Journal of Heredity最新文献

Correction to: A haplotype-resolved genome assembly of the bocaccio rockfish. 更正：bocaccio岩鱼的单倍型解决基因组组装。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-08 DOI: 10.1093/jhered/esaf078

引用次数: 0

A Reference Genome for Colusa Grass, Neostapfia colusana, a Threatened and Endangered California Vernal Pool Plant. 一种受威胁和濒临灭绝的加利福尼亚春池植物——Colusa Grass， Neostapfia colusana的参考基因组。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-07 DOI: 10.1093/jhered/esaf075

Lillie K Pennington, Merly Escalona, Daniel J Toews, Noravit Chumchim, Robert Cooper, Colin W Fairbairn, Mohan P A Marimuthu, Courtney Miller, Oanh H Nguyen, Dannise Ruiz-Ramos, William E Seligmann, Molly Stephens, Erin Toffelmeier, H Bradley Shaffer, Rachel S Meyer, Jason P Sexton

{"title":"A Reference Genome for Colusa Grass, Neostapfia colusana, a Threatened and Endangered California Vernal Pool Plant.","authors":"Lillie K Pennington, Merly Escalona, Daniel J Toews, Noravit Chumchim, Robert Cooper, Colin W Fairbairn, Mohan P A Marimuthu, Courtney Miller, Oanh H Nguyen, Dannise Ruiz-Ramos, William E Seligmann, Molly Stephens, Erin Toffelmeier, H Bradley Shaffer, Rachel S Meyer, Jason P Sexton","doi":"10.1093/jhered/esaf075","DOIUrl":"https://doi.org/10.1093/jhered/esaf075","url":null,"abstract":"Colusa grass, Neostapfia colusana, is a listed California endangered plant endemic to the vernal pools of California. Vernal pool habitat is highly degraded and threatened by further anthropological development, with only 10% of its historical range remaining. With only 42 confirmed extant populations, it is a major conservation concern to understand patterns of genomic diversity. Here we report the first complete genome assembly of Colusa grass. The assembly includes two haplotypes: haplotype one spans 2.13 Gb with contig N50 of 10.62 Mb, scaffold N50 of 112.31 Mb, and BUSCO completeness of 98.1%. Haplotype two spans 2.04 Gb with contig N50 of 10.05 Mb and scaffold N50 of 138.31 Mb, with a BUSCO completeness of 97.6%. This genome assembly will allow for in-depth analysis of genomic variation and gene flow in populations of this threatened grass and will be a major asset to studies supporting its conservation. This genome was assembled as part of the California Conservation Genomics Project (CCGP), which contributes to a collection of resources and tools to support state-wide conservation efforts.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240267","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}

引用次数: 0

Reference Genome of an Irruptive Migrant, the Pine Siskin (Spinus pinus). 入侵候鸟松雀（Spinus pinus）的参考基因组。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-07 DOI: 10.1093/jhered/esaf076

Jair Cortez, Joel W G Slade, Tricia A Van Laar

{"title":"Reference Genome of an Irruptive Migrant, the Pine Siskin (Spinus pinus).","authors":"Jair Cortez, Joel W G Slade, Tricia A Van Laar","doi":"10.1093/jhered/esaf076","DOIUrl":"https://doi.org/10.1093/jhered/esaf076","url":null,"abstract":"Pine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de novo using long-read sequencing and scaffolded with a reference-guided approach. Synteny analyses also showed that our assembly can reliably reveal genomic rearrangements relative to other finches. Using reference-based annotation, we identified thousands of protein-coding genes, including loci relevant to metabolism and immune function that demonstrate the utility of this assembly for downstream studies. We also found evidence of gene duplications and pseudogenization in immune loci, showing the utility of our assembly for immunogenetic studies. Our analysis provides the first genome-wide view of transposable element (TE) activity in Spinus, revealing multiple bursts of long terminal repeat (LTR) retrotransposon expansion, including a recent one that coincides with the estimated diversification of North and South American siskins approximately 2.7 million years ago. We also detected putative lineage-specific LTR sequences, suggesting recent or ongoing TE diversification. This assembly fills a critical gap in passerine genomic resources and provides a resource for comparative, transcriptomic, and population-level studies across species with diverse migratory strategies.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240314","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}

