Genetics最新文献_第8页

Genome size and chromosome number are critical metrics for accurate genome assembly assessment in Eukaryota. 基因组大小和染色体数目是准确评估真核生物基因组组装的关键指标。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae099

Carl E Hjelmen

{"title":"Genome size and chromosome number are critical metrics for accurate genome assembly assessment in Eukaryota.","authors":"Carl E Hjelmen","doi":"10.1093/genetics/iyae099","DOIUrl":"10.1093/genetics/iyae099","url":null,"abstract":"The number of genome assemblies has rapidly increased in recent history, with NCBI databases reaching over 41,000 eukaryotic genome assemblies across about 2,300 species. Increases in read length and improvements in assembly algorithms have led to increased contiguity and larger genome assemblies. While this number of assemblies is impressive, only about a third of these assemblies have corresponding genome size estimations for their respective species on publicly available databases. In this paper, genome assemblies are assessed regarding their total size compared to their respective publicly available genome size estimations. These deviations in size are assessed related to genome size, kingdom, sequencing platform, and standard assembly metrics, such as N50 and BUSCO values. A large proportion of assemblies deviate from their estimated genome size by more than 10%, with increasing deviations in size with increased genome size, suggesting nonprotein coding and structural DNA may be to blame. Modest differences in performance of sequencing platforms are noted as well. While standard metrics of genome assessment are more likely to indicate an assembly approaching the estimated genome size, much of the variation in this deviation in size is not explained with these raw metrics. A new, proportional N50 metric is proposed, in which N50 values are made relative to the average chromosome size of each species. This new metric has a stronger relationship with complete genome assemblies and, due to its proportional nature, allows for a more direct comparison across assemblies for genomes with variation in sizes and architectures.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312096","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

Tools and methods for cell ablation and cell inhibition in Caenorhabditis elegans. 在秀丽隐杆线虫中进行细胞消融和细胞抑制的工具和方法。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae119

Dennis Rentsch, Amelie Bergs, Jiajie Shao, Nora Elvers, Christiane Ruse, Marius Seidenthal, Ichiro Aoki, Alexander Gottschalk

引用次数: 0

Analysis of meiotic recombination in Drosophila simulans shows no evidence of an interchromosomal effect. 对模拟果蝇减数分裂重组的分析表明，没有证据表明存在染色体间效应。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae084

Bowen Man, Elizabeth Kim, Alekhya Vadlakonda, David L Stern, K Nicole Crown

{"title":"Analysis of meiotic recombination in Drosophila simulans shows no evidence of an interchromosomal effect.","authors":"Bowen Man, Elizabeth Kim, Alekhya Vadlakonda, David L Stern, K Nicole Crown","doi":"10.1093/genetics/iyae084","DOIUrl":"10.1093/genetics/iyae084","url":null,"abstract":"Chromosome inversions are of unique importance in the evolution of genomes and species because when heterozygous with a standard arrangement chromosome, they suppress meiotic crossovers within the inversion. In Drosophila species, heterozygous inversions also cause the interchromosomal effect, whereby the presence of a heterozygous inversion induces a dramatic increase in crossover frequencies in the remainder of the genome within a single meiosis. To date, the interchromosomal effect has been studied exclusively in species that also have high frequencies of inversions in wild populations. We took advantage of a recently developed approach for generating inversions in Drosophila simulans, a species that does not have inversions in wild populations, to ask if there is an interchromosomal effect. We used the existing chromosome 3R balancer and generated a new chromosome 2L balancer to assay for the interchromosomal effect genetically and cytologically. We found no evidence of an interchromosomal effect in D. simulans. To gain insights into the underlying mechanistic reasons, we qualitatively analyzed the relationship between meiotic double-stranded break (DSB) formation and synaptonemal complex (SC) assembly. We found that the SC is assembled prior to DSB formation as in D. melanogaster; however, we show that the SC is assembled prior to localization of the oocyte determination factor Orb, whereas in D. melanogaster, SC formation does not begin until the Orb is localized. Together, our data show no evidence that heterozygous inversions in D. simulans induce an interchromosomal effect and that there are differences in the developmental programming of the early stages of meiosis.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141066010","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

Single nucleotide polymorphism profile for quantitative trait nucleotide in populations with small effective size and its impact on mapping and genomic predictions. 小有效规模种群中数量性状核苷酸的 SNP 图谱及其对制图和基因组预测的影响。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae103

