Journal of Heredity最新文献

{"title":"Dissecting Genotype-Environment interactions with functional implications for parental selection in Cannabis Breeding.","authors":"Anna Halpin-McCormick, Robert Thomson, Robert C Clarke, Jeffrey Neyhart, Michael B Kantar","doi":"10.1093/jhered/esaf048","DOIUrl":"https://doi.org/10.1093/jhered/esaf048","url":null,"abstract":"<p><p>As climate variability continues to impact agricultural systems, identifying genetic factors that contribute to environmental adaptation will be essential for optimizing breeding strategies for the development of climate resilient varieties. Through human cultivation and naturalization, Cannabis sativa has dispersed globally, adapting to a range of environmental conditions across various climates and latitudes. We combined raw data from multiple public sources to conduct an Environmental Genomic Selection (EGS) analysis on 149 C. sativa samples, to assess how different populations of Cannabis relate to their environmental conditions. Exploring Genomic Estimated Adaptive Values (GEAVs) across bioclimatic variables can facilitate the selection of parental material adapted for a specific condition. We further explore potential mechanisms of local adaptation by characterizing the individual marker effects which underlie these GEAV scores. To facilitate interpretation, we used previously described genetic groupings (Basal, Hemp-type, Drug-type feral, Drug-type). Distinct patterns emerged across population groups with the drug-type (Type I) group showing consistently narrow GEAV ranges, whereas the drug-type feral group showed a broader distribution, often having high GEAVs for precipitation variables. A key climate variable difference was seen in monthly average values, revealing a seasonal response to precipitation in drug-type feral samples. By examining monthly differences in marker effects associated with precipitation, we identify potential genomic mechanisms underlying seasonal environmental responses in drug-type feral samples. As these samples are sourced from geographic regions that have seasonal monsoons, they may have traits conferring flood tolerance (water logging) that could be introgressed into other backgrounds. The basal group also exhibited broad GEAV ranges across several bioclimatic traits, indicating they may be a valuable genetic resource for introgression to enhance environmental resilience. These findings underscore the importance of incorporating diverse germplasm into breeding programs to improve Cannabis resilience to changing environmental conditions. EGS provides a fast method to enable climate-conscious parental selection while gaining mechanistic information. Ultimately, we hope that such a strategy could support the development of climate-resilient Cannabis varieties tailored to both current and future environmental challenges.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621143","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":"High-quality genome assembly of the endemic, threatened, White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.","authors":"K L Vinay, Chiti Arvind, Naman Goyal, V V Robin","doi":"10.1093/jhered/esaf049","DOIUrl":"https://doi.org/10.1093/jhered/esaf049","url":null,"abstract":"<p><p>The White-bellied Sholakili (Sholicola albiventris) is an endemic, elevationally restricted species occurring in the Shola Sky Islands of the Western Ghats of India. This unique understory bird, with a complex vocal repertoire, exhibits impacts of anthropogenic habitat fragmentation on gene flow. Here, we present the first genome assembly for Sholicola albiventris, which was assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.083 Gbp, consisting of 975 scaffolds with an N50 of 68.64 Mbp and L50 of 6. Our genome assembly's completeness is supported by a number of metrics - high BUSCOs (99.9%), and a total of 4887 ultraconserved element (UCE) loci retrieved. We also report the complete mitochondrial genome comprising 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. We identified 11.82% of the nuclear genome as repetitive and 36,000 putative genes, with 12017 genes functionally annotated. Our assembly showed a great synteny between Taeniopygia guttata and Gallus gallus chromosome level assemblies. This reference will be pivotal for investigating landscape connectivity, sub-population genetics, local adaptation, and conservation genetics of this high-elevation, range-restricted endemic bird species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621144","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 genome assembly for Lahontan Cutthroat Trout, Oncorhynchus clarkii henshawi.","authors":"Cheyenne Y Payne, Merly Escalona, Shannon R Kieran Blair, Amanda J Finger, Richard E Green, Devon Pearse, Jeff Rodzen, John Carlos Garza","doi":"10.1093/jhered/esaf050","DOIUrl":"https://doi.org/10.1093/jhered/esaf050","url":null,"abstract":"<p><p>Cutthroat Trout (Oncorhynchus clarkii) are diverse Pacific salmonids widely distributed throughout