引用次数: 0

Genomic Architecture of the Pole Borer, Neandra brunnea (Cerambycidae: Parandrinae), Sheds Light on the Evolution of Wood-Feeding in Longhorn Beetles. 极孔虫，Neandra brunnea（天牛科：天牛科）的基因组结构，揭示了长角甲虫取食木材的进化。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-04 DOI: 10.1093/jhered/esaf080

Terrence Sylvester, Richard Adams, Robert F Mitchell, Rongrong Shen, Duane D McKenna

{"title":"Genomic Architecture of the Pole Borer, Neandra brunnea (Cerambycidae: Parandrinae), Sheds Light on the Evolution of Wood-Feeding in Longhorn Beetles.","authors":"Terrence Sylvester, Richard Adams, Robert F Mitchell, Rongrong Shen, Duane D McKenna","doi":"10.1093/jhered/esaf080","DOIUrl":"https://doi.org/10.1093/jhered/esaf080","url":null,"abstract":"Neandra brunnea, commonly known as the pole borer, is a species of wood-boring (xylophagous) longhorn beetle (family Cerambycidae) found throughout most of eastern North America. We sequenced, assembled and annotated the genome of N. brunnea and compared it to publicly available genomes of other Cerambycidae. The 1.23 Gb N. brunnea genome assembly was distributed across 78 contigs, with an N50 of 38.88 Mb and largest contig of 74.28 Mb. Most of the genome was comprised of repetitive sequences, with 81.39% comprising interspersed repeats. Most (99.7%) of the expected orthologous genes (BUSCOs) were present and fully assembled, with only 2.5 % duplicated. The genome annotation identified 13,003 genes (15,574 transcripts), including 301 putative horizontally transferred loci from a diversity of both prokaryotic and eukaryotic donors. The assembled mitochondrial genome is relatively large at 17 kb and shows an unusual repeating array of d-loop segments. As the first representative of the longhorn beetle subfamily Parandrinae with a sequenced genome, N. brunnea provides an important new point of reference for the comparative study of beetle genomes and a further resource for studies of the evolution and genomic basis of xylophagy.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226418","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}

引用次数: 0

Reduced gene expression and missense mutations in the transporter protein SLC45A2 in a hypopigmented egyptian rousette fruit bat (Rousettus aegyptiacus). 在低色素的埃及果蝠（Rousettus aegyptiacus）中，转运蛋白SLC45A2的基因表达和错义突变减少。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-03 DOI: 10.1093/jhered/esaf070

Kalina T J Davies, Rosie Drinkwater, Liliana M Dávalos, Nicolas Nesi, Mads F Bertelsen, Stephen J Rossiter

{"title":"Reduced gene expression and missense mutations in the transporter protein SLC45A2 in a hypopigmented egyptian rousette fruit bat (Rousettus aegyptiacus).","authors":"Kalina T J Davies, Rosie Drinkwater, Liliana M Dávalos, Nicolas Nesi, Mads F Bertelsen, Stephen J Rossiter","doi":"10.1093/jhered/esaf070","DOIUrl":"https://doi.org/10.1093/jhered/esaf070","url":null,"abstract":"Oculocutaneous albinism-characterised by absent or decreased melanin in the skin, eyes and hair-often co-occurs with sensory, skin and immunity disorders. The genetic basis of albinism in humans is complex, with many loci implicated in multiple forms of the disorder. Less is known about the underlying genetic causes of albinism and leucism in other species, and cross-species studies of the molecular correlates of hypopigmentation could highlight common and conserved pathways underlying mammalian pigmentation disorders. We characterise the putative causal loci of reduced pigmentation in an Egyptian fruit bat (Rousettus aegyptiacus) that displayed features indicative of albinism. Despite albino or leucistic individuals having been reported in > 100 bat species, the associated genetic backgrounds have not previously been studied. We used a digital gene expression panel to quantify mRNA levels in wing membrane samples of four candidate pigmentation genes in the focal albino fruit bat and control individuals. Significantly reduced SLC45A2 mRNA expression was found in the albino compared to five bats with typical colouration. Additionally, intraspecific sequence analyses of the albino bat SLC45A2 coding sequence identified two missense mutations, E18A and Q298R, the former of which was private to the albino bat. Position 18 of SLC45A2 was otherwise found to be highly conserved across 60 bat species and has not been previously linked to human albinism. By identifying SLC45A2 as the likely contributing locus, our results also indicate further support for the necessity of genetic testing for the reliable categorisation of hypopigmented animals as either albino or leucistic.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214471","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}

