{"title":"Comparative analyses of olfactory receptor repertoires reveal evolutionary dynamics and adaptation of freshwater and seawater gobies based on the chromosome-level genomes.","authors":"Huayan Zhao, Minmin Xie, Fang Zhao, Mingpeng Zheng, Chuang Zhou","doi":"10.1093/jhered/esag027","DOIUrl":"10.1093/jhered/esag027","url":null,"abstract":"<p><p>The olfactory receptor (OR) genes underpin vertebrates' detection of environmental chemical signals; the expansion, functional differentiation, and genomic diversity of the OR gene family drive niche adaptation. Aquatic OR genes evolve in response to salinity and odorant spectra to maintain olfactory adaptability, shaping distinct olfactory traits in freshwater and seawater fish. To explore OR gene evolution linked to salinity adaptation, we systematically identified and analyzed the OR genes of three freshwater and four seawater gobiid species (Perciformes, Gobiidae) at the chromosome-level genomes. The analysis of the OR gene composition of gobies revealed significant habitat-related differentiation: the seawater gobiid species exhibited a higher average number of OR genes (115.50) compared to the freshwater gobiid species (89.67). This distribution pattern indicated an adaptive expansion of the OR gene family to accommodate the more complex chemical signaling environment in seawater habitats. Sequence analysis of the conserved motifs of the OR gene confirmed that the conserved motifs across different gobies exhibited similar sequence compositions, underscoring the evolutionary conservation of the OR gene sequence during adaptive evolution. Phylogenetic analysis of the OR gene families (ζ, η, δ, ε) demonstrated a distinct habitat-specific distribution pattern among gobiid species: the ε family was consistently present in seawater gobiid species but absent in freshwater gobiid species, whereas the η family maintained a dominant proportion in both seawater and freshwater gobiid species. A comparative analysis of the OR gene subfamilies identified a total of 89 OR gene subfamilies among freshwater and seawater gobiid species. Of these, 38 subfamilies were unique to freshwater gobiid species, while 67 subfamilies were exclusively found in four seawater gobiid species. Chromosome-level genomic analysis indicated that OR genes were not randomly distributed throughout the genome but were organized in clusters, forming gene clusters. Our findings about the changes in the OR gene family associated with habitat divergence in gobiid species would provide new insights into the olfactory adaptation in fish.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"809-821"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147476538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Henry K Baker, Cheyenne Y Payne, Merly Escalona, Jeff Rodzen, Steve Parmenter, Russell M Barabe, Claire Ingel, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Robert D Cooper, Courtney Miller, Erin Toffelmier, J Carlos Garza, H Bradley Shaffer, Diana J Rennison, Jonathan B Shurin
{"title":"The genome assemblies of the Tui chub, Siphateles bicolor, and Arroyo chub, Gila orcuttii.","authors":"Henry K Baker, Cheyenne Y Payne, Merly Escalona, Jeff Rodzen, Steve Parmenter, Russell M Barabe, Claire Ingel, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Robert D Cooper, Courtney Miller, Erin Toffelmier, J Carlos Garza, H Bradley Shaffer, Diana J Rennison, Jonathan B Shurin","doi":"10.1093/jhered/esag002","DOIUrl":"10.1093/jhered/esag002","url":null,"abstract":"<p><p>We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1,148,084,093 base pairs, has a scaffold N50 of 45.9 mb, a contig N50 of 23.7 mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1,263,410,250 base pairs, has a scaffold N50 of 50.5 mb, a contig N50 of 13.1 mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34,090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28,193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species' phylogeographic histories and delineating the role of hybridization in their evolution.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"843-855"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145991902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christina M McCosker, Lynda Doughty, Nicole Hunter, Ashley Stokes, Wendy B Puryear, Jonathan A Runstadler, Kristina M Cammen
{"title":"Whole genome sequencing reveals variation in immune and nervous systems associated with harbor seal susceptibility to phocine distemper virus.","authors":"Christina M McCosker, Lynda Doughty, Nicole Hunter, Ashley Stokes, Wendy B Puryear, Jonathan A Runstadler, Kristina M Cammen","doi":"10.1093/jhered/esag017","DOIUrl":"10.1093/jhered/esag017","url":null,"abstract":"<p><p>Anthropogenic pressures have increased the emergence and spread of infectious diseases in wildlife in recent decades, with cascading impacts on ecosystem dynamics and elevated risk to public health. Understanding factors that contribute to disease severity, and population- and community-level impacts, is critical to predicting and mitigating infectious disease outbreaks. We aimed to investigate how host genetic factors contribute to harbor seal susceptibility to phocine distemper virus (PDV), a virus that has caused variable levels of mortality among pinniped populations across the North Atlantic. We conducted whole-genome sequencing of harbor