G3: Genes|Genomes|Genetics最新文献

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In vivo regulation of an endogenously-tagged protein by a light-regulated kinase.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-07 DOI: 10.1093/g3journal/jkaf073
Mengjing Bao, Katarzyna Lepeta, Gustavo Aguilar, Sophie Schnider, Markus Affolter, Maria Alessandra Vigano
{"title":"In vivo regulation of an endogenously-tagged protein by a light-regulated kinase.","authors":"Mengjing Bao, Katarzyna Lepeta, Gustavo Aguilar, Sophie Schnider, Markus Affolter, Maria Alessandra Vigano","doi":"10.1093/g3journal/jkaf073","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf073","url":null,"abstract":"<p><p>Post-translational modifications (PTMs) are indispensable modulators of protein activity. Most cellular behaviours, from cell division to cytoskeletal organization, are controlled by PTMs, their mis-regulation being associated with a plethora of human diseases. Traditionally, the role of PTMs has been studied employing biochemical techniques. However, these approaches fall short when studying PTM dynamics in vivo. In recent years, functionalized protein binders have allowed the post-translational modification of endogenous proteins by bringing an enzymatic domain in close proximity to the protein they recognize. To date, most of these methods lack the temporal control necessary to understand the complex effects triggered by PTMs. In this study, we have developed a method to phosphorylate endogenous Myosin in a light-inducible manner. The method relies both on nanobody-targeting and light-inducible activation in order to achieve both tight specificity and temporal control. We demonstrate that this technology is able to disrupt cytoskeletal dynamics during Drosophila embryonic development. Together, our results highlight the potential of combining optogenetics and protein binders for the study of the proteome in multicellular systems.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-07 DOI: 10.1093/g3journal/jkaf071
Manning Y Huang, Matthew J Nalley, Patrick Hecht, Hiten D Madhani
{"title":"An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans.","authors":"Manning Y Huang, Matthew J Nalley, Patrick Hecht, Hiten D Madhani","doi":"10.1093/g3journal/jkaf071","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf071","url":null,"abstract":"<p><p>Cryptococcus neoformans is the top-ranked W.H.O. fungal priority pathogen, but tools for generating conditional mutations are limited. Auxin-inducible degron systems permit rapid and effective cellular depletion of a tagged protein of interest upon adding a small molecule. These tools are invaluable, particularly for studying essential genes, which may play important roles in pathogen biology. AID2 is one such system that improves on previous strategies. This system achieves greater sensitivity and specificity through an auxin derivative, 5-Ph-IAA, alongside an OsTIR1F74G mutant. We adapted the AID2 system for C. neoformans by codon optimizing OsTIR1F74G and tested its use in multiple scenarios. We demonstrate that the C. neoformans optimized AID2 system enables effective degradation of proteins, including essential proteins, and can be used to help discriminate essential from non-essential genes. This tool enables the study of unexplored parts of the C. neoformans genome.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
The draft genome of the Wisconsin Miniature SwineTM, a valuable biomedical research tool.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-07 DOI: 10.1093/g3journal/jkaf067
Alex C Veith, Jennifer J Meudt, Jamie L Reichert, Jennifer M Frank, Derek M Pavelec, Bridget Ladell, James Speers, Molly Zeller, Taeyoung Shin, Joshua R Hyman, Christopher A Bradfield, Charles M Konsitzke, Dhanansayan Shanmuganayagam, C Dustin Rubinstein, Mark E Berres
{"title":"The draft genome of the Wisconsin Miniature SwineTM, a valuable biomedical research tool.","authors":"Alex C Veith, Jennifer J Meudt, Jamie L Reichert, Jennifer M Frank, Derek M Pavelec, Bridget Ladell, James Speers, Molly Zeller, Taeyoung Shin, Joshua R Hyman, Christopher A Bradfield, Charles M Konsitzke, Dhanansayan Shanmuganayagam, C Dustin Rubinstein, Mark E Berres","doi":"10.1093/g3journal/jkaf067","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf067","url":null,"abstract":"<p><p>Porcine biomedical models have emerged as valuable tools in biomedical research due to their physiological, anatomical, metabolic, immunological, and genetic similarities to humans. As a result, they offer greater relevance for translational studies than rodent models. Moreover, compared to nonhuman primates, porcine models are more cost-effective, easier to manipulate genetically, and raise fewer ethical concerns. However, the conventional breeds of swine most commonly used in research have rapid growth rates, which lead to logistical challenges such as increased space requirements, making them impractical as biomedical models. The Wisconsin Miniature SwineTM (WMSTM) was developed to address these shortcomings. The WMSTM porcine model grows slower, reaching and maintaining human sizes at adulthood. The model was also specifically designed to possess more human-like physiology that allows for easy modeling of comorbidities like obesity and metabolic syndrome that affect a large portion of the human population affected by chronic diseases. Thus, WMS™ is an ideal porcine gene editing platform for modeling complex multifactorial diseases. Here, we present the first draft genome assembly representative of the WMSTM line. The primary assembly was generated with approximately 20X coverage of long reads from Oxford Nanopore Technologies and independently error-corrected using 23X Pacific Biosciences reads. Arima Genomics Hi-C data was used to improve contiguity. Largely congruent with the existing Sus scrofa genome, we also show the utility of WMSTM as a model through comparisons between two WMSTM genes and human homologs. Finally, we show the utility of genotyping by sequencing (GBS) across WMSTM herds. The WMSTM genome generated here is highly complete and supports investigators utilizing WMSTM in biomedical research.