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.

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next generation sequencing technologies and the resulting reduction of associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.21 gigabase, 20,330-contig nuclear assembly with an N50 of 98.9 Mb and a 17,108 bp mitogenome. The nuclear assembly had 31x average coverage and was comparable in completeness to other primate reference genomes, with a 95.47% BUSCO completeness score for primate-specific genes. As the first reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

The Mozambique tilapia (Oreochromis mossambicus) is a species of significant ecological and economic importance in Southern Africa. However, urbanization and water management challenges have led to the species being classified as threatened by the International Union for Conservation of Nature. Despite its widespread distribution and significance as a key food source, the genetic architecture of Southern African O. mossambicus remains inadequately characterized. This gap in knowledge hinders efforts to conserve and manage the species effectively. This study presents a high-quality chromosome-level genome assembly for a South African O. mossambicus assembled using both PacBio HiFi and Dovetail Omni-C sequencing. The 1.09 Gb assembly is highly contiguous, with 99.4% of sequences anchored into 22 chromosomes and a BUSCO completeness of 99.5%. We annotated 27,544 protein-coding genes. This genome provides an essential resource for preserving native biodiversity and enabling genomic selection for traits like disease resistance and growth performance within the South African aquaculture context.

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.

Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: Hypothymis azurea), Indian Yellow Tit (Paridae: Machlolophus aplonotus), Brown-cheeked Fulvetta (Leiothrichidae: Alcippe poioicephala), Malabar Trogon (Trogonidae: Harpactes fasciatus), Blue-bearded Bee-eater (Meropidae: Nyctyornis athertoni), Malabar Whistling-Thrush (Muscicapidae: Myophonus horsfieldii), Orange-headed Thrush (Turdidae: Geokichla citrina). Using a hybrid Oxford Nanopore long reads - Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores >97%, UCEs >4799). Repeat masking identified [~]10% of the genomes as interspersed repeats, and functional annotations yielded an average of 9,619 protein-coding genes per species. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxson test, p = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.

The eastern three-lined skink (Bassiana duperreyi) inhabits the Australian high country in the southwest of the continent including Tasmania. It is an oviparous species that is distinctive because it undergoes sex reversal (from XX genotypic females to phenotypic males) at low incubation temperatures. We present a chromosome-scale genome assembly of a Bassiana duperreyi XY male individual, constructed using a combination of PacBio HiFi and ONT long reads scaffolded using Illumina HiC data. The genome assembly length is 1.57 Gb with a scaffold N50 of 222 Mbp, N90 of 26 Mbp, 200 gaps and 43.10% GC content. Most (95%) of the assembly is scaffolded into 6 macrochromosomes, 8 microchromosomes and the X chromosome, corresponding to the karyotype. Fragmented Y chromosome scaffolds (n=11 > 1 Mbp) were identified using Y-specific contigs generated by genome subtraction. We identified two novel alpha-satellite repeats of 187 bp and 199 bp in the putative centromeres that did not form higher order repeats. The genome assembly exceeds the standard recommended by the Earth Biogenome Project; 0.02% false expansions, 99.63% kmer completeness, 94.66% complete single copy BUSCO genes and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. The B. duperreyi genome assembly has one of the highest completeness levels for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity, and for other comparative genomics studies of the Scincidae. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Scincidae; Lygosominae; Eugongylini; Bassiana (=Acritoscincus); Bassiana duperreyi (Gray, 1838) (NCBI: txid316450).

BackgroundObtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome. Of chelonians, terrestrial tortoises are considered one of the most endangered taxa, which calls for more genomic resources. Here we make the most of high synteny conservation in chelonians to produce the first chromosome-level genome assembly of genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: T. graeca. ResultsWe used high quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome level assembly of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25998 protein-coding genes, and a 41.2% fraction was determined as repetitive in our assembled genome. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) consistent with previously suggested phylogeographic patterns for the species. This outlines the value of genomes like this for phylogeographic studies. ConclusionsOur results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our Testudo graeca annotated genome paves the way to delve deeper into the species evolutionary history and provides a valuable resource to increase making direct conservation efforts on their threatened populations.

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ~90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. A phylogenetic analysis revealed the isolate used in our genomic analysis belongs to Subspecies B, one of the two known genetic subspecies of F. auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.

Rapid evolution of long-read sequencing technologies requires accurate, fast and user-friendly genome assembly and scaffolding tools. In this article we present Digital Scaffolding (dScaff), a bioinformatics tool that performs scaffolding of de novo genome assemblies based on reference scaffolds or chromosomes. dScaff makes use of a series of bash and R scripts in order to create a minimal complete scaffold from a genome assembly, with future features to be implemented. Herein, we demonstrate the functionality of dScaff on a novel genome assembly pertaining to a recently sequenced local strain of Drosophila suzukii.

