broad range of regional satellite imagery resulted in the detection of 3353 gray whales, as well as opportunistic detections of humpback, blue and fin whales, in and going from December 28th 2009 to March 26th 2023. It also provided meaningful data points concerning the migration routes of gray whales within the Channel Islands and Southern California Bight. The large number of high-confidence detections indicates the capacity for a large-scale monitoring approach to support state and federal conservation policies such as gear mitigation, vessel speed reduction programs, or shipping lane redefinition that could also be expanded to other areas and for other species.

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.

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.

Nematodes belonging to the Cystidicolidae Skrjabin, 1946 constitute more than 23 genera of 111 recognized species in fish from many habitats including the deep-sea, continental shelves, estuarine and freshwater habitats. The taxonomy of many species within the Cystidicolidae is unsettled due to their small size and correspondingly small morphological characters requiring use of scanning electron microscopy and supported more recently by molecular studies. The type species, Ascarophis morrhuae Van Beneden, 1870, which belongs to one of the first described and most speciose cystidicolid genera with 46 species, is based on a two-sentence description of a single female specimen from an Atlantic cod, Gadus morhua, presumably captured off the coast of Belgium in the North Sea (Van Beneden, 1870). New material was collected/examined from Atlantic cod and haddock, Melanogrammus aeglefinus, from Iceland and the North Sea and specimens present in the Natural History Museum, London were also studied. Based on these materials, A. morrhuae is morphologically redescribed and the first DNA sequences of this species are provided, it is differentiated from other Ascarophis species present in the North Atlantic and previous records are reviewed. This information provides a foundation for taxonomic and phylogenetic reconsideration of all cystidicolid nematodes and related families.

The fully mycoheterotrophic, non-photosynthetic Afrothismia fonensis Cheek & G.Delhaye sp. nov. (Afrothismiaceae), is described and illustrated from two sites in submontane forest in or adjacent to the Pic de Fon Foret Classee, Simandou Range, Republic of Guinea. This is the first record of the genus and family in West Africa west of Nigeria. The new species is remarkable for its small size, and for being unique in the genus in the entirely connate intertepaline lobes (in other species of the genus they are free or only partly united) and the longitudinal ridges on the outer perianth tube (unknown in other species). The provisional extinction risk assessment for Afrothismia fonensis is Critically Endangered (CR B1ab (iii)+2ab(iii)+D1) using the IUCN 2012 categories and criteria, due to less than 50 individuals being recorded, and due to the both the very small range and the immediate threats from foraging by red river hogs, trampling by cattle and from de-watering of the adjacent Oueleba iron-ore body where mining began in 2025. It should be noted that mitigation actions are expected to adequately address the risks associated with mining activities, and direct impacts to both areas of Afrothismia fonensis habitat have been fully avoided through relocation of planned infrastructure. We review the importance of the Boyboyba forest, Simandou range, as the West African centre of diversity for non-photosynthetic heteromycotrophs. This new discovery is examined in the context of other recently discovered range extensions to Guinea of Central African genera and families.

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).