Journal of Heredity最新文献_第2页

Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi. 濒危、基因细分的北部潮水虾虎鱼 Eucyclogobius newberryi 的参考基因组。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae053

David K Jacobs, Andrew Kinziger, Mira Abrecht, W Tyler McCraney, Benjamin A Hà, Brenton T Spies, Elizabeth Heath-Heckman, Mohan P A Marimuhtu, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Merly Escalona, Courtney Miller, H Bradley Shaffer

{"title":"Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi.","authors":"David K Jacobs, Andrew Kinziger, Mira Abrecht, W Tyler McCraney, Benjamin A Hà, Brenton T Spies, Elizabeth Heath-Heckman, Mohan P A Marimuhtu, Oanh Nguyen, Colin W Fairbairn, William E Seligmann, Merly Escalona, Courtney Miller, H Bradley Shaffer","doi":"10.1093/jhered/esae053","DOIUrl":"10.1093/jhered/esae053","url":null,"abstract":"The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby, NTG) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980 Mb E. newberryi reference genome has an N50 of 34 Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the NTG, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"170-178"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378628","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}

引用次数: 0

Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow). 微塑料暴露与模式生物黑头鲦鱼（Pimephales promelas）的表观基因组效应有关。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae027

Miranda J Wade, Kennedy Bucci, Chelsea M Rochman, Mariah H Meek

{"title":"Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow).","authors":"Miranda J Wade, Kennedy Bucci, Chelsea M Rochman, Mariah H Meek","doi":"10.1093/jhered/esae027","DOIUrl":"10.1093/jhered/esae027","url":null,"abstract":"Microplastics have evolutionary and ecological impacts across species, affecting organisms' development, reproduction, and behavior along with contributing to genotoxicity and stress. As plastic pollution is increasing and ubiquitous, gaining a better understanding of organismal responses to microplastics is necessary. Epigenetic processes such as DNA methylation are heritable forms of molecular regulation influenced by environmental conditions. Therefore, determining such epigenetic responses to microplastics will reveal potential chronic consequences of this environmental pollutant. We performed an experiment across two generations of fathead minnows (Pimephales promelas) to elucidate the transgenerational epigenetic effects of microplastic exposure. We exposed the first generation of fish to four different treatments of microplastics: two concentrations of each of pre-consumer polyethylene (PE) and PE collected from Lake Ontario. We then raised the first filial generation with no microplastic exposure. We used enzymatic methylation sequencing on adult liver tissue and homogenized larvae to evaluate DNA methylation differences among treatments, sexes, and generations. Our findings show the origin of the plastic had a larger effect in female minnows whereas the effect of concentration was stronger in the males. We also observed transgenerational effects, highlighting a mechanism in which parents can pass on the effects of microplastic exposure to their offspring. Many of the genes found within differentially methylated regions in our analyses are known to interact with estrogenic chemicals associated with plastic and are related to metabolism. This study highlights the persistent and potentially serious impacts of microplastic pollution on gene regulation in freshwater systems.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"113-125"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923715","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}

引用次数: 0

Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli). 转录组学的敏感性：不同样本和方法改变了海湾琵琶鱼（Syngnathus scovelli）的结论。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae067

Bernadette D Johnson, Emily Rose, Adam G Jones

{"title":"Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).","authors":"Bernadette D Johnson, Emily Rose, Adam G Jones","doi":"10.1093/jhered/esae067","DOIUrl":"10.1093/jhered/esae067","url":null,"abstract":"Transcriptome analysis has become a central tool in evolutionary and functional genomics. However, variation among biological samples and analysis techniques can greatly influence results, potentially compromising insights into the phenomenon under study. Here, we evaluate differences in the brain transcriptome between female and male Gulf pipefish (Syngnathus scovelli). We perform comparisons between results from entire pipelines for brain transcriptome assembly, quantification, and analysis. We also offer a unique biological comparison between two sampling instances (Redfish Bay: n = 15, Port Lavaca: n = 7). Our results demonstrate crucial shortcomings with current experimental approaches. We found high variation within our results that was driven by both technical differences between pipelines and biological differences between pipefish samples. In our analysis of highly expressed genes, we found that the choice of methods influenced the degree of contamination or noise included in the identified genes. Notably, genes identified within the same pipeline were more similar than any other comparison. Our differential expression analysis revealed that both methodology and sampling location influenced the quantity and consistency of statistically significant transcripts. In the context of these results, we offer modifications to current practices that may increase the robustness of transcriptome-based conclusions. In particular, the use of a reference-guided assembly and an increase in sample sizes are likely to improve resistance to noise or error.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"139-148"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640233","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}

