Journal of Heredity最新文献

{"title":"Extraordinary variation in radiation tolerance: mechanisms and evolution.","authors":"Erin S Kelleher, Shahrzad Hajiarbabi, Llewellyn Green","doi":"10.1093/jhered/esaf015","DOIUrl":"https://doi.org/10.1093/jhered/esaf015","url":null,"abstract":"<p><p>Ionizing radiation is a potent environmental mutagen, producing damaged bases and single and double-stranded DNA breaks. Acute high-dose radiation exposure is therefore toxic, causing cellular and organismal mortality, while lower doses can give rise to high mutation rates and cancer. Radiation sensitivity furthermore varies dramatically between organisms and cell types, with certain organisms exhibiting extreme tolerance to ionizing radiation. It is puzzling however, how such radiotolerance evolved in nature, as toxic radiation doses are not observed outside of medical and nuclear settings. In this review, we explore the mechanisms and evolution of extraordinary radiotolerance in metazoans. We contrast two extensively studied genetic models, mammals and Caenorhabditis elegans, as well as two lineages known to tolerate extreme radiation when compared to closely related species: naked mole rats and tardigrades. We describe similar strategies employed by these disparate lineages to protect DNA, repair DNA, and attenuate cellular responses following radiation exposure. We further discuss how these mechanisms may have evolved in response to other extreme conditions tolerated by each species in their natural environment, giving rise to radiotolerance as a correlated response.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175865","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}

{"title":"Chromosomal Fusions Reshape Gene Expression and Environmental Responses in Corbicula Clams.","authors":"Yu Wang, Yitian Bai, Gang Ni, Shikai Liu, Lingfeng Kong, Qi Li","doi":"10.1093/jhered/esaf030","DOIUrl":"https://doi.org/10.1093/jhered/esaf030","url":null,"abstract":"<p><p>Genome-structural evolution on a large scale is prevalent in various organisms. The role of genome-structural rearrangements, including chromosome fusions, has been revealed in genome evolution and species divergence. However, the empirical evidence in adaptation remains debated at the current time. We investigated the phylogenetic relationship, genomic divergence and environmental associations of closely related Asian clams: the freshwater species Corbicula fluminea and brackish-freshwater species Corbicula mortoni. The chromosome-level genome assembly of brackish-freshwater C. mortoni using single-molecule and Hi-C sequencing revealed a chromosome-scale rearrangement relative to freshwater C. fluminea. Strikingly, genomic characterization studies including outgroup species Archivesica marissinica indicated two independent fusion events in these closely related species. Transcriptome analysis under salinity stress identified differentially expressed genes (DEGs) and revealed a significant enrichment of significantly down-regulated genes (SDGs) on the fused chromosome of C. mortoni, suggesting possible regulatory shifts associated with fusion. In summary, our genomic and transcriptomic analyses document important chromosome-scale evolutionary events during Corbicula speciation and provides insights into the relationship between genomic reorganization and gene regulation in response to environmental variation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082163","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}

{"title":"A Chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica.","authors":"Nicolas Alexandre, Jennifer Balacco, Tatiana Tilley, Linelle Abueg, Nadolina Brajuka, Lucas R Moreira, Conor Whelan, Erika Schwarz Taylor, Erich D Jarvis, Olivier Fedrigo, Beth Shapiro, Anna L Keyte","doi":"10.1093/jhered/esaf031","DOIUrl":"https://doi.org/10.1093/jhered/esaf031","url":null,"abstract":"<p><p>The Nicobar pigeon (Caloenas nicobarica), the closest living relative of the extinct Dodo (Raphus cucullatus), is endemic to Southeast Asia with a fragmented distribution across numerous small islands. It suffers from habitat loss, hunting, and predation from invasive species, resulting in its classification as Near-Threatened by the International Union for the Conservation of Nature (IUCN). We have generated a haplotype-resolved and chromosome-level genome assembly of the Nicobar pigeon using a combination of PacBio HiFi long-read sequencing and Arima Hi-C chromatin interaction mapping. This assembly includes two haplotypes, each spanning approximately 1.2 Gb. Haplotype 1 has a contig N50 of 25.2 Mb and a scaffold N50 of 79.7 Mb, while haplotype 2 has a contig N50 of 24.7 Mb and a scaffold N50 of 107.9 Mb. As the first high-quality genome assembly of any bird in the Columbidae Indo-Pacific clade, this resource provides valuable insights for phylogenetic studies. Furthermore, the phylogenetic proximity of the Nicobar pigeon to the Dodo (Raphus cucullatus) and the Rodrigues Solitaire (Pezophaps solitaria) offers a unique opportunity to study these extinct species, making this assembly a critical resource for evolutionary studies. It also offers a unique model for studying genetic diversity, adaptation, and speciation in island environments. This genomic resource will not only enhance our understanding of the evolutionary history of the Nicobar pigeon but also serves as a valuable tool for future conservation efforts aimed at preserving this unique species and its fragile island ecosystem.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082160","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}