western North America. Distinct lineages of Cutthroat Trout have been defined based on morphology, geography, and genetic differences. Several of these, including Lahontan Cutthroat Trout (Oncorhynchus clarkii henshawi), are classified as threatened or in danger of extinction. Despite their precarious conservation status, few genomic resources have been developed for these lineages. In an effort to promote the development and application of genomic approaches for research and conservation of this group, we present the first high-quality reference genome for Lahontan Cutthroat Trout. We use this genome assembly to describe genomic synteny and structural rearrangements with their sister species, Rainbow Trout (O. mykiss), as well as with the diverged Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) lineage.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610323","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 Snow Leopard, Panthera Uncia.","authors":"Plasil Martin, Winter Sven, Stejskalova Karla, Vychodilova Leona, Jelinek April, Futas Jan, Burger A Pamela, Horin Petr","doi":"10.1093/jhered/esaf046","DOIUrl":"https://doi.org/10.1093/jhered/esaf046","url":null,"abstract":"<p><p>The snow leopard (Panthera uncia), a vulnerable big cat native to Central Asia, faces an ongoing population decline due to habitat loss and human activities. Despite its conservation importance, genomic resources for this species remain limited. High-quality reference genomes are essential for assessing genetic diversity, structural variation, and evolutionary history. To address this gap, we have generated a long-read-based and proximity-ligation scaffolded de novo genome assembly of a male snow leopard. The final assembly has a total length of 2.46 Gb in 280 scaffolds, of which the 19 largest correspond to the 18 autosomes and the X chromosome. The scaffold N50 is 145.76 Mb, and the L50 is seven scaffolds. BUSCO and compleasm scores are 98.7% and 98.9% of identified Carnivora orthologs. Telomeric sequences were identified on at least one end of 18 out of 19 chromosomes. Scaffolds corresponding to the Y chromosome were identified and mapped. Additionally, the assembly's annotation identified a repeat content of 42.27% and 25 391 genes. We produced a high-quality, long-read-based chromosome-level assembly of a male snow leopard, as evidenced by the data above. As a first assembly of a male genome, it can serve as a suitable reference genome for the species. The Y chromosome scaffolds provide a glimpse into the chromosome organization and interspecies differences.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592966","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":"Correction to: Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations.","authors":"","doi":"10.1093/jhered/esaf044","DOIUrl":"https://doi.org/10.1093/jhered/esaf044","url":null,"abstract":"","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585651","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 genome assembly for a textbook mammalian study species, the California ground squirrel (Otospermophilus beecheyi).","authors":"Matthew L Holding, Sree Rohit Raj Kolora, Jennifer E Smith, Shana L McDevitt, Peter H Sudmant, Rebecca D Tarvin","doi":"10.1093/jhered/esaf045","DOIUrl":"https://doi.org/10.1093/jhered/esaf045","url":null,"abstract":"<p><p>Squirrels (Rodentia; Sciuridae) are a well-known and diverse group of rodents, including the charismatic ground-dwelling members of the Tribe Marmotini. In particular, the California ground squirrel (Otospermophilus beecheyi) is an emerging model system for the study of social and risk-sensitive behaviors in a rapidly changing world, as well as the physiology of resistance to snake venoms. To complement extensive natural history information for O. beecheyi, we provide a chromosome-scale genome to facilitate molecular studies focused on the genetic basis of ecologically important traits, population genetics, comparative genomics, and social evolution. The final scaffolded genome was 2.27 Gb contained in 9960 contigs and placed into 1383 scaffolds. The scaffold N50 was just over 125 Mb. We used the presence of 10 248 complete genes detected by BUSCO v5 specifically to compare broad patterns of chromosomal synteny between chromosomal scaffolds for O. beecheyi and two other sciurid rodents. The recovered pattern of synteny suggests several fusion and fission events for O. beecheyi in relation to the other two species. Taken together, this new information should advance our understanding of O. beecheyi and comparative studies of mammalian genomic biology and evolution.