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PubMed2025

Genomic resources for comparative analyses of obligate avian brood parasitism.

Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.

assemblies↗

PubMed2025

Genetic and genomic resources for turfgrasses: status, applications, and prospects.

Turfgrasses are integral to urban landscapes, providing social, economic, and ecological benefits. With increasing urbanization, there is a growing demand for turfgrasses that remain visually appealing while being resilient to environmental stresses. In this review, we highlight the current state of genetic and genomic resources for turfgrasses, focusing on advancements in the understanding of genes and pathways associated with traits such as disease resistance, stress tolerance, and environmental adaptability. Additionally, we discuss recent progress in implementing genome editing technologies for turfgrasses and their transformative potential for breeding and functional genomics. We examine progress, challenges, and future prospects in leveraging genomic tools for turfgrass improvement. By synthesizing knowledge from diverse studies, we provide a comprehensive overview of the techniques, discoveries, and innovations shaping the future of turfgrass breeding and management.

Poaceae↗

PubMed2025

Largest-Scale Genomic Resource Reconstructing the Genetic Origin, Population Structure, and Biological Adaptations of the Hui People.

Historical and archaeological records indicate that the Maritime and Land Silk Roads played a pivotal role in facilitating Trans-Eurasian migrations and cultural exchanges. However, the extent to which population movements or the spread of ideas shape Chinese Hui populations remains debated. We present the largest genomic resource to date, including 2,280 Hui individuals sequenced or genotyped from 30 diverse regions, to examine the genetic origins, population structure, and biological adaptations of this underrepresented group in global human genome research. We identified a detailed population structure characterized by five distinct genetic lineages of the Hui, influenced by geography and varying gene flow. The admixture history and demographic events suggest that the northwestern and northern Hui lineages emerged from demic diffusion during the Tang and Yuan Dynasties via the Land Silk Road. In contrast, the southern and island Hui lineages reflect cultural diffusion along the Maritime Silk Road, while the mixed southern-northern lineage likely developed through a combination of demic and cultural diffusion. Our findings support a hybrid model for Hui formation, indicating that both demographic processes and sociocultural transmissions contributed to their population history. We identified east-west highly differentiated variants and pre- and post-admixture adaptations in Hui genomes, demonstrating that admixture-driven adaptive or neutral variants impacted susceptibility to cardiovascular diseases and immune- and diet-related traits. These adaptive signatures include post-admixture signals of SLC24A5 and ECHDC1 in the Hui, as well as pre-admixture signals of the HLA region, BCL2A1, and KCNH8 in the East Asian source. Overall, our study suggests that Han-related genetic components helped the Hui population rapidly adapt to new local environments. Additionally, the frequency spectrum of clinically essential variants differed significantly between Hui and Han individuals, emphasizing the importance of including underrepresented populations in genomic research to promote health equity.

Humans↗

PubMed2026

Strong phylogenetic signal from chloroplast genomes of three Barringtonia species provides the first genomic resources for their conservation.