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Multimerized Epitope Tags for High Sensitivity Protein Detection.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-07 DOI: 10.1093/g3journal/jkaf070
R Steven Stowers
{"title":"Multimerized Epitope Tags for High Sensitivity Protein Detection.","authors":"R Steven Stowers","doi":"10.1093/g3journal/jkaf070","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf070","url":null,"abstract":"<p><p>A detailed understanding of the function of a gene requires knowledge of the cellular and subcellular distribution of its encoded protein(s). For proteins expressed at low levels, antibodies that recognize single epitopes may not be sufficient for visualizing expression. To enhance the sensitivity of protein detection, tandem repeat multimers of the commonly used epitope tags V5, HA, MYC, FLAG, ALFA, and OLLAS were developed that encode up to 80X copies of each tag, an eight-fold increase over currently available options for epitope multimer tagging. As proof-of-principle, conditional alleles of vGlut containing the 40XV5 and 40XMYC epitope tag multimers were validated in vivo in Drosophila. Both epitope-tagged proteins were determined to exhibit synaptic localization in the adult brain and larval neuromuscular junction similar to that of endogenous vGlut. They were also conditionally expressed in subsets of adult brain neurons and observed to exhibit robust, easily detectable expression in presynaptic terminals even in single neurons. These highly multimerized epitope tags will facilitate any type of experiment using antibody detection of proteins that would benefit from enhanced sensitivity.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
The Genome of the MZM-0403 Strain of the African Turquoise Killifish, Nothobranchius furzeri. MZM-0403 株系非洲松石鳉(Nothobranchius furzeri)的基因组。
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-07 DOI: 10.1093/g3journal/jkaf075
Bernadette D Johnson, Balan Ramesh, Adam G Jones
{"title":"The Genome of the MZM-0403 Strain of the African Turquoise Killifish, Nothobranchius furzeri.","authors":"Bernadette D Johnson, Balan Ramesh, Adam G Jones","doi":"10.1093/g3journal/jkaf075","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf075","url":null,"abstract":"<p><p>The African turquoise killifish, Nothobranchius furzeri, is an emerging model for functional genomics research. Interest in N. furzeri stems from its extremely short lifespan, and the breadth of research on this fish is rapidly expanding. All currently available whole-genome assemblies for N. furzeri are based on the GRZ strain. However, N. furzeri shows substantial phenotypic differences among populations. Here, we present a whole-genome assembly of the MZM-0403 strain of N. furzeri, which differs from the GRZ strain with respect to lifespan and male coloration patterns. We used PacBio HiFi sequencing to sequence the genome of an MZM-0403 male to approximately 48X coverage. The PacBio reads were de novo assembled and then scaffolded against an existing N. furzeri genome assembly. This strategy resulted in a chromosome-level assembly. Our MZM-0403 assembly differs from previous N. furzeri assemblies in that it is closer to the expected genome size based on independent estimates (∼1.5 Gb) and it has substantially fewer gaps, particularly in the vicinity of genes and within introns. A repeat analysis shows that about two-thirds of the genome is composed of repetitive elements. In addition, our assembly approach allowed us to recover phased fragments of the X- and Y-chromosomes. Analysis of these regions identify 20 genes that are likely in the non-recombining region of the sex chromosomes. Overall, this novel genome assembly will be useful for future functional and comparative genomics studies of fishes in the genus Nothobranchius.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Arsenic impairs Drosophila neural stem cell mitotic progression and sleep behavior in a tauopathy model.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-07 DOI: 10.1093/g3journal/jkaf049
Temitope H Adebambo, Fernanda Medina-Flores, Shirley Zhang, Dorothy A Lerit