引用次数: 0

Genetic diversity of US Rambouillet in NSIP compared to other sheep breeds. 美国朗布依在NSIP中与其他绵羊品种的遗传多样性。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-03 DOI: 10.1093/jhered/esaf079

Emily J Schulz, Sara M Nilson, Tom W Murphy, Brenda M Murdoch, Luiz F Brito, Ronald M Lewis, Jessica L Petersen

{"title":"Genetic diversity of US Rambouillet in NSIP compared to other sheep breeds.","authors":"Emily J Schulz, Sara M Nilson, Tom W Murphy, Brenda M Murdoch, Luiz F Brito, Ronald M Lewis, Jessica L Petersen","doi":"10.1093/jhered/esaf079","DOIUrl":"https://doi.org/10.1093/jhered/esaf079","url":null,"abstract":"Breed management and genomic evaluation rely on understanding population structure and genetic diversity. The primary objective of this study was to evaluate genetic diversity in Rambouillet enrolled in the National Sheep Improvement Program (NSIP) in comparison to other U.S. and international sheep breeds. We considered genotypes of 667 NSIP Rambouillet from a 50K single nucleotide polymorphism (SNP) array and 600K SNP genotypes on 64 each of NSIP Rambouillet, Suffolk, and Katahdin sheep. Pedigree analyses were also conducted on the NSIP Rambouillet. International comparisons incorporated 50K SNP data from 9 international breeds. After genomic quality control measures to reduce bias in analyses, the NSIP Rambouillet had the greatest diversity among the 3 NSIP breeds (expected heterozygosity: 0.404; average individual inbreeding: 9.94%). Conversely, the NSIP Rambouillet had the lowest genetic diversity when compared to the international breeds. Based on principal component analyses, NSIP Rambouillet were divergent from the international populations except for evidence of connectivity between the NSIP and European Rambouillet. Population structure within the NSIP Rambouillet, demonstrated by cluster analysis and a significant loss of heterozygosity (FIS) was driven primarily by one flock. Using complete pedigrees of the NSIP population, effective population size, effective number of founders, and average generation interval was 87 to 218, 95, and 3.4 yr, respectively. This pedigree and genomic assessment of genetic diversity provides the basis for genomic selection and monitoring of the NSIP Rambouillet.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214537","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}

引用次数: 0

A high-quality reference genome for the ornate shrew (Sorex ornatus). 华丽鼩鼱（Sorex ornatus）的高质量参考基因组。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-10-03 DOI: 10.1093/jhered/esaf074

Isaac J Linn, Merly Escalona, Oanh Nguyen, Mohan P A Marimuthu, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Eric Beraut, Christopher J Conroy, Rauri C K Bowie, Michael W Nachman

引用次数: 0

Mixed evidence for intralocus sexual conflict from male-limited selection in Drosophila melanogaster. 黑腹果蝇雄性有限选择引起的室内性冲突的混合证据。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-29 DOI: 10.1093/jhered/esaf072

Harshavardhan Thyagarajan, Imran Sayyed, Mindy G Baroody, Joshua A Kowal, Troy Day, Adam K Chippindale