BACKGROUND: The genus Barringtonia (Lecythidaceae) is a vital component of tropical coastal forests and mangrove ecosystems. Among its members, B. racemosa and B. fusicarpa are classified as Endangered and Vulnerable, respectively, due to habitat degradation and anthropogenic pressures, underscoring the urgent need for genetic studies to guide conservation. Chloroplast (cp.) genomes serve as essential resources for phylogenetic reconstruction and conservation genetics. However, the scarcity of cp. genome data for Barringtonia has limited comprehensive evolutionary and conservation-oriented investigations. RESULTS: We assembled and annotated the first complete cp. genomes of B. racemosa, B. fusicarpa, and B. acutangula. All three genomes exhibit the typical quadripartite structure, ranging from 158,959 bp (B. racemosa) to 159,837 bp (B. acutangula), and contain 132 genes (87 protein-coding, 37 tRNA, 8 rRNA) with a GC content of 36.68%-36.86%. Collinearity and IR boundary analyses revealed high structural conservation without large-scale rearrangements. Interspecific sequence-level variations were detected in simple sequence repeats (SSRs) and long repeats. Nucleotide diversity (π) analysis identified highly polymorphic regions, including rpl20 (π = 0.080), rpoA (π = 0.064), rps3 (π = 0.063), and ndhF (π = 0.060), which represent promising molecular markers for population genetics within the genus. Codon-based selection analyses (Ka/Ks) showed that all protein-coding genes are under strong purifying selection (mean Ka/Ks 0.32-0.37), with no evidence of positive selection. Pairwise genetic distances (p-distances) among Barringtonia species are extremely low (mean 0.0046), while distances to the related genus Bertholletia are ~ 6-fold higher, supporting their generic distinction. CONCLUSIONS: Phylogenetic analysis robustly supports Barringtonia as a monophyletic clade (bootstrap = 100%), with B. racemosa and B. fusicarpa forming a sister lineage to B. acutangula. This study provides the first high-quality cp. genome resources for the two threatened Barringtonia species, revealing strong structural and sequence conservation but no direct chloroplast genomic correlates of endangerment. The identified polymorphic regions and repeat markers lay a foundation for future population genetics, phylogeographic studies, and conservation-oriented genetic management of these ecologically important coastal plants.

Genome, Chloroplast↗

PubMed2025

The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid Wheat Triticum turgidum cv. Kronos.

Triticum turgidum cv. Kronos is a tetraploid wheat cultivar that underpins one of the richest community platforms for functional genomics. Over the past decade, about 3,000 exome- and promoter-capture datasets, linked to mutagenized seed stocks, and transcriptomic and phenotypic resources have accumulated, yet the absence of a reference genome has constrained their impact. Here, we present a chromosome-scale reference genome of Kronos with high-confidence annotations, including manual curation of over 1,000 disease resistance (NLR) genes. This reference revealed previously hidden NLR diversity and clarified their genomic organization at chromosomal ends. Re-analysis of exome- and promoter-capture datasets enabled high-resolution mutation discovery in genes and regulatory regions that were previously inaccessible, uncovering the full standing variation present in Kronos mutant lines. We further re-curated transcriptomic and small RNA datasets, generating improved, genome-wide maps of microRNAs and phasiRNAs important for wheat development. Collectively, these resources elevate Kronos to reference quality and establish it as a versatile platform for functional and translational wheat research.

Journal Article↗

PubMed2026

Improved Genomic Resources for the swordtail cricket, Laupala kohalensis Otte 1994.

Advances in genetic tools such as next and third generation sequencing, paired with a focus on representative clades, provide insight into how processes including adaptation, admixture, and genome structure shape the evolution and maintenance of species. However, our understanding of the genomics of speciation is dominated by systems where ecological adaptations are thought to cause initial barriers to gene exchange. In contrast to other model systems, the 38 species of the genus Laupala constitute a very rapid radiation, where evolution of reproductive barriers and speciation is thought to be driven by sexual selection. Here, with novel PacBio HiFi reads and RNA- and Iso-Seq data, we provide a highly contiguous, chromosome-level genome and markedly improved annotation of the endemic Hawaiian cricket, Laupala kohalensis Otte, 1994. Our new resources advance previous efforts, placing 99% of 47 scaffolds on 7 autosomes and 1 sex chromosome in the 1.67 Gb assembly, with a 98.8% BUSCO score (insecta_db10), N50 of ~268 Mb, and L50 of 3. Using a custom repeat library, we estimate the genome to have 46.09% repeat content, and the new annotation includes an increased estimate of 17,670 genes, which coincides with that known from other Orthopterans. Notably, we find a large nuclear DNA segment of mitochondrial origin on chromosome 7. This new resource provides a powerful tool to identify and compare genomic causes of phenotypic diversification in a system characterized by strong signatures of sexual differentiation, representing an underappreciated but potentially widespread cause of speciation.

