G3: Genes|Genomes|Genetics最新文献_第3页

When is it subfunctionalization and when is it not? 什么时候是子功能化，什么时候不是？

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae269

James A Birchler

引用次数: 0

Detection and annotation of unique regions in mammalian genomes. 哺乳动物基因组中独特区域的检测与注释

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae257

Beatriz Vieira Mourato, Bernhard Haubold

引用次数: 0

The vertebrate small leucine-rich proteoglycans: amplification of a clustered gene family and evolution of their transcriptional profile in jawed vertebrates. 脊椎动物富含亮氨酸的小蛋白聚糖：一个集群基因家族的扩增及其在颚脊椎动物中转录谱的进化。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkaf003

Nathan Gil, Nicolas Leurs, Camille Martinand-Mari, Mélanie Debiais-Thibaud

{"title":"The vertebrate small leucine-rich proteoglycans: amplification of a clustered gene family and evolution of their transcriptional profile in jawed vertebrates.","authors":"Nathan Gil, Nicolas Leurs, Camille Martinand-Mari, Mélanie Debiais-Thibaud","doi":"10.1093/g3journal/jkaf003","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf003","url":null,"abstract":"Small Leucine-Rich Proteoglycans (SLRPs) are a major family of vertebrate proteoglycans. In bony vertebrates, SLRPs have a variety of functions from structural to signaling and are found in extracellular matrices, notably in skeletal tissues. However, there is little or no data on the diversity, function and expression patterns of SLRPs in cartilaginous fishes, which hinders our understanding of how these genes evolved with the diversification of vertebrates, in particular regarding the early events of whole genome duplications that shaped gnathostome and cyclostome genomes. We used a selection of chromosome-level assemblies of cartilaginous fish and other vertebrate genomes for phylogeny and synteny reconstructions, allowing better resolution and understanding of the evolution of this gene family in vertebrates. Novel SLRP members were uncovered together with specific loss events in different lineages. Our reconstructions support that the canonical SLRPs have originated from different series of tandem duplications that preceded the extant vertebrate last common ancestor, one of them even preceding the extant chordate last common ancestor. They then further expanded with additional tandem and whole-genome duplications during the diversification of extant vertebrates. Finally, we characterized the expression of several SLRP members in the small-spotted catshark Scyliorhinus canicula and from this, inferred conserved and derived SLRP expression in several skeletal and connective tissues in jawed vertebrates.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947398","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

Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola. 葡萄霜霉病病原菌重组景观与核型变异的连锁定位研究。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae259

Etienne Dvorak, Isabelle D Mazet, Carole Couture, François Delmotte, Marie Foulongne-Oriol

{"title":"Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola.","authors":"Etienne Dvorak, Isabelle D Mazet, Carole Couture, François Delmotte, Marie Foulongne-Oriol","doi":"10.1093/g3journal/jkae259","DOIUrl":"10.1093/g3journal/jkae259","url":null,"abstract":"Plasmopara viticola, the causal agent of grapevine downy mildew, is a biotrophic oomycete engaged in a tight coevolutionary relationship with its host. Rapid adaptation of the pathogen is favored by annual sexual reproduction that generates genotypic diversity. With the aim of studying the recombination landscape across the P. viticola genome, we generated 2 half-sibling F1 progenies (N = 189 and 162). Using targeted SNP sequencing, between 1,405 and 1,894 markers were included in parental linkage maps, and a consensus map was obtained by integrating 4,509 markers. The reference genome could be assembled into 17 pseudochromosomes, anchoring 88% of its physical length. We observed a strong collinearity between parental genomes and extensive synteny with the downy mildew Peronospora effusa. In the consensus map, the median recombination rate was 13.8 cM/Mb. The local recombination rate was highly variable along chromosomes, and recombination was suppressed in putative centromeric regions. Recombination rate was found negatively correlated with repeats' coverage and positively correlated with gene coverage. However, genes encoding secreted proteins and putative effectors were underrepresented in highly recombining regions. In both progenies, about 5% of the individuals presented karyotypic anomalies. Aneuploidies and triploidies almost exclusively originated from the male-transmitted chromosomes. Triploids resulted from fertilization by diploid gametes, but also from dispermy. Obligatory sexual reproduction each year may explain the lower level of karyotypic variation in P. viticola compared to other oomycetes. The linkage maps will be useful to guide future de novo chromosome-scale assemblies of P. viticola genomes and to perform forward genetics.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754938","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

Wild yeast isolation by middle-school students reveals features of populations residing on North American oaks. 中学生对野生酵母的分离揭示了北美橡树种群的特征。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae270

Randi Yeager, Lydia R Heasley, Nolan Baker, Vatsal Shrivastava, Julie Woodman, Michael A McMurray