引用次数: 0

Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia. mpv17 基因突变会导致罗非鱼线粒体功能障碍而失去虹膜。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae034

Jia Xu, Peng Li, Mengmeng Xu, Chenxu Wang, Thomas D Kocher, Deshou Wang

{"title":"Mutation of mpv17 results in loss of iridophores due to mitochondrial dysfunction in tilapia.","authors":"Jia Xu, Peng Li, Mengmeng Xu, Chenxu Wang, Thomas D Kocher, Deshou Wang","doi":"10.1093/jhered/esae034","DOIUrl":"10.1093/jhered/esae034","url":null,"abstract":"Mpv17 (mitochondrial inner membrane protein MPV17) deficiency causes severe mitochondrial DNA depletion syndrome in mammals and loss of pigmentation of iridophores and a significant decrease of melanophores in zebrafish. The reasons for this are still unclear. In this study, we established an mpv17 homozygous mutant line in Nile tilapia. The developing mutants are transparent due to the loss of iridophores and aggregation of pigment granules in the melanophores and disappearance of the vertical pigment bars on the side of the fish. Transcriptome analysis using the skin of fish at 30 dpf (days post fertilization) revealed that the genes related to purine (especially pnp4a) and melanin synthesis were significantly downregulated. However, administration of guanine diets failed to rescue the phenotype of the mutants. In addition, no obvious apoptosis signals were observed in the iris of the mutants by TUNEL staining. Significant downregulation of genes related to iridophore differentiation was detected by qPCR. Insufficient ATP, as revealed by ATP assay, α-MSH treatment, and adcy5 mutational analysis, might account for the defects of melanophores in mpv17 mutants. Several tissues displayed less mtDNA and decreased ATP levels. Taken together, these results indicated that mutation of mpv17 led to mitochondrial dTMP deficiency, followed by impaired mtDNA content and mitochondrial function, which in turn, led to loss of iridophores and a transparent body color in tilapia.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"101-112"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472787","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

Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution. 定量性状位点集中在墨西哥洞穴鱼基因组的特定区域，揭示了洞穴相关进化的关键候选基因。

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-03-01 DOI: 10.1093/jhered/esae040

Jonathan Wiese, Emilie Richards, Johanna E Kowalko, Suzanne E McGaugh

{"title":"Quantitative trait loci concentrate in specific regions of the Mexican cavefish genome and reveal key candidate genes for cave-associated evolution.","authors":"Jonathan Wiese, Emilie Richards, Johanna E Kowalko, Suzanne E McGaugh","doi":"10.1093/jhered/esae040","DOIUrl":"10.1093/jhered/esae040","url":null,"abstract":"A major goal of modern biology is connecting phenotype with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here, we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. These analyses revealed that QTL clusters in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics associated with increased opportunities for mutation, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb, which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific regions of the genome may play significant roles in driving adaptation to the cave environment in A. mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"89-100"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857224","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-length genome assembly for the Pismo clam, Tivela stultorum, a long-lived bivalve species severely impacted by overfishing.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-02-19 DOI: 10.1093/jhered/esaf008

Kyle A Emery, Melissa B DeBiasse, Merly Escalona, Mohan P A Marimuthu, Oanh H Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Nicholas K Schooler, David M Hubbard, Jenifer E Dugan, Michael N Dawson