Hawaii↗

PubMed2026

An improved chromosome-level genome resource for the sheep scab mite, Psoroptes ovis.

Sheep scab, caused by infestation with the ectoparasitic mite, Psoroptes ovis, represents a major welfare and economic challenge for the livestock industry. We present an updated 62.7 Mb genome assembly containing 10 chromosome-level scaffolds with 10,516 annotated protein-coding genes, which provides a useful resource for studies into resistance and control.

Psoroptes ovis↗

PubMed2026

The genomic resource of Lysinibacillus fusiformis KBD-5, a biocontrol agent with antifungal activity against Botrytis cinerea.

Lysinibacillus fusiformis strain KBD-5, previously known for its antiviral activity against Tobacco mosaic virus, was investigated for its biocontrol potential against the fungal pathogen Botrytis cinerea. In plate assays, conducted with three independent biological replicates and incubated at 28 °C for 5 days, KBD-5 significantly inhibited the mycelial growth of B. cinerea by 76.42%. Whole-genome sequencing revealed a 4.69 Mb genome with a GC content of 37.28%, encoding 4719 proteins. Bioinformatics analysis identified genes involved in antimicrobial functions, including 195 carbohydrate-active enzymes (potentially aiding in fungal cell wall degradation) and 8 gene clusters for secondary metabolite synthesis (e.g., T3PKS with 30% similarity to bacillibactin biosynthetic clusters and NRPS), indicating the production of antifungal metabolites like bacillibactin-like polyketides. The strain also showed a high safety profile with no significant virulence or drug resistance risks. These findings indicate that genomic analysis of KBD-5 reveals the potential for multiple biocontrol mechanisms, supporting its potential development as a biocontrol agent. The draft genome sequence is available under NCBI accession PRJNA1335659.

Botrytis↗

PubMed2026

Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (Phaseolus vulgaris L.).

Seed coat color and patterning are key quality traits in common bean (Phaseolus vulgaris L.) that define market classes and strongly influence consumer preference and market value. These traits are controlled by a complex network of major genes (sometimes with epistatic interactions), which complicates the recovery of desired market class phenotypes following inter-market class hybridization. Although many of the underlying loci have been genetically mapped, diagnostic, high-throughput molecular markers for efficient allele tracking across the Middle American and Andean gene pools remain limited. In this study, we developed and validated 24 gene-specific PCR Allele Competitive Extension (PACE) markers targeting seven major seed coat color genes (G, B, V, J, Rk, T, and Z) and two patterning genes (CPi and CSt), together with a previously reported marker associated with the postharvest seed coat darkening locus (Psd). An additional PACE marker targeting the Phaseolin (Phs) locus was developed to distinguish Middle American (S-type) and Andean (T-type) gene pools, providing a complementary tool for assessing genetic background alongside seed coat-specific loci. Marker performance was evaluated across three diverse panels, revealing high diagnostic accuracy for most loci (90%-100%). However, for loci such as J, V, Rk, T, and Z, allele-specific markers or marker combinations were required to capture full allelic diversity. Haplotype analysis further revealed substantial allelic diversity across market classes and identified background-specific interactions. Collectively, these results provide a comprehensive set of high-resolution, gene-anchored PACE markers for seed coat color, patterning, and gene pool classification in common bean. These markers enable rapid and precise allele tracking in breeding populations and germplasm collections, facilitating marker-assisted selection for market class-specific seed coat traits and accelerating genetic improvement.

Phaseolus↗

PubMed2026

AEGIS: an annotation extraction and genomic integration resource.