{"title":"Arsenic impairs Drosophila neural stem cell mitotic progression and sleep behavior in a tauopathy model.","authors":"Temitope H Adebambo, Fernanda Medina-Flores, Shirley Zhang, Dorothy A Lerit","doi":"10.1093/g3journal/jkaf049","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf049","url":null,"abstract":"<p><p>Despite established exposure limits, arsenic remains the most significant environmental risk factor detrimental to human health and is associated with carcinogenesis and neurotoxicity. Arsenic compromises neurodevelopment, and it is associated with peripheral neuropathy in adults. Exposure to heavy metals, such as arsenic, may also increase the risk of neurodegenerative disorders. Nevertheless, the molecular mechanisms underlying arsenic-induced neurotoxicity remain poorly understood. Elucidating how arsenic contributes to neurotoxicity may mitigate some of the risks associated with chronic sublethal exposure and inform future interventions. In this study, we examine the effects of arsenic exposure on Drosophila larval neurodevelopment and adult neurologic function. Consistent with prior work, we identify significant developmental delays and heightened mortality in response to arsenic. Within the developing larval brain, we identify a dose-dependent increase in brain volume. This aberrant brain growth is coupled with impaired mitotic progression of the neural stem cells (NSCs), progenitors of the neurons and glia of the central nervous system. Live imaging of cycling NSCs reveals significant delays in cell cycle progression upon arsenic treatment, leading to genomic instability. In adults, chronic arsenic exposure reduces neurologic function, such as locomotion. Finally, we show arsenic selectively impairs circadian rhythms in a humanized tauopathy model. These findings inform mechanisms of arsenic neurotoxicity and reveal sex-specific and genetic vulnerabilities to sublethal exposure.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
CRISPR/Cas9-induced breaks are insufficient to break linkage drag surrounding the ToMV locus of Solanum lycopersicum.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-02 DOI: 10.1093/g3journal/jkaf068
Jillis Grubben, Gerard Bijsterbosch, Burak Aktürk, Richard G F Visser, Henk J Schouten
{"title":"CRISPR/Cas9-induced breaks are insufficient to break linkage drag surrounding the ToMV locus of Solanum lycopersicum.","authors":"Jillis Grubben, Gerard Bijsterbosch, Burak Aktürk, Richard G F Visser, Henk J Schouten","doi":"10.1093/g3journal/jkaf068","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf068","url":null,"abstract":"<p><p>Despite the success of CRISPR/Cas9 in inducing DNA double-strand breaks (DSBs) for genome editing, achieving targeted recombination in somatic cells remains challenging, particularly at recombination cold spots like the Tomato Mosaic Virus (ToMV) resistance locus in Solanum lycopersicum. We investigated the potential of CRISPR/Cas9-induced targeted recombination in somatic cells to overcome linkage drag surrounding the ToMV locus. We employed two strategies: first, inducing DSBs in both alleles of F1 tomato seedlings to promote non-homologous end joining (NHEJ) and homology-directed repair (HDR); second, targeting a single allele in a heterozygous background to induce HDR in seedlings. CRISPR/Cas9 activity was confirmed in F₁ seedlings by detecting NHEJ-mediated mutations at the target sites in ToMV. We developed a bioinformatics pipeline to identify targeted recombinants by analyzing single nucleotide polymorphisms (SNPs) between parental haplotypes, allowing precise tracking of SNP variations. A two-dimensional pooling strategy was employed to distinguish genuine recombination events from PCR artifacts. Despite these advances and the active CRISPR/Cas9 system in F1 progeny, no reliable targeted recombinations were found. We extended our research to protoplasts to assess whether CRISPR/Cas9 could induce targeted recombination under different cellular conditions at the same locus. Consistent with our findings in F1 plants, we observed no increase in recombinant patterns compared to wild-type controls in protoplasts. Our findings suggest that CRISPR/Cas9-induced DSBs were insufficient to break the genetic linkage at the ToMV locus on chromosome 9 at a detectable level.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-04-02 DOI: 10.1093/g3journal/jkaf062
George Chung, Fabio Piano, Kristin C Gunsalus
{"title":"TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads.","authors":"George Chung, Fabio Piano, Kristin C Gunsalus","doi":"10.1093/g3journal/jkaf062","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf062","url":null,"abstract":"<p><p>Telomeres are eukaryotic chromosome end structures that guard against sequence loss and aberrant chromosome fusions. Telomeric repeat motifs (TRMs), the minimal repeating unit of a telomere, vary from species to species, with some evolutionary clades experiencing a rapid sequence divergence. To explore the full scope of this evolutionary divergence, many bioinformatic tools have been developed to infer novel TRMs using repetitive sequence search on short sequencing reads. However, novel telomeric motifs remain unidentified in up to half of the sequencing libraries assayed with these tools. A possible reason may be that short reads, derived from extensively sheared DNA, preserve little to no positional context of the repetitive sequences assayed. On the other hand, if a sequencing read is sufficiently long, telomeric sequences must appear at either end rather than in the middle. The TeloSearchLR algorithm relies on this to help identify novel TRMs on long reads, in many cases where short-read search tools have failed. In addition, we demonstrate that TeloSearchLR can reveal unusually long telomeric motifs not maintained by telomerase, and it can also be used to anchor terminal scaffolds in new genome assemblies.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Tetracycline has no long-term effects on gut physiology and microbiome of the New World screwworm, Cochliomyia hominivorax, which has positive implications for transgenic male-only rearing systems.