{"title":"Wild yeast isolation by middle-school students reveals features of populations residing on North American oaks.","authors":"Randi Yeager, Lydia R Heasley, Nolan Baker, Vatsal Shrivastava, Julie Woodman, Michael A McMurray","doi":"10.1093/g3journal/jkae270","DOIUrl":"10.1093/g3journal/jkae270","url":null,"abstract":"Features of the natural life cycle of the budding yeast Saccharomyces cerevisiae were crucial to its domestication as a laboratory experimental model, especially the ability to maintain stable haploid clones and cross them at will to combine alleles via meiosis. Stable haploidy results from mutations in HO, which encodes an endonuclease required for haploid-specific mating-type switching. Previous studies found an unexpected diversity of HO alleles among natural isolates within a small geographic area. We developed a hands-on field and laboratory activity for middle-school students in Denver, CO, USA, to isolate wild yeast from oak bark, identify species via DNA sequencing, and sequence HO from S. cerevisiae isolates. We find limited HO diversity in North American oak isolates, pointing to efficient, continuous dispersal across the continent. In contrast, we isolated the \"dairy yeast,\" Kluyveromyces lactis, from a tree <10 m away and found that it represents a new population distinct from an oak population in an adjacent state. The outreach activity partnered middle-school, high-school, and university students in making scientific discoveries and can be adapted to other locations and natural yeast habitats. Indeed, a pilot sampling activity in southeast Texas yielded S. cerevisiae oak isolates with a new allele of HO and, from a nearby prickly pear cactus, a heat-tolerant isolate of Saccharomyces paradoxus.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Establishment of a locally adaptive allele in multidimensional continuous space. 在多维连续空间建立局部适应性等位基因

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae266

Takahiro Sakamoto

{"title":"Establishment of a locally adaptive allele in multidimensional continuous space.","authors":"Takahiro Sakamoto","doi":"10.1093/g3journal/jkae266","DOIUrl":"10.1093/g3journal/jkae266","url":null,"abstract":"Local adaptation is widely seen when species adapt to spatially heterogeneous environments. Although many theoretical studies have investigated the dynamics of local adaptation using 2-population models, there remains a need to extend the theoretical framework to continuous space settings, reflecting the real habitats of species. In this study, we use a multidimensional continuous space model and mathematically analyze the establishment process of local adaptation, with a specific emphasis on the relative roles of mutation and migration. First, the role of new mutations is evaluated by deriving the establishment probability of a locally adapted mutation using a branching process and a diffusion approximation. Next, the contribution of immigrants from a neighboring region with similar environmental conditions is considered. Theoretical predictions of the local adaptation rate agreed with the results of Wright-Fisher simulations in both mutation-driven and migration-driven cases. Evolutionary dynamics depend on several factors, including the strength of migration and selection, population density, habitat size, and spatial dimensions. These results offer a theoretical framework for assessing whether mutation or migration predominantly drives convergent local adaptation in spatially continuous environments in the presence of patchy regions with similar environmental conditions.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim. 蜜蜂感染锥虫寄生虫 Lotmaria passim 的索米进化。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae258

Lindsey M Markowitz, Anthony Nearman, Zexuan Zhao, Dawn Boncristiani, Anzhelika Butenko, Luis Miguel de Pablos, Arturo Marin, Guang Xu, Carlos A Machado, Ryan S Schwarz, Evan C Palmer-Young, Jay D Evans

{"title":"Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim.","authors":"Lindsey M Markowitz, Anthony Nearman, Zexuan Zhao, Dawn Boncristiani, Anzhelika Butenko, Luis Miguel de Pablos, Arturo Marin, Guang Xu, Carlos A Machado, Ryan S Schwarz, Evan C Palmer-Young, Jay D Evans","doi":"10.1093/g3journal/jkae258","DOIUrl":"10.1093/g3journal/jkae258","url":null,"abstract":"Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome-which was completed before its differentiation from the closely related Crithidia mellificae-has remained the reference for this species despite lacking improvements from newer methodologies. Here, we report the updated sequencing, assembly, and annotation of the BRL-type (Bee Research Laboratory) strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provided evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

GenoTools: an open-source Python package for efficient genotype data quality control and analysis. GenoTools：用于高效基因型数据质量控制和分析的开源 Python 软件包。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae268

Dan Vitale, Mathew J Koretsky, Nicole Kuznetsov, Samantha Hong, Jessica Martin, Mikayla James, Mary B Makarious, Hampton Leonard, Hirotaka Iwaki, Faraz Faghri, Cornelis Blauwendraat, Andrew B Singleton, Yeajin Song, Kristin Levine, Ashwin Ashok Kumar-Sreelatha, Zih-Hua Fang, Mike Nalls