MOTIVATION: Genome annotation files (GFF3/GTF) are the standard for storing genomic feature data, yet their flexibility often results in formatting inconsistencies that create bottlenecks for downstream bioinformatics analyses. A robust, unified framework is required to parse, standardise, and validate these files to ensure interoperability and facilitate complex comparative genomic tasks. RESULTS: We present AEGIS (Annotation Extraction and Genomic Integration Suite), a comprehensive toolkit designed to parse, correct, and standardise genome annotations. Beyond quality control, AEGIS provides advanced modules for flexible feature extraction (e.g., coding sequences, promoters) and comparative genomic analysis. Uniquely, it integrates multiple lines of evidence, including sequence homology, synteny, and coordinate-based lift-overs, to assess gene model correspondence and infer orthology. We demonstrate the utility of AEGIS by quantifying complex structural changes between Arabidopsis annotation versions and identifying high-confidence orthologues across diverse plant genomes. AVAILABILITY: AEGIS is implemented in Python. Source code and documentation are freely available under the GPL-3 license at https://github.com/Tomsbiolab/aegis and as a Docker container at https://hub.docker.com/r/tomsbiolab/aegis. The package is also available on PyPI (pip install aegis-bio).

Software↗

PubMed2026

Reference-Guided Chromosome-Scale Genome Assembly With Insights on Population Genomics of the Atlantic Goliath Grouper (Epinephelus itajara), Islas del Rosario, Colombia.

Epinephelus itajara, commonly known as the Atlantic Goliath grouper, is the largest species among the western North Atlantic groupers and is critically endangered. This species plays a crucial ecological, cultural, and economic role and has been the focus of captive breeding efforts at the Oceanario of the Rosario Islands, Colombia. However, despite its ecological and conservation importance, genomic resources and population genomic data for E. itajara remain scarce, particularly in the Colombian Caribbean. This study presents a reference-guided chromosome-scale genome assembly and an analysis of the population genomic structure of E. itajara using PacBio HiFi sequencing and Illumina technologies. The assembled genome has a total size of 1.12 Gb, with a contig N50 of 42.69 Mb and a scaffold N50 of 46.30 Mb. A total of 22,692 protein-coding genes were identified after masking 46% of the genome, which consists of repetitive elements. Comparative genomic analyses revealed a high degree of collinearity with closely related Epinephelus species and identified E. lanceolatus as the closest relative, supporting recent divergence and conserved genome architecture within the genus. Additionally, a population genomics analysis was conducted using 7706 high-quality SNPs to assess the genomic structure of captive populations. The results revealed four distinct genomic lineages, with moderate genetic differentiation among the sampled individuals. In the Colombian Caribbean, two unique lineages were identified, associated with the localities of Bahía Cispatá and Bahía Barbacoas, suggesting possible geographic isolation. These genomic resources provide valuable tools and new opportunities to better understand the genomic diversity, evolutionary history, and reproductive mechanisms of E. itajara. Moreover, they serve as a foundation for conservation strategies, including selective breeding programs aimed at increasing genomic diversity in captive populations and guiding restoration efforts in its natural habitat.

Epinephelus itajara↗

PubMed2025

Toward an integrated resource for pharmacogenomics (PGx): Survey findings from the genomic medicine communities.

PURPOSE: Pharmacogenomics (PGx) is a critical component of precision health care that aims to improve drug efficacy and reduce adverse events. Terminologies and standards have not always aligned between PGx and broader genomic medicine communities, which is a barrier to PGx implementation. An updated assessment of community barriers, needs, and perspectives is critical to enable more standardized terminologies and interpretation frameworks. METHODS: The Clinical Genome Resource's PGx Interpretation Committee (PGxIC, formerly referred to as the PGx Working Group, PGxWG) conducted 2 surveys targeting the PGx and genomic medicine communities (n = 508) to evaluate perspectives on PGx clinical validity and actionability frameworks, as well as other barriers to PGx implementation. Surveys were tailored toward self-reported familiarity with PGx. Data primarily consisted of free text, which were analyzed using qualitative content analysis methods. RESULTS: Survey responses indicated conflation of terminology across disciplines, including confusion around differing definitions of terms in PGx and non-PGx contexts. Data also indicated broad support for leveraging existing PGx guidelines and framework structures alongside the standardization of approaches and centralization of resources. CONCLUSION: These novel survey results demonstrate broad consensus on the importance of integrating PGx into clinical practice, including support for development of gene-drug response clinical validity and actionability frameworks aligned with Clinical Genome Resource's frameworks for gene-disease relationships.