{"title":"Mixed evidence for intralocus sexual conflict from male-limited selection in Drosophila melanogaster.","authors":"Harshavardhan Thyagarajan, Imran Sayyed, Mindy G Baroody, Joshua A Kowal, Troy Day, Adam K Chippindale","doi":"10.1093/jhered/esaf072","DOIUrl":"https://doi.org/10.1093/jhered/esaf072","url":null,"abstract":"Sexual conflict over shared traits-intralocus sexual conflict (IaSC)-may be common and consequential, but experimental tests of its relative magnitude are challenging and limited in number. We use a sex-limited selection experiment, designed to subject haplotypes of Drosophila melanogaster to selection for male fitness without opposing selection acting on female fitness. Importantly, we use three novel base populations to compare results with those from the LHM population, the sole population investigated using this technique. In contrast with previous studies, we find that male fitness of haplotypes subject to male-limited selection (ML populations) are not consistently better than their matched (MC) controls when tested in the 'wildtype' state. Males from ML lines did not outperform controls in competitive fitness assays, mate choice trials, fecundity induction or sperm offense tests. As predicted, genetic variation for male fitness was reduced, with low fitness haplotypes apparently removed by selection, but this was only surveyed in one replicate population pair and included a potential artefact in the protocol. Female fitness was markedly reduced by carriage of ML haplotypes, as predicted by sexual antagonism. Hence, our results are only partially consistent with the IaSC hypothesis, raising questions about the relative contribution of sexual conflict to the standing genetic variation in these populations and the potential role of artefacts in the protocol that may have obscured our ability to detect IaSC.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187234","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}

引用次数: 0

Development, history, and impact of "Recent Advances in Conservation Genetics", the ConGen Global training course. ConGen全球培训课程“保护遗传学最新进展”的发展、历史和影响。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-25 DOI: 10.1093/jhered/esaf060

Taras K Oleksyk, Klaus-Peter Koepfli, Stephen J O'Brien

{"title":"Development, history, and impact of \"Recent Advances in Conservation Genetics\", the ConGen Global training course.","authors":"Taras K Oleksyk, Klaus-Peter Koepfli, Stephen J O'Brien","doi":"10.1093/jhered/esaf060","DOIUrl":"https://doi.org/10.1093/jhered/esaf060","url":null,"abstract":"The ConGen Global course \"Recent Advances in Conservation Genetics\" was established to educate and empower new generations of researchers and practitioners in genetic and genomic approaches to biodiversity conservation. Since its first offering in 1996, the course has evolved from a focus on sample collection, population diversity assessment, and molecular phylogeography using (polymerase chain reaction (PCR) and Sanger sequencing to a curriculum centered on next-generation sequencing, whole-genome assembly, demographic inference, and bioinformatic analyses. Originally hosted at venues near Washington, D.C., the course expanded internationally in 2011 and has since been held near biodiversity hotspots across the globe, incorporating local researchers, and drawing an increasingly diverse global audience from every part of the world. Each edition integrates region-specific conservation challenges with hands-on tutorials, case studies, and personal narratives from leading conservation geneticists. This combination of rigorous science, practical applications, and international participation has created a uniquely impactful and inclusive program. Here, we review the last decade of ConGen Global (2015 to 2025), highlighting its contributions to conservation genetics education, its role in standardizing and disseminating new genomic methods, and its influence on policy-relevant research agendas. Beyond training, the course has shaped the broader field of conservation genetics by accelerating the adoption of genomic tools, strengthening global research networks, and translating genetic insights into conservation practice. Drawing on nearly three decades of experience, ConGen Global continues to serve as a model for advancing conservation genetics education and for inspiring future training programs worldwide.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139537","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}

引用次数: 0

A chromosome-level genome assembly of the forked fungus beetle Bolitotherus cornutus, a model system for studying social evolution in the wild. 分叉真菌甲虫Bolitotherus cornutus的染色体水平基因组组装，这是研究野生社会进化的模式系统。

IF 2.5 2区生物学

Journal of Heredity Pub Date : 2025-09-24 DOI: 10.1093/jhered/esaf071

Kyle M Benowitz, Zachery M Esterline, Allina A Win, Vincent A Formica, Edmund D Brodie

引用次数: 0