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-03-25 DOI: 10.1093/g3journal/jkaf058
Alex P Arp, Mackenzie Tietjen, Agustin Sagel, Mario Vasquez, Gladys Quintero, Deanna Bodine, Perot Saelao, Paul V Hickner
{"title":"Tetracycline has no long-term effects on gut physiology and microbiome of the New World screwworm, Cochliomyia hominivorax, which has positive implications for transgenic male-only rearing systems.","authors":"Alex P Arp, Mackenzie Tietjen, Agustin Sagel, Mario Vasquez, Gladys Quintero, Deanna Bodine, Perot Saelao, Paul V Hickner","doi":"10.1093/g3journal/jkaf058","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf058","url":null,"abstract":"<p><p>Tetracycline repressible (Tet-Off) male-only sexing systems have great potential for improving the efficacy of sterile insect control programs in addition to reducing rearing cost. The relationship between insects and their microbial symbionts, as well as potential physiological stress caused by tetracycline class antibiotics, pose concerns that Tet-Off strains could have reduced fitness in nature. Here we evaluated the biological performance, midgut microbiome, and midgut transcriptomes of wild-type screwworm, Cochliomyia hominivorax, reared in diet without Tc (control), with Tc (on-Tc), or a pseudo \"male-only\" condition where offspring of the Tc fed line were reared without Tc (post-Tc), like Tet-Off strains previously developed for this species. Biological performance was not significantly changed by the inclusion of Tc in the diet, and in most cases the flies reared with Tc were generally more fit than lines reared without Tc. The gut microbiome and transcriptome revealed interesting and similar pattens. In both surveys, the greatest changes were between both control and post-Tc treatments and the on-Tc treatment. Very few differences were observed between control and post-Tc treatments, suggesting that there are few negative persistent effects of Tc exposure to fly colonies, and flies revert to their natural state rapidly after the removal of Tc. These results suggest there are limited negative impacts of Tet-Off regulatory systems for use by the C. hominivorax eradication program, and differences observed in Tet-Off strain performance are likely not related to Tc exposure.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis).
IF 2.1 3区 生物学
G3: Genes|Genomes|Genetics Pub Date : 2025-03-25 DOI: 10.1093/g3journal/jkaf066
Laurie Lecomte, Anne-Laure Ferchaud, Eric Normandeau, Claire Mérot, Isabelle Langlois-Parisé, Jean-Christophe Therrien, Pierre Bérubé, Haig Djambazian, Pubudu Manoj Nawarathna, Jiannis Ragoussis, Dylan Fraser
{"title":"Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis).","authors":"Laurie Lecomte, Anne-Laure Ferchaud, Eric Normandeau, Claire Mérot, Isabelle Langlois-Parisé, Jean-Christophe Therrien, Pierre Bérubé, Haig Djambazian, Pubudu Manoj Nawarathna, Jiannis Ragoussis, Dylan Fraser","doi":"10.1093/g3journal/jkaf066","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf066","url":null,"abstract":"<p><p>Brook trout (Salvelinus fontinalis) is a socioeconomically important fish species for fisheries, aquaculture and aquatic conservation. We produced a 2.5 Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- and long-read sequencing of a fully homozygous mitotic gynogenic doubled haploid fish, which facilitates assembly of highly complex salmonid genomes. The assembly has an N50 of 50.98 Mb and 88.9% of the total assembled sequence length is anchored into 42 main chromosomes, of which 63.44% represents repeated contents, including 1,461,010 DNA transposons. 56,058 genes were found, with 98.6% of the 3,640 expected conserved orthologs BUSCO genes (actinopterygii_odb10 lineage database). Additionally, we found significant homology within the 42 chromosomes, as expected for this pseudo-tetraploid species, as well as with the sister species lake trout (Salvelinus namaycush) and Atlantic salmon (Salmo salar). This assembly will serve as a reliable genomic resource for brook trout, thus enabling a wider range of reference-based applications to support ongoing research and management decision-making for the species.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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