seals that were stranded during and after a PDV outbreak that occurred in the Northeastern United States in 2018 and used genome-wide association and FST-based approaches to identify genetic variants putatively associated with survival. A subset of harbor seals (10 cases, 10 controls) were sequenced at high coverage (~58×) to generate a reference haplotype panel and impute genotypes in the remaining samples (37 cases, 45 controls), which were sequenced at a lower coverage (~4×). On investigation of 148,644 filtered single nucleotide polymorphisms, we identified 33 candidate genes related to innate and adaptive immunity and 37 genes related to the nervous system that were associated with harbor seal survival. These results provide further evidence for the importance of immunogenetic variation and highlight additional key pathways and biological processes that may confer resistance to PDV. Genome-wide approaches, which can reveal the complexity of genetic variation underpinning disease-associated traits, are critical tools to help us understand and potentially predict the impact of future disease outbreaks.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"718-729"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147312541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carlos Daniel Cadena, Laura Pabón, Andrés Felipe Díaz-Salazar, Maria Elisa Mendiwelso, Natalia Ocampo-Peñuela, Nelsy Niño-Rodríguez, Juliana Soto-Patiño, Glenn F Seeholzer, Suzette G A Flantua, Linelle Abueg, Jennifer Balacco, Nadolina Brajuka, Giulio Formenti, Tatiana Tilley, Conor Whelan, Erich D Jarvis, Brian Tiltson Smith, Andrés M Cuervo
{"title":"New genomic resources and the historical demography of the Tourmaline Sunangel (Trochilidae, Heliangelus exortis) in the Colombian Andes.","authors":"Carlos Daniel Cadena, Laura Pabón, Andrés Felipe Díaz-Salazar, Maria Elisa Mendiwelso, Natalia Ocampo-Peñuela, Nelsy Niño-Rodríguez, Juliana Soto-Patiño, Glenn F Seeholzer, Suzette G A Flantua, Linelle Abueg, Jennifer Balacco, Nadolina Brajuka, Giulio Formenti, Tatiana Tilley, Conor Whelan, Erich D Jarvis, Brian Tiltson Smith, Andrés M Cuervo","doi":"10.1093/jhered/esag016","DOIUrl":"10.1093/jhered/esag016","url":null,"abstract":"<p><p>Understanding the demographic history of tropical montane species offers insights into how climate-driven habitat dynamics shape genetic diversity and population structure. The Tourmaline Sunangel (Heliangelus exortis), a hummingbird endemic to the Northern Andes of Colombia and Ecuador, inhabits high-elevation ecosystems that were repeatedly impacted by Pleistocene glacial-interglacial cycles. To enable genomic and evolutionary studies in this system, we generated a high-quality, chromosome-level reference genome using PacBio HiFi long reads and Hi-C scaffolding. The resulting 1.05 Gb assembly has contig and scaffold N50s of 8.4 mb and 73.9 mb, respectively, with >94% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Using this reference, we analyzed whole-genome resequencing data from 10 individuals collected at a single locality in the Eastern Andes of Colombia and reconstructed demographic history with pairwise sequentially Markovian coalescent models. Our results indicate a pronounced population expansion between ~1 Mya and ~300 kya, likely driven by increased habitat connectivity during glacial periods when highland vegetation was displaced downslope, followed by a decline likely associated with interglacial fragmentation. These trends broadly align with paleoecological records, suggesting that populations of forest-associated species such as H. exortis responded to Pleistocene climatic oscillations, though demographic patterns did not strictly mirror known glacial-interglacial dynamics. This work establishes a foundation for future genomic studies in Andean birds and highlights the potential of combining genomic and paleoecological data to unravel how biodiversity responds to environmental change.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"868-876"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147277782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Olivia R Boven, Karilyn Alex, Kristen D King, Patrick Thompson, Lynnea Wiens, Samantha Pham, Michael A Russello
{"title":"Kokanee-sockeye salmon hybridization predominantly leads to a resident life history with outcomes for a long-term reintroduction program.","authors":"Olivia R Boven, Karilyn Alex, Kristen D King, Patrick Thompson, Lynnea Wiens, Samantha Pham, Michael A Russello","doi":"10.1093/jhered/esag024","DOIUrl":"10.1093/jhered/esag024","url":null,"abstract":"<p><p>Stocking programs have been widely implemented to restore extirpated fish species to their historical ranges, and must include careful consideration of potential hybridization dynamics. The sockeye salmon (Oncorhynchus nerka) reintroduction project in Skaha Lake (British Columbia, Canada) provides an excellent opportunity to investigate the outcomes of hybridization between anadromous (migratory) sockeye and resident kokanee over a two-decade-long program. Prior research established the presence of hybrids, with the vast majority of F1 spawners exhibiting a resident life history. Yet, it remains unknown whether anadromous hybrid smolts exhibit fitness effects in the form of reduced survival during migration or whether they predominantly remain resident. Here, we paired