{"title":"GenoTools: an open-source Python package for efficient genotype data quality control and analysis.","authors":"Dan Vitale, Mathew J Koretsky, Nicole Kuznetsov, Samantha Hong, Jessica Martin, Mikayla James, Mary B Makarious, Hampton Leonard, Hirotaka Iwaki, Faraz Faghri, Cornelis Blauwendraat, Andrew B Singleton, Yeajin Song, Kristin Levine, Ashwin Ashok Kumar-Sreelatha, Zih-Hua Fang, Mike Nalls","doi":"10.1093/g3journal/jkae268","DOIUrl":"10.1093/g3journal/jkae268","url":null,"abstract":"GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control, and genome-wide association studies capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools' \"Ancestry\" module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization specified to the user's genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIH's Center for Alzheimer's and Related Dementias and the Global Parkinson's Genetics Program, GenoTools was used to process and analyze the UK Biobank and major Alzheimer's disease and Parkinson's disease datasets with over 400,000 genotypes from arrays and 5,000 whole genome sequencing samples and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous quality control, and conducted genetic ancestry-specific genome-wide association studies to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotyping and sequencing (whole genome sequencing and exome) data with reproducible and scalable ancestry, quality control, and genome-wide association studies pipelines.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Marginal interaction test for detecting interactions between genetic marker sets and environment in genome-wide studies. 边际交互检验，用于检测全基因组研究中遗传标记集与环境之间的交互作用。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae263

Linchuan Shen, Amei Amei, Bowen Liu, Gang Xu, Yunqing Liu, Edwin C Oh, Xin Zhou, Zuoheng Wang

{"title":"Marginal interaction test for detecting interactions between genetic marker sets and environment in genome-wide studies.","authors":"Linchuan Shen, Amei Amei, Bowen Liu, Gang Xu, Yunqing Liu, Edwin C Oh, Xin Zhou, Zuoheng Wang","doi":"10.1093/g3journal/jkae263","DOIUrl":"10.1093/g3journal/jkae263","url":null,"abstract":"As human complex diseases are influenced by the interaction between genetics and the environment, identifying gene-environment interactions (G×E) is crucial for understanding disease mechanisms and predicting risk. Developing robust quantitative tools for G×E analysis can enhance the study of complex diseases. However, many existing methods that explore G×E focus on the interplay between an environmental factor and genetic variants, exclusively for common or rare variants. In this study, we developed MAGEIT_RAN and MAGEIT_FIX to identify interactions between an environmental factor and a set of genetic markers, including both rare and common variants, based on the MinQue for Summary statistics. The genetic main effects in MAGEIT_RAN and MAGEIT_FIX are modeled as random and fixed effects, respectively. Simulation studies showed that both tests had type I error under control, with MAGEIT_RAN being the most powerful test. Applying MAGEIT to a genome-wide analysis of gene-alcohol interactions on hypertension and seated systolic blood pressure in the Multiethnic Study of Atherosclerosis revealed genes like EIF2AK2, CCNDBP1, and EPB42 influencing blood pressure through alcohol interaction. Pathway analysis identified 1 apoptosis and survival pathway involving PKR and 2 signal transduction pathways associated with hypertension and alcohol intake, demonstrating MAGEIT_RAN's ability to detect biologically relevant gene-environment interactions.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa). 为水稻（Oryza sativa）多样化育种应用设计的数千种特异性 KASP 标记。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-01-08 DOI: 10.1093/g3journal/jkae251

Katherine Steele, Mark Quinton-Tulloch, Darshna Vyas, John Witcombe

{"title":"Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).","authors":"Katherine Steele, Mark Quinton-Tulloch, Darshna Vyas, John Witcombe","doi":"10.1093/g3journal/jkae251","DOIUrl":"10.1093/g3journal/jkae251","url":null,"abstract":"This study aimed to broaden applicability of KASP for Oryza sativa across diverse genotypes through incorporation of ambiguous (degenerate) bases into their primer designs and to validate 4,000 of them for genotyping applications. A bioinformatics pipeline was used to compare 129 rice genomes from 89 countries with the indica reference genome R498 and generate ∼1.6 million KASP designs for the more common variants between R498 and the other genomes. Of the designs, 98,238 were for predicted functional markers. Up to 5 KASP each for 1,024 breeder-selected loci were assayed in a panel of 178 diverse rice varieties, generating 3,366 validated KASP. The 84% success rate was within the normal range for KASP demonstrating that the ambiguous bases do not compromise efficacy. The 3,366-trait-specific marker panel was applied for population structure analysis in the diversity panel and resolved them into 4 expected groups. Target variations in 13 genomes used for designs were compared with the corresponding KASP genotypes in different accessions of the same 13 varieties in the diversity panel. There was agreement for 79% or more markers in 12 varieties; 10 having agreement >88%. One variety, a selection from a landrace, had only 46.5% marker agreement. Breeders can search for the validated KASP and more than a million so-far untested designs in three reference genomes (including Niponbare MSU7) with a search tool, that includes designs in proximity to previously published microsatellite markers, and retrieve target variations for 129 rice genomes plus their genomic locations with ±25 bp flanking sequences.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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