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546229","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":"Near-Gapless Genome Assemblies of the Domestic Cat (Felis silvestris catus) and the African Serval (Leptailurus serval) Derived from Trio-Binning.","authors":"Andrew J Harris, Terje Raudsepp, Nicole M Foley, Wesley C Warren, Leslie A Lyons, William J Murphy","doi":"10.1093/jhered/esaf047","DOIUrl":"https://doi.org/10.1093/jhered/esaf047","url":null,"abstract":"<p><p>The Savannah cat is a popular cat breed derived from an interspecific hybrid cross between the domestic cat (Felis silvestris catus) and the African serval (Leptailurus serval). Within the family Felidae, Savannahs represent the most divergent interspecific hybrid breed, with ~13 million years separating the parental species. Here, we apply trio-binning of an F1 interspecific hybrid to achieve near-gapless chromosome-level genome assemblies for the domestic cat and serval. Using a hybrid assembly approach combining PacBio HiFi and CLR reads, we generated domestic cat and serval genome assemblies, each comprising ~2.5 Gb of sequence with contig N50s of 107.4Mb and 112.3Mb, respectively. We anchored >99% of the contigs into 19 chromosome-length scaffolds for each species, supported by base-quality (QV) metrics exceeding 61. The serval reference genome assembly represents the first for the species, providing an essential resource for future population and comparative genomic studies. The new domestic cat assembly adds an average of 36-Mb of novel sequence to chromosomes missing in earlier long-read assemblies. These sequence gains include the first resolution of multi-megabase FA-SAT macrosatellite arrays with putative functions in cell cycle regulation. These new assemblies add to the growing list of highly complete chromosome-level felid genomes and improve our understanding of complex genome architecture and satellite evolution within mammals.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546231","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":"Correction to: Forensic assessment of kinship, genomic ancestry, and natural history of an iconic tiger of Harlem, New York City.","authors":"","doi":"10.1093/jhered/esaf043","DOIUrl":"https://doi.org/10.1093/jhered/esaf043","url":null,"abstract":"","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546230","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":"Small snakes, big cities: population genetics of urban Dekay's brown snake (Storeria dekayi) in New Jersey.","authors":"Tianqi Huang, Isaac Overcast, Arianna Kuhn, Peter J Morin, Sara Ruane","doi":"10.1093/jhered/esaf042","DOIUrl":"https://doi.org/10.1093/jhered/esaf042","url":null,"abstract":"<p><p>Despite the unprecedented rate of global urbanization, a diverse array of taxa are supported in urban areas. However, the long-term persistence of urban wildlife cannot be guaranteed due to the various adverse effects that come with urbanization, such as resource depletion and reduced gene flow. Accordingly, it is imperative to evaluate the health and viability of urban wildlife, particularly of species that are underrepresented in the existing literature, like herpetofauna. Genomic techniques can provide critical insights into urban wildlife health and population viability. Here, we generated a ddRADseq dataset of 162 Dekay's brown snakes (Storeria dekayi) among 11 locations with different urbanization magnitudes across New Jersey, USA, and examined the population genetic patterns of this common urban reptile. While genetic diversity was not severely reduced within those populations, we uncovered the presence of genetic differentiation and structuring across them, especially for those from the most urbanized areas. Deviations of interpopulation structure from their geographic distributions might reflect either habitat alteration or human intervention in recent history. Landscape genetic analyses revealed the presence of an isolation-by-distance relationship that was only significant within a short spatial distance of 1500 m. Most urban populations also displayed lower-than-expected historic migration and diversity rates, but some remained genetically connected and diverse. To conclude, our study can serve as a useful guide for population genomic studies on urban herpetofauna. Based on our results, urbanization is likely to impact interpopulation genetic connectivity, but to have limited effects on intrapopulation genetic diversity of small-bodied, terrestrial urban dwellers.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487155","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 reference genome assembly for Gilbert's skink Plestiodon gilberti.","authors":"Jonathan Q Richmond, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Benjamin R Karin, Robert D Cooper, Robert N Fisher, Ian J Wang, H Bradley Shaffer","doi":"10.1093/jhered/esaf040","DOIUrl":"https://doi.org/10.1093/jhered/esaf040","url":null,"abstract":"<p><p>Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert's skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project (CCGP). This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization events present challenges to disentangling the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the CCGP, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531180","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}