Humans↗

PubMed2026

An Updated Evidence Assessment of the Genetic Causes of Dilated Cardiomyopathy.

BACKGROUND: Evidence of the diverse genetic architecture of dilated cardiomyopathy (DCM) continues to emerge and requires reassessment of the clinical relevance of implicated disease genes. Building on the 2019-2020 Clinical Genome Resource evaluation, the DCM gene curation expert panel reconvened in 2024-2025 to conduct a reassessment of genes in DCM. METHODS: The Clinical Genome Resource semiquantitative clinical validity classification framework was applied with specifications to DCM to classify genes into categories on the basis of strength of published evidence for a DCM phenotype. Previously curated genes were reassessed, and newly reported gene-disease-mode of inheritance (MOI) relationships, termed "curations," were evaluated. RESULTS: Sixty-eight genes were evaluated, inclusive of 72 unique gene-disease-MOI relationships across 51 previously evaluated and 17 newly assessed genes. Thirty-five curations were classified as high evidence (16 Definitive, 10 Strong, 9 Moderate), increasing by 16 from the prior assessment. Nine newly assessed genes were classified as high evidence: BAG5, FLII, LMOD2, MYLK3, MYZAP, NRAP, PPA2, PPP1R13L, and RPL3L. Twelve genes (11 newly appraised) were rated as high evidence with an autosomal recessive (AR) MOI. Five reevaluated genes from 2019-2020 had clinically significant changes in classification. Except for JPH2, for which curation was modified to separate autosomal dominant and AR MOI curations, clinically significant changes involved upgrades from low- to high-evidence categories (PLEKHM2, PRDM16, TBX20, TNNI3K), demonstrating the robustness of the Clinical Genome Resource gene curation process over time. An additional 29 gene-disease-MOI curations were classified as Limited, including 6 newly evaluated genes and 1 new MOI for a previously evaluated gene, MYBPC3-AR; 4 were classified as No Known Disease Relationship, and remained Disputed. Four previously evaluated genes were curated for both AD and AR MOIs: JPH2 (AD-Strong, AR-Limited), LDB3 (AD-Limited, AR-Strong), MYBPC3 (AD-Limited, AR-Limited), and TNNI3 (AD- and AR- Strong). CONCLUSIONS: With substantial new evidence, the genetic architecture of DCM has rapidly expanded. This updated assessment of genes reported in DCM yielded 35 high-evidence curations, an increase from 19 only 5 years ago. The results of this evidence-based evaluation process inform clinical interpretation of genetic information in the care of DCM patients and families.

dilated cardiomyopathy↗

PubMed2026

The Gabriella Miller Kids First Data Resource for genomic research in pediatric cancer and congenital anomalies.

Nine-year-old brain tumor patient Gabriella Miller challenged members of Congress to "stop talking and start doing" when providing federal funding for research into cures for pediatric cancer and congenital anomalies. Though she ultimately lost her life to that cancer, her advocacy efforts resulted in the 2014 Gabriella Miller Kids First Research Act, launching the Gabriella Miller Kids First Pediatric Research Program at the National Institutes of Health (NIH). The overarching goal of the Gabriella Miller Kids First Pediatric Research Program is to help researchers uncover new insights into the biology of childhood cancer and congenital anomalies. Following the signing of the Gabriella Miller Kids First Research Act 2.0 in January 2025, the program has been extended at NIH through 2028 to advance the groundwork laid in the program's first ten years. The Gabriella Miller Kids First Data Resource Center has since honored her legacy by building a comprehensive data resource for genomic research into pediatric conditions. Data from more than 30,000 participants annotated with demographic and clinical information related to their diagnoses have been released for secondary research and analysis using the center's web-based platforms. This paper analyzes the outcomes of the initiative and highlights breakthroughs made by the larger research community resulting from the availability of this data resource. We explore the future expansion of the data resource to include new modalities and tools for supporting life-saving research for children like Gabriella Miller.