{"title":"Genome assembly of the endangered Santa Marta Harlequin Toad, Atelopus laetissimus, endemic to the Sierra Nevada de Santa Marta of Colombia.","authors":"Victor L N Araújo, José H Grau, Luis Alberto Rueda-Solano, José D Barros-Castañeda, Sandra V Flechas, Andrew J Crawford","doi":"10.1093/jhered/esaf029","DOIUrl":"https://doi.org/10.1093/jhered/esaf029","url":null,"abstract":"<p><p>Despite the critical conservation status of many harlequin toads (Anura: Bufonidae: Atelopus) and their significance in elucidating the impacts of emerging diseases on amphibians, genomic data for this genus are scarce. Here, we present a de novo genome assembly of the Santa Marta Harlequin Toad, Atelopus laetissimus, using PacBio HiFi sequencing data, representing the first published Atelopus genome assembly and only the second amphibian genome assembly from Colombia. The assembly consists of 1,487 contigs at 35X coverage with an N50 of 31 Mb and a total length of 3.5 Gb. A Tetrapoda BUSCO score of 92% suggests our assembly is very nearly complete. Analysis revealed a high repeat content, with 70% of the genome consisting of interspersed repeats. This high-contiguity draft assembly will drive the search for a possible genetic basis of pathogen resistance in these endangered toads of the Sierra Nevada de Santa Marta, as well as facilitate ongoing evolutionary studies.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082166","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}

{"title":"A chromosome-level genome assembly of the Chinese herring (Ilisha elongata) uncovered its population dynamics and genes related to lipid metabolism.","authors":"Tianqin Wu, Jiantao Hu, Vanthu Giap, Qian Wang, Liang Lu, Chenhong Li","doi":"10.1093/jhered/esaf028","DOIUrl":"https://doi.org/10.1093/jhered/esaf028","url":null,"abstract":"<p><p>The Chinese herring (Ilisha elongata) is an economically important clupeiform fish, mostly found along the coast of China and Japan in the western Pacific Ocean. Overfishing and climate change have caused a substantial decline in its annual catch, which may have impacted its population size and structure. Here, we present a chromosome-level genome assembly of the Chinese herring, generated using a combination of Nanopore sequencing, Illumina sequencing, and high-throughput chromatin conformation capture (Hi-C) technologies. The total length of this assembly is802.47 Mbp, anchored to 24 chromosomes, with contig N50 and scaffold N50 values of 13.22 Mbpand 33.10 Mbp, respectively. BUSCO analysis indicated high completeness of this assembly, with 94.9% of universal single-copy orthologs. Analysis of resequencing samples from various coastal regions of China and Japan revealed four distinct genetic populations of Chinese herring along the East Asian coast. The Dandong population (Yellow Sea) diverged earliest, exhibiting unique genetic structures and selective sweep signals, whereas the other three populations expanded from a tropical South China Sea ancestral population to the East China Sea and to Japanese waters. Among 23,366 protein-coding genes, several families related to metabolism of very-long-chain unsaturated fatty acids are particularly contracted compared to the American shad. Additionally, several genes associated with fatty acid synthesis formation have undergone accelerated positive selection. These findings may explain the differential fatty acid ratios in marine versus riverine migratory clupeiforms. This high-quality genome assembly of the Chinese herring may provide valuable resources for comparative study of coastal fishes and benefit the development of a sustainable management strategy for fisheries of the Chinese herring.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058365","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}