{"title":"A chromosome-length genome assembly for the Pismo clam, Tivela stultorum, a long-lived bivalve species severely impacted by overfishing.","authors":"Kyle A Emery, Melissa B DeBiasse, Merly Escalona, Mohan P A Marimuthu, Oanh H Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Nicholas K Schooler, David M Hubbard, Jenifer E Dugan, Michael N Dawson","doi":"10.1093/jhered/esaf008","DOIUrl":"https://doi.org/10.1093/jhered/esaf008","url":null,"abstract":"The Pismo clam, Tivela stultorum, is an ecologically and economically important species that inhabiting sandy beaches and subtidal zones in central and southern California, USA, and northern Baja California, Mexico. This long lived venerid clam species is of great management, cultural and conservation interest in California where it was harvested for centuries by indigenous people and then nearly extirpated by intense commercial and recreational overfishing in the mid 1900's. A recreational fishery continues today in California, however T. stultorum faces pressure from poaching, overharvest, and the loss of sandy beaches from rising sea levels and beach erosion. Understanding the susceptibility and resilience of Pismo clams to these pressures is essential for their conservation. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to assemble a highly contiguous genome of 763 Mb. The genome had a contig N50 of 13 Mb and a scaffold N50 of 38 Mb with a BUSCO completeness score of 95%. Most of the genome sequences (96%) were contained in 19 scaffolds at least 10MB long, consistent with prior evidence that venerid clam genomes are composed of 19 autosomes. This reference genome will enable a more complete understanding of the ecology and evolutionary dynamics of T. stultorum via population genomic analyses, which will help assess risks from climate, fishing, environmental change, and susceptibilities due to life history. Our goal is to better support the continued recovery, informed management and conservation, and future persistence of T. stultorum, a long lived and highly valued clam species.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451004","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

Decoding Cattle (Bos taurus) Diacylglycerol Acyltransferase (DGAT) Gene Families: A Pathway to Functional Understanding.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-02-11 DOI: 10.1093/jhered/esae079

Effat Nasre Esfahani, Saeid Ansari Mahyari, Peymaneh Davoodi, Mostafa Ghaderi-Zefrehei, Bluma J Lesch

{"title":"Decoding Cattle (Bos taurus) Diacylglycerol Acyltransferase (DGAT) Gene Families: A Pathway to Functional Understanding.","authors":"Effat Nasre Esfahani, Saeid Ansari Mahyari, Peymaneh Davoodi, Mostafa Ghaderi-Zefrehei, Bluma J Lesch","doi":"10.1093/jhered/esae079","DOIUrl":"https://doi.org/10.1093/jhered/esae079","url":null,"abstract":"Diacylglycerol acyltransferases (DGAT) are key enzymes in fat storage, converting diacylglycerol and fatty acyl CoA into triacylglycerol. In cattle (Bos taurus), the DGAT1 and DGAT2 genes are well-known for their significant influence on milk production traits, particularly milk fat yield and percentage. However, the cattle genome contains twelve other DGAT gene family members that remain largely uncharacterized. The research examined the genetic makeup of these DGAT proteins, revealing differences in exon count, isoforms, amino acid composition, molecular weight, isoelectric points, and predicted SNP locations. The genes are distributed across five chromosomes (2, 14, 15, 25, and X), and the expansion of this gene family in cattle is likely the result of gene duplication events, driven by specific motifs that favor such duplication. By identifying these distinctions, the study provides foundational insights into the lesser-known DGAT genes, which could be involved in regulating important traits like milk fat production. This comprehensive in silico analysis of the DGAT gene family offers valuable insights into the genetic and structural diversity of these enzymes in cattle. It also establishes a platform for future research into functional SNPs and their potential role in improving milk fat production traits, contributing to the advancement of cattle genetics and dairy production optimization. To this end, the identification of previously uncharacterized DGAT genes and their possible involvement in milk fat synthesis could pave the way for innovative breeding strategies focused on improving both milk yield and fat content in dairy cattle.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392483","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