Australia is remarkable for its lizard diversity, with very high endemicity because of continental-scale diversification and adaptive radiation during prolonged isolation. We here employed stLFR linked-read technology to generate male and female draft genomes of the jacky dragon Amphibolurus muricatus, an Australian dragon lizard (family Agamidae; the agamids). The assemblies are 1.8 Gb in size and have a repeat content (39%) and GC content (42%) similar to other dragon lizards. The longest scaffold was 39.7 Mb (female) and 9.6 Mb (male), with corresponding scaffold N50 values of 6.8 Mb and 1.6 Mb. The BUSCO (Sauropsida database) completeness percentages were 90.2% and 88.8% respectively. Phylogenetic comparisons show that Australian and Asian agamids split from a common ancestor about 80 million years ago, while the Australian genera Amphibolurus, Pogona, and the basal Intellagama split [~]37 million years ago. The draft A. muricatus assemblies will be a valuable resource for understanding lizard sex determination and the evolution and conservation of Australian dragon lizards.

Clam digging has a long history in Hong Kong, but unregulated clam digging activities depletes clam populations and threatens the ecosystem. Population genomics is useful to unravel the connectivity of clams at different geographical locations and to provide necessary conservation measures; and yet, only limited number of clams in Hong Kong have genomic resources. Here, we present chromosomal-level genome assemblies for two clams commonly found in Hong Kong, Anomalocardia flexuosa and Meretrix petechialis, using a combination of PacBio HiFi and Omni-C reads. We assembled each genome ([~]1.04-1.09 Gb) into 19 pseudochromosomes with high sequence continuity (scaffold N50 = 58.5 Mb and 53.5 Mb) and high completeness (BUSCO scores 94.4% and 95.7%). A total of 20,881 and 20,084 gene models were also predicted for A. flexuosa and M. petechialis respectively using transcriptomes generated in this study. The two new genomic resources established in this study will be useful for further study of the biology, ecology, and evolution of clams, as well as setting up a foundation for evidence-informed decision making in conservation measures and implementation.

The rails are a phenotypically diverse family of birds that includes around 130 species and displays a wide distribution around the world. Here we present annotated genome assemblies for four rails from Aotearoa New Zealand: two native volant species, p[u]keko Porphyrio melanotus and mioweka Gallirallus philippensis, and two endemic flightless species takah[e] Porphyrio hochstetteri and weka Gallirallus australis. The quality checks and comparison with other rallid genomes showed that the new assemblies were of high quality and that the annotations could be trusted. Using the sequence read data, heterozygosity was found to be lowest in the endemic flightless species and this probably reflects their relatively small populations. This study significantly increases the number of available rallid genomes and will enable future genomic studies on the evolution of this family.

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.

Citrus reticulata (Blanco) fruit is native to South East Asia which owns many of the nutritional, medicinal and economic advantages, locally known as "Kinnow" and one of the priced mandarin varieties (Dancy, Fuetrells Early and Honey) of Citrus genera renowned for its exclusive taste, vitamin richness, thin peel, long shelf-life and seedless characteristics in Pakistan. However, genetic improvement and breeding strategies of this valued variety are lacking due to the in-housed insufficient genomic and technical resources. Therefore, the current research was initiated to provide the base-line de-novo genome assembly of C. reticulata (seedless kinnow) at a depth of 151x with Illumina paired-end short-read sequencing technology using HiSeq 2500. Whole-genome sequencing resulted in 139,436,350 raw reads ([~]20.09 GB) of data, however, after removing the low-quality reads (1.08%), duplicated sequences (10.5%) and Illumina adaptors, 137,901,462 clean reads were obtained with ([~]18.87 GB) of clean data which was further used for downstream variant calling analysis. In total, 348,861 scaffolds were generated with N50 value of 4827 which constitute 263,018,9 contigs ranging from 71-36,213 with total of 179,984,763 nucleotides. The GC content of the final draft assembly at 71-mer was 34.1%. Moreover, annotation was performed with "Hayai-Annotation Plants" tool which marked the whole-genome mapping with three main functional databases of interpro, Pfam and gene ontology. Additionally, in-silico identification of 111,032 Simple Sequence Repeats (SSR) was also accomplished with the help of GMATA tool, which may be used for further screening and genetic improvement of the citrus varieties by means of this current assembly as a resource of local reference genome.

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.5 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 84.3%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 53 Actinopterygii species and two outgroups was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.