Humans↗

PubMed2026

Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships in Fraxinus (Fraxinus mandshurica).

Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.

Fraxinus↗

PubMed2026

Genomes of the ex-type strains of Elsinoë mangiferae and E. perseae, the causal agents of scab on mango and avocado.

Elsinoë species are slow-growing, hemibiotrophic to necrotrophic fungi that cause scab diseases on economically important fruit crops. Genome resources for many host-specific species remain limited. We report high-quality draft genome assemblies for the ex-type strains of Elsinoë mangiferae (CBS 226.50) and E. perseae (CBS 406.34), causal agents of mango and avocado scab, respectively. Among 5 approaches tested, a Nanopore-only NextDenovo assembly produced the most contiguous genomes, yielding 24.5 Mb (E. mangiferae) and 25.1 Mb (E. perseae) assemblies with 13 and 18 contigs, respectively, BUSCO completeness scores of ∼94%, and multiple putative telomere-to-telomere chromosomes. Gene prediction identified 9,134 and 9,243 genes, respectively. Functional annotation revealed enrichment of metabolic and regulatory pathways, including those involved in posttranslational modification, protein transport, and secondary metabolism. Carbohydrate-active enzyme repertoires were small but conserved, consistent with stealth pathogenicity strategies and low plant cell wall degradation. Both genomes encoded large secretomes (>850 proteins), diverse protease repertoires (>300 proteins), Ecp2-like effector proteins, and multiple biosynthetic gene clusters, including clusters with similarity to those associated with elsinochrome and ACT-toxin II biosynthesis, some of which may contribute to host-pathogen interactions and disease development. A large fraction of genes lacked functional characterization, suggesting incomplete databases and/or the presence of lineage-specific genes potentially involved in virulence or host adaptation. These genome resources fill critical gaps for underrepresented Elsinoë species and provide taxonomically anchored references essential for diagnostics, comparative genomics, and research into the molecular basis of host specificity and pathogenicity in scab-causing fungi.

Persea↗

PubMed2024

Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats.

INTRODUCTION: Comprehensive genomic resources offer insights into biological features, including traits/disease-related genetic loci. The current reference genome assembly for the domestic cat (Felis catus), Felis_Catus_9.0 (felCat9), derived from sequences of the Abyssinian cat, may inadequately represent the general cat population, limiting the extent of deducible genetic variations. OBJECTIVES: The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly. METHODS: In contrast to prior assemblies relying on Abyssinian cat sequences, AnAms1.0 was constructed from the sequences of more popular American Shorthair breed, which is related to more breeds than the Abyssinian cat. By combining advanced genomics technologies, including PacBio long-read sequencing and Hi-C- and optical mapping data-based sequence scaffolding, we compared AnAms1.0 to existing Felidae genome assemblies (20 scaffolds, scaffolds N50 > 150 Mbp). Homology-based and ab initio gene annotation through Iso-Seq and RNA-Seq was used to identify new coding genes and splice variants. RESULTS: AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variants and 29 million repetitions compared to felCat9. Additionally, we identified > 1,600 novel protein-coding genes. Notably, olfactory receptor structural variants and cardiomyopathy-related variants were identified. CONCLUSION: AnAms1.0 facilitates the discovery of novel genes related to normal and disease phenotypes in domestic cats. The analyzed data are publicly accessible on Cats-I (https://cat.annotation.jp/), which we established as a platform for accumulating and sharing genomic resources to discover novel genetic traits and advance veterinary medicine.

Animals↗

PubMed2025

Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes' tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Animals↗