cohort-based sampling (age-0 fry, age-1 smolts, adult spawners) in Skaha Lake with SNP genotyping, otolith microchemistry, and morphometrics to (1) reconstruct trends in stock proportions of sockeye, kokanee, and hybrids (F1, B1 sockeye, B1 kokanee) over a 15-year time series and (2) investigate the morphological, behavioural, and fitness outcomes of sockeye-kokanee hybridization. Genetic assignments revealed stock proportions varied widely over time and across cohorts, with hybrids making up a substantial proportion of the population despite earlier suggestions that hybrids may exhibit reduced fitness. Approximately 94% of F1 and 100% of B1 kokanee spawners exhibited microchemical evidence of a resident life history. Conversely, B1 sockeye spawners were evenly split between resident and anadromous, displaying a significant difference in fork length associated with life history and providing further evidence for a genetic basis to migratory behaviour. More broadly, our findings have important management implications for habitat restoration and underscore the need for continued monitoring with consistent sampling among partner organizations.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"778-791"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147446025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ellie Kolb, Mayra N Mendoza Cerna, Brian W Davis, Roscoe Stanyon, Terje Raudsepp
{"title":"Comprehensive cytogenetic analysis of the aardwolf (Proteles cristatus) and comparative chromosome painting with the domestic cat (Felis catus).","authors":"Ellie Kolb, Mayra N Mendoza Cerna, Brian W Davis, Roscoe Stanyon, Terje Raudsepp","doi":"10.1093/jhered/esag008","DOIUrl":"10.1093/jhered/esag008","url":null,"abstract":"<p><p>Aardwolf (Proteles cristatus) is one of the four extant hyenas. Up to now, chromosome analysis of the aardwolf is limited to the knowledge that this insectivorous hyena shares the same 2n = 40 diploid chromosome number with the three bone-crushing hyena species. Here we present a detailed conventional banding and molecular cytogenetic characterization of the aardwolf karyotype. A chromosome-by-chromosome comparison with the spotted hyena (Crocuta crocuta) shows extensive conservation of chromosome size, morphology, and banding patters between the two hyenas. Karyotype conservation in hyenas is further supported by cat-aardwolf Zoo-FISH revealing almost identical patterns with previously available cat-spotted hyena Zoo-FISH, as well as extensive conserved synteny between cats and hyenas. Notably, hyena Chr12 and cat E1 share conserved synteny and carry the single nucleolus organizer region in both groups of species. Telomere-FISH in aardwolf and cat revealed only canonical telomeres and no interstitial sites, thus consistent with the overall karyotype conservation. However, there are also differences between aardwolf and spotted hyena Chr15, Chr16, and Chr19 due to heterochromatic additions in the aardwolf. Of these, the metacentric aardwolf Chr16 serves as a genomic feature that distinguishes this species from the spotted hyena in which the homeologous chromosome is acrocentric. In conclusion, improved cytogenetic and molecular characterization of the aardwolf karyotype expands the comparative knowledge about mammalian karyotypes and chromosome evolution, supports karyotypic conservation in feliform carnivores, and facilitates the construction of a high-quality chromosome-level annotated genome assemblies for the aardwolf and other hyenas.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"740-749"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miguel Camacho-Sanchez, Noor Haliza Hasan, Arlo Hinckley, Fred Tuh Yit Yu, Javier Juste, Jennifer A Leonard
{"title":"Effective population size associated with sky-island distribution in the summit rat, Rattus baluensis, a mountain Bornean endemic.","authors":"Miguel Camacho-Sanchez, Noor Haliza Hasan, Arlo Hinckley, Fred Tuh Yit Yu, Javier Juste, Jennifer A Leonard","doi":"10.1093/jhered/esaf106","DOIUrl":"10.1093/jhered/esaf106","url":null,"abstract":"<p><p>Tropical mountains are hotspots of biodiversity, and they can harbor species with sky-island distributions on mountaintops. The summit rat, Rattus baluensis, is a Bornean endemic previously known from two populations in the Kinabalu range. Here, we report the discovery of a third, genetically distinct population on Mt. Trusmadi, Sabah, Borneo. Using 27 nuclear introns genotyped in 44 individuals, we show that this population is genetically isolated and more differentiated than those in the Kinabalu range. ABC analyses reveal the three populations likely became isolated in mountain tops during the Holocene. Genetic diversity and effective population size across the three populations correlate with the area of high-elevation habitat on each mountain. Despite relatively large population sizes and well-preserved habitats, the species' strict association with montane forest and confinement to three mountaintops make it particularly vulnerable to climate change, stochastic events, and localized anthropogenic impacts.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"688-698"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146055210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marco Bürger, Chenjiao Deng, Charmaine F Soco, Sowmya Poosapati, Adam C Schneider, Daniel Potter