{"title":"A Chromosome-level Genome Assembly of the Beavertail Cactus, Opuntia basilaris.","authors":"Susan Fawcett, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Eric Beraut, William Seligmann, Colin W Fairbairn, Erin Toffelmier, Courtney Miller, H Bradley Shaffer, Lucas C Majure","doi":"10.1093/jhered/esaf027","DOIUrl":"https://doi.org/10.1093/jhered/esaf027","url":null,"abstract":"<p><p>Few genomic resources currently exist for the American endemic family Cactaceae, a group of around 1850 species, which are world renowned for their amazing growth forms and succulent habits. These icons of arid landscapes across the Americas are threatened in many parts of their range, including in parts of California, and developing more comprehensive genomic data will aid efforts to better understand and preserve these plants. We sequenced and assembled the genome of the beavertail cactus, Opuntia basilaris, which is represented by three varieties in California, one of which is threatened, and another endangered. The genome assembly has a BUSCO complete score of 98.1%, and a total scaffold length of 980 Mb, with a scaffold N50 length of 83 Mb. The genome size of diploid O. basilaris is markedly smaller than other diploid members of Cactaceae that have been assembled to date. This is the first nuclear genome sequenced in subfamily Opuntioideae and the most complete nuclear genome for Cactaceae to date and will lay the foundation for future genomic work across the biologically and taxonomically complicated prickly pear cacti.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065078","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}

{"title":"A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.","authors":"Rishi De-Kayne, Stacy Li, Merly Escalona, Runyang Nicolas Lou, Gregory L Owens, Sree Rohit Raj Kolora, Conner Jainese, Katelin Seeto, Merit McCrea, Oanh Nguyen, Noravit Chumchim, Ruta M Sahasrabudhe, Colin W Fairbairn, Richard E Green, William E Seligmann, Milton Love, Peter H Sudmant","doi":"10.1093/jhered/esaf026","DOIUrl":"https://doi.org/10.1093/jhered/esaf026","url":null,"abstract":"<p><p>Rockfishes (genus Sebastes) are one of the most diverse clades amongst teleosts (ray-finned fishes). The genus includes more than 110 species which are distributed broadly across the North Pacific Ocean, North and South Atlantic Ocean, and Southeastern Pacific Ocean. Rockfishes exhibit particularly high diversity along the western coast of the United States, where their abundance plays a critical role in local marine ecosystems and fisheries. Sebastes paucispinis (\"bocaccio\") is a rockfish species most commonly found off the coast of California. In 2005, Bocaccio were federally declared overfished following massive depletion by commercial and recreational fisheries from the 1980s to early 2000s. Implementation of significant restrictions have bolstered recovery of critical rockfish populations along the California and Oregon coasts, but the impact of anthropogenic stressors on bocaccio, and other Sebastes species, has yet to be fully evaluated. Here, we present the first de novo reference-quality genome assembly of Sebastes paucispinis, as part of the California Conservation Genomics Project (CCGP).</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057898","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}

{"title":"Reference genome of the Gophersnake, Pituophis catenifer (Serpentes: Colubridae).","authors":"Jesse L Grismer, Merly Escalona, Courtney Miller, Mohan P A Marimuthu, Oanh Nguyen, Eric Beraut, Sam Sacco, Erin Toffelmier, Robert Cooper, Ian J Wang, Robert N Fisher, H Bradley Shaffer","doi":"10.1093/jhered/esaf024","DOIUrl":"https://doi.org/10.1093/jhered/esaf024","url":null,"abstract":"<p><p>The Gophersnake, Pituophis catenifer, is a habitat generalist that ranges throughout the western half of the United Sates and southward into México. Five of the six subspecies, P. catenifer affinis (Sonoran Gophersnake), P. catenifer annectens (San Diego Gophersnake), P. catenifer catenifer (Pacific Gophersnake), P. catenifer deserticola (Great Basin Gophersanke), and P. catenifer pumilus (Santa Cruz Island Gophersnake), occur in California and span virtually all the state's diverse terrestrial habitats. These subspecies are ecologically and morphologically distinct from one another, although existing genetic data indicate there is genetic admixture across some of their contact zones. Given that these subspecies occur in such different environments they will not all respond to climate change and anthropogenic stressors equally. Here, we report a new, chromosome-level assembly of P. catenifer as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 426 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.5 Mb, a scaffold N50 of 161 Mb, and BUSCO completeness score of 95.3%. This genome will be a foundational resource for future studies on the conservation, adaptation, biogeography, and the systematics of P. catenifer.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999616","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}