The yellowfin seabream, Acanthopagrus latus, is widely distributed throughout the Indo-West Pacific. This fish is an ideal model species in which to study the mechanism of sex reversal since it exhibits a specific feature: sequential hermaphrodite. Here, we report a chromosome-scale assembly of the A. latus based on PacBio and Hi-C data. 22,485 protein-coding genes were annotated in whole genome level using transcriptome data. Taken together, this highly accurate, chromosome-level reference genome can provide a valuable resource to elucidate the mechanism of sex reversal for A. latus. Background & SummaryEvolution of sex, especially the evolution of different sexual systems, is a fascinating subject in evolutionary biology. The Sparidae, commonly known as seabreams or progies, is a family of fishes of the order Perciformes. And this family consist about 150 species in the world, which are mainly coastal fish1. Previous researchers mentioned that Sparidae is an ideal taxon to study the evolution history and adaptive significance of sexual systems, particularly for both types of sequential hermaphroditism, given that this group contains many protogyny, protandry and genochorist species2. The yellowfin seabream, Acanthopagrus latus is a protandry species which belongs to the Sparidae family. It is widely distributed in Indo-West Pacific area3. It has a great relevance for marine aquaculture and its biology is well focused on reproductive physiology and nutrition4. Interestingly, A. latus has a special gender feature is that it belongs to protandrous sexual system (initially as male and change later to female)5. Most of the past studies of A. latus mainly focused on the reproductive biology, population structure, aquaculture and taxonomy3,4,6-8. Although some sex reversal related genes were found in A. latus, the lack of genomic resources still limit us to elucidate the mechanism of sex reversal for this species.9,10. In addition, this lack was also limited the studies of evolution of sexual systems for Sparidae. In this study, long-read (PacBio SMRT) sequencing and Hi-C sequencing technologies were applied to construct a high quality reference genome for yellowfin seabream. This high-quality genome can provide a valuable resource to elucidate the mechanism of sex reversal for A. latus. Furthermore, this genome can also facilitate the studies of evolution of sexual systems for Sparidae.

The number of high-quality genomes is rapidly growing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with a coverage of 94.5x, the genome of the Sapphire Devil, Chrysiptera cyanea was assembled and annotated. The final assembly consisted of 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%. 28,173 genes were identified. Comparative analyses with available chromosome-scale assemblies for related species identified contig-chromosome correspondences. This genome will be useful to use as a comparison to study the specific adaptations linked to symbiosis life of the closely related anemonefish. Furthermore, this species is present in most tropical coastal areas in the Indo-West Pacific and could become a model for environmental monitoring. This work will allow to expand coral reef research efforts and highlights the power of long-read assemblies to retrieve high quality genomes.

BackgroundThe central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated telomere to telomere phased assembly of the genome of a female ZW central bearded dragon. ResultsGenome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single copy BUSCO genes and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model rDNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudoautosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies and their resultant transcription factors and intermediaries, determines sex in the bearded dragon. ConclusionThis high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Iguania; Agamidae; Amphibolurinae; Pogona; Pogona vitticeps (Ahl, 1926) (NCBI:txid103695). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/651798v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1a9d5fforg.highwire.dtl.DTLVardef@1206061org.highwire.dtl.DTLVardef@97acf7org.highwire.dtl.DTLVardef@1dc939d_HPS_FORMAT_FIGEXP M_FIG C_FIG

BackgroundWith high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensive genome resource is of great importance. ResultsHerein, we constructed a BAC library for broomcorn millet, generated BAC end sequences based on the clone-array pooled shotgun sequencing strategy and Illumina sequencing technology, and integrated BAC clones into genome by a novel pipeline for BAC end profiling. The BAC library is consisted of 76,023 clones with an average insert length of 123.48 Kb, covering about 9.9-fold of the 850 Mb genome. Of 9,216 clones tested using our pipeline, 8,262 clones were mapped on the broomcorn millet cultivar longmi4 genome. These mapped clones covered 308 of the 829 gaps left by the genome. To our knowledge, this is the only BAC resource for broomcorn millet. ConclusionsWe constructed a high-quality BAC libraray for broomcorn millet and designed a novel pipeline for BAC end profiling. BAC clones can be browsed and obtained from our website (http://eightstarsbio.com/gresource/JBrowse-1.16.5/index.html). The high-quality BAC clones mapped on genome in this study will provide a powerful genomic resource for genome gap filling, complex segment sequencing, FISH, functional research, and genetic engineering of broomcorn millet.

The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome using high-fidelity (HiFi) long-read sequencing. This resulted in a highly contiguous contig assembly with 90% of the genome in 10 contigs. The contig assembly was placed in a chromosomal context using synteny with a closely related species, A. ludens, as both are members of the A. fraterculus group. The resulting assembly represents the five autosomes and the X chromosome which represents 95.9% of the genome, and 199 unplaced contigs representing the remaining 4.1%. Orthology analysis across the structural annotation sets of high quality tephritid genomes demonstrates the gene annotations are robust, and identified genes unique to Anastrepha species that may help define their pestiferous nature that can be used as a starting point for comparative genomics. This genome assembly represents the first of this species and will serve as a foundation for future genetic and genomic research in support of its management as an agricultural pest.