{"title":"Whole-genome sequences confirm Castilleja lassenensis (Orobanchaceae) as a distinct species from Castilleja lemmonii.","authors":"Marco Bürger, Chenjiao Deng, Charmaine F Soco, Sowmya Poosapati, Adam C Schneider, Daniel Potter","doi":"10.1093/jhered/esag015","DOIUrl":"10.1093/jhered/esag015","url":null,"abstract":"<p><p>Castilleja lassenensis, a species of root-parasitic plants endemic to the Mt. Lassen region in northern California, has been subject to taxonomic debate since its first description in 1940. While morphological and ecological distinctions from its close relative Castilleja lemmonii have been documented, many regional floras do not list C. lassenensis or treat it as a synonym of C. lemmonii. We sequenced the nuclear genomes of C. lassenensis and C. lemmonii and performed comparative genomic analyses including gene content, functional enrichment, and phylogenetic placement. The genome of C. lassenensis, although slightly smaller than that of C. lemmonii, shows higher gene content, with different patterns of gene duplication. Functional genomic analysis revealed distinct enrichment patterns in the two species, with metabolic and transport functions enriched in C. lassenensis versus cellular organization in C. lemmonii. The taxa also show divergence in peptidase and CAZyme distributions, as well as in KAI2d proteins involved in strigolactone perception. Population-level validation using diagnostic gene markers across multiple individuals from geographically separate populations confirmed stable genomic differences. Our results support the recognition of C. lassenensis as a distinct species and underscore the need for measures to ensure its conservation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"647-655"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146121204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lianming Du, Lian Wang, Jiahao Chen, Songwen Tan, Peng Guo, Qin Liu
{"title":"Reference genome assembly of the mandarin rat snake (Euprepiophis mandarinus).","authors":"Lianming Du, Lian Wang, Jiahao Chen, Songwen Tan, Peng Guo, Qin Liu","doi":"10.1093/jhered/esag029","DOIUrl":"10.1093/jhered/esag029","url":null,"abstract":"<p><p>The mandarin rat snake (Euprepiophis mandarinus), a widely distributed and ecologically important species endemic to Asia, serves as an ideal candidate for establishing a reference genome for the genus Euprepiophis. This is due to its wide distribution, and its overlapping distribution with and morphological similarities to the endangered Euprepiophis perlaceus. Here we present the first high-quality, chromosome-level reference genome of E. mandarinus, assembled using PacBio HiFi long-read and Hi-C sequencing. The final assembly has a length of 1.65 Gb contained in 56 scaffolds, a scaffold N50 of 210 Mb, a benchmarking universal single-copy orthologs completeness of 98.2%, and 99.12% bases anchored onto 19 chromosomes. We identified 22,332 protein-coding genes, 3,440 noncoding RNAs, and approximately 7 million repeat elements accounting for 58.38% of the assembled genome. This reference genome provides a valuable resource for taxonomic, phylogenetic, comparative, and conservation studies of the genus Euprepiophis.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"834-842"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147516994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alasdair J Taylor, Nicole M Foley, Isabella R Childers, William J Murphy, Scott V Dindot
{"title":"A de novo genome assembly of an Angelman syndrome pig (Sus scrofa domesticus) model to resolve SNHG14.","authors":"Alasdair J Taylor, Nicole M Foley, Isabella R Childers, William J Murphy, Scott V Dindot","doi":"10.1093/jhered/esag019","DOIUrl":"10.1093/jhered/esag019","url":null,"abstract":"<p><p>Pigs (Sus scrofa domesticus) are used as biomedical and preclinical models for their comparable anatomy, physiology, and neurodevelopment to humans. Angelman syndrome is a rare genetic neurodevelopmental disorder, caused by the loss of the maternal Ubiquitin protein ligase E3A (UBE3A) allele, that was recently modeled and characterized in Yorkshire/Landrace pigs. The paternal UBE3A allele is intact but silenced in neurons of the central nervous system by the long non-coding RNA and polycistronic transcription unit Small Nuclear Host Gene 14 (SNHG14). Targeting SNHG14 to reactivate the paternal UBE3A allele is a therapeutic approach for Angelman syndrome currently under investigation. However, the current pig reference genome (Sscrofa11.1) misassembles the highly complex SNHG14 locus, hindering accurate targeting and regulatory studies in this model. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly for an Angelman syndrome pig model and fully resolved the SNHG14 locus without gaps. We show that the current pig reference genome contains extensive tandem repeat collapse within SNHG14, misrepresenting both its size and organization. The resolved locus reveals a previously unknown bipartite architecture of SNORD116 tandem repeats, comprising two distinct groups in both sequence and structure. This resolution and genome resource remove the genomic hindrance to SNHG14-focused studies in pigs.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"918-926"},"PeriodicalIF":2.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147379582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}