{"title":"Life history and chromosome organization determine chemoreceptor gene expression in rattlesnakes.","authors":"Michael P Hogan, Matthew L Holding, Gunnar S Nystrom, Kylie C Lawrence, Emilie M Broussard, Schyler A Ellsworth, Andrew J Mason, Mark J Margres, H Lisle Gibbs, Christopher L Parkinson, Darin R Rokyta","doi":"10.1093/jhered/esae078","DOIUrl":"https://doi.org/10.1093/jhered/esae078","url":null,"abstract":"<p><p>Predatory species who hunt for their prey rely on a suite of integrated characters, including sensory traits that are also used for nonpredatory behaviors. Linking the evolution of sensory traits to specific selection pressures therefore requires a deep understanding of the underlying genetics and molecular mechanisms producing these complex phenotypes. However, this relationship remains poorly understood for complex sensory systems that consist of proteins encoded by large gene families. The chemosensory repertoire of rattlesnakes includes hundreds of type-2 vomeronasal receptors and olfactory receptors, representing the two largest gene families found in the genome. To investigate the biological importance of this chemoreceptor diversity, we assessed gene expression in the eastern diamondback rattlesnake (Crotalus adamanteus) and identified sex- and age-biased genes. We found type-2 vomeronasal receptor expression in the vomeronasal epithelium was limited to juvenile snakes, suggesting the sensory programming of this tissue may be correlated with early life development. In the olfactory epithelium, we found subtle expression biases that were more indicative of life history rather than development. We also found transcriptional evidence for dosage compensation of sex-linked genes and trait integration in the expression of transcription factors. We overlay our molecular characterizations in Crotalus adamanteus onto updated olfactory receptor and type-2 vomeronasal receptor phylogenies, providing a genetic road map for future research on these receptors. Finally, we investigated the deeper macroevolutionary context of the most highly expressed type-2 vomeronasal receptor gene spanning the rise of tetrapods and estimated the strength of positive selection for individual amino acid residues in the predicted protein structure. We hypothesize that this gene may have evolved as a conserved signaling subunit to ensure consistent G-protein coupled receptor functionality, potentially relaxing signaling constraints on other type-2 vomeronasal receptor paralogs and promoting ligand binding specificity.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057397","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}

{"title":"Genomic data from the extinct California brown bear suggests a source population for reintroduction to California.","authors":"T Brock Wooldridge, Ming-Shan Wang, Nedda F Saremi, Joshua D Kapp, Katherine L Moon, Peter D Heintzman, John P Dumbacher, Peter S Alagona, Barney Long, Beth Shapiro","doi":"10.1093/jhered/esaf018","DOIUrl":"https://doi.org/10.1093/jhered/esaf018","url":null,"abstract":"<p><p>California brown bears, also known as California grizzlies or golden bears, are an extinct group that once thrived in North America's western coastal habitats. Despite being common in the region as recently as the early 19th century, intense poisoning, trapping, and hunting led to their extinction by 1924. Today, California is emerging as a candidate for brown bear reintroduction as a component of larger ecosystem restoration efforts. Questions remain, however, about whether living brown bears are suitable proxies for the bears that once inhabited California. While recent work suggests that brown bears from California were similar in size and overall diet to brown bears living today in continental North America, the a) extent to which California bears were genetically differentiated from other populations, and b) what this means for proposed reintroductions, remain outstanding questions. We generated genomes from two of the last living California brown bears and compared them to genomes from living brown bears. Genomic estimates of divergence time combined with radiocarbon dating points towards brown bears arriving recently to California, having diverged within the last 10,000 years from a common ancestor with brown bears found today in Yellowstone National Park, Wyoming. This timeline, the overall genetic similarity between the California and Yellowstone populations, and the strong pattern of isolation-by-distance we observe all suggest that no closer living relatives are likely to be found. If genetic background is to be a consideration for reintroduction efforts in California, brown bears from Yellowstone might serve as a source population.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045298","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}