Pea aphid wing plasticity variation has a multigenic basis.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-02-04 DOI: 10.1093/jhered/esaf006

Rose M H Driscoll, Xiaomi Liu, Julia McDonough, James Schmidt, Jennifer A Brisson

{"title":"Pea aphid wing plasticity variation has a multigenic basis.","authors":"Rose M H Driscoll, Xiaomi Liu, Julia McDonough, James Schmidt, Jennifer A Brisson","doi":"10.1093/jhered/esaf006","DOIUrl":"https://doi.org/10.1093/jhered/esaf006","url":null,"abstract":"Phenotypic plasticity, the ability of a single genotype to produce a range of phenotypes in response to environmental cues, can exhibit genetic variation like any trait. Discovering the genetic basis of plasticity and plasticity variation is critical to understand how populations will respond to the ongoing environmental challenges brought about by, for example, climate change. Here, we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing plasticity variation. In this species, genetically identical, highly fecund wingless and dispersive winged individuals are produced by pea aphid mothers in uncrowded versus crowded environments, respectively. We focus specifically on the genetic basis of the propensity to produce winged individuals in response to crowding. We crossed a low to a high plasticity line and examined plasticity variation in backcross progeny (F1 x low parent), finding that differences between lines had a strong genetic component and that multiple loci likely to contribute to this variation. Transcriptional profiling revealed a candidate gene, yellow-h, which was found within a genomic locus contributing to plasticity variation. Overall, we provide novel information about the genetic basis of an ecologically-relevant trait and contribute to the growing literature recognizing the importance of understanding the genetic basis of plasticity variation.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124106","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 structure of the northern house mosquito (Diptera: Culicidae) in a WNV-susceptible area.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-30 DOI: 10.1093/jhered/esaf005

Ingrid E Alvial, Noemi Rojas-Hernández, Nicolas Guerra, David Véliz, Christian R González, Laura M Pérez, Hugo A Benítez

{"title":"Genetic structure of the northern house mosquito (Diptera: Culicidae) in a WNV-susceptible area.","authors":"Ingrid E Alvial, Noemi Rojas-Hernández, Nicolas Guerra, David Véliz, Christian R González, Laura M Pérez, Hugo A Benítez","doi":"10.1093/jhered/esaf005","DOIUrl":"https://doi.org/10.1093/jhered/esaf005","url":null,"abstract":"Mosquitoes from the Culex pipiens complex are found worldwide and have been the focus of numerous studies due to their role as vectors of human pathogens. We investigated the population genetic structure of Cx. pipiens s.l. by analyzing SNPs and the COI gene, focusing on the genetic grouping signals of the ecotypes pipiens and molestus. Our analysis revealed no genetic association between the ecotypes and the SNPs, suggesting that the classification is based on ecological traits rather than genetic factors. Using data from 2,641 SNPs and 164 genotypes, our Bayesian clustering analysis categorized the populations into six distinct genetic groups, distinguishing the Rapa Nui island population from those on the American mainland. The estimated effective migration rates (EEMR) showed low levels of migration between island and continental populations, with significant migration occurring only among populations between 29° S and 33° S. Genetic differentiation between Rapa Nui island and the American continent was observed. In contrast, no significant differentiation was noted in other regions. The haplotype network suggests a possible migration pathway from that area of the South Pacific. Additionally, demographic history analysis indicates a relatively recent founder effect of Cx. pipiens s.l. on the island. Geographic isolation and variations in genetic makeup can limit the spread of pathogens regionally and globally. However, these same factors can also promote specialization and enhance adaptation to new ecological niches, thereby improving the ability of pathogens to function as effective vectors in isolated environments.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069194","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

Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.

IF 3 2区生物学

Journal of Heredity Pub Date : 2025-01-29 DOI: 10.1093/jhered/esaf001

Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver

{"title":"Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.","authors":"Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver","doi":"10.1093/jhered/esaf001","DOIUrl":"https://doi.org/10.1093/jhered/esaf001","url":null,"abstract":"The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n=38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long RoHs require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069192","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