Ivan Pocrnic, Daniela Lourenco, Ignacy Misztal

{"title":"Single nucleotide polymorphism profile for quantitative trait nucleotide in populations with small effective size and its impact on mapping and genomic predictions.","authors":"Ivan Pocrnic, Daniela Lourenco, Ignacy Misztal","doi":"10.1093/genetics/iyae103","DOIUrl":"10.1093/genetics/iyae103","url":null,"abstract":"Increasing SNP density by incorporating sequence information only marginally increases prediction accuracies of breeding values in livestock. To find out why, we used statistical models and simulations to investigate the shape of distribution of estimated SNP effects (a profile) around quantitative trait nucleotides (QTNs) in populations with a small effective population size (Ne). A QTN profile created by averaging SNP effects around each QTN was similar to the shape of expected pairwise linkage disequilibrium (PLD) based on Ne and genetic distance between SNP, with a distinct peak for the QTN. Populations with smaller Ne showed lower but wider QTN profiles. However, adding more genotyped individuals with phenotypes dragged the profile closer to the QTN. The QTN profile was higher and narrower for populations with larger compared to smaller Ne. Assuming the PLD curve for the QTN profile, 80% of the additive genetic variance explained by each QTN was contained in ± 1/Ne Morgan interval around the QTN, corresponding to 2 Mb in cattle and 5 Mb in pigs and chickens. With such large intervals, identifying QTN is difficult even if all of them are in the data and the assumed genetic architecture is simplistic. Additional complexity in QTN detection arises from confounding of QTN profiles with signals due to relationships, overlapping profiles with closely spaced QTN, and spurious signals. However, small Ne allows for accurate predictions with large data even without QTN identification because QTNs are accounted for by QTN profiles if SNP density is sufficient to saturate the segments.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447368","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

From heterosis to outbreeding depression: genotype-by-environment interaction shifts hybrid fitness in opposite directions. 从异花授粉到外交抑制：基因型与环境的相互作用使杂种优势向相反的方向转移。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae090

Haolong Wang, Baofeng Su, Ying Zhang, Mei Shang, Shangjia Li, De Xing, Jinhai Wang, Logan Bern, Andrew Johnson, Jacob Al-Armanazi, Tasnuba Hasin, Darshika Hettiarachchi, Abel Paladines Parrales, Hamza Dilawar, Timothy J Bruce, Rex A Dunham, Xu Wang

{"title":"From heterosis to outbreeding depression: genotype-by-environment interaction shifts hybrid fitness in opposite directions.","authors":"Haolong Wang, Baofeng Su, Ying Zhang, Mei Shang, Shangjia Li, De Xing, Jinhai Wang, Logan Bern, Andrew Johnson, Jacob Al-Armanazi, Tasnuba Hasin, Darshika Hettiarachchi, Abel Paladines Parrales, Hamza Dilawar, Timothy J Bruce, Rex A Dunham, Xu Wang","doi":"10.1093/genetics/iyae090","DOIUrl":"10.1093/genetics/iyae090","url":null,"abstract":"In F1 hybrids, phenotypic values are expected to be near the parental means under additive effects or close to one parent under dominance. However, F1 traits can fall outside the parental range, and outbreeding depression occurs when inferior fitness is observed in hybrids. Another possible outcome is heterosis, a phenomenon that interspecific hybrids or intraspecific crossbred F1s exhibit improved fitness compared to both parental species or strains. As an application of heterosis, hybrids between channel catfish females and blue catfish males are superior in feed conversion efficiency, carcass yield, and harvestability. Over 20 years of hybrid catfish production in experimental settings and farming practices generated abundant phenotypic data, making it an ideal system to investigate heterosis. In this study, we characterized fitness in terms of growth and survival longitudinally, revealing environment-dependent heterosis. In ponds, hybrids outgrow both parents due to an extra rapid growth phase of 2-4 months in year 2. This bimodal growth pattern is unique to F1 hybrids in pond culture environments only. In sharp contrast, the same genetic types cultured in tanks display outbreeding depression, where hybrids perform poorly, while channel catfish demonstrate superiority in growth throughout development. Our findings represent the first example, known to the authors, of opposite fitness shifts in response to environmental changes in interspecific vertebrate hybrids, suggesting a broader fitness landscape for F1 hybrids. Future genomic studies based on this experiment will help understand genome-environment interaction in shaping the F1 progeny fitness in the scenario of environment-dependent heterosis and outbreeding depression.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162728","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

Calcium influx rapidly establishes distinct spatial recruitments of Annexins to cell wounds. 钙离子的流入会迅速在细胞伤口处形成不同的附件蛋白空间招募。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae101

Mitsutoshi Nakamura, Susan M Parkhurst

引用次数: 0

The cytidine deaminase APOBEC3C has unique sequence and genome feature preferences. 胞苷脱氨酶 APOBEC3C 具有独特的序列和基因组特征偏好。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae092

Grant W Brown

引用次数: 0

The Caenorhabditis elegans cuticle and precuticle: a model for studying dynamic apical extracellular matrices in vivo. 秀丽隐杆线虫的角质层和前角质层：研究体内动态顶端细胞外基质的模型。

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae072

Meera V Sundaram, Nathalie Pujol

{"title":"The Caenorhabditis elegans cuticle and precuticle: a model for studying dynamic apical extracellular matrices in vivo.","authors":"Meera V Sundaram, Nathalie Pujol","doi":"10.1093/genetics/iyae072","DOIUrl":"10.1093/genetics/iyae072","url":null,"abstract":"Apical extracellular matrices (aECMs) coat the exposed surfaces of animal bodies to shape tissues, influence social interactions, and protect against pathogens and other environmental challenges. In the nematode Caenorhabditis elegans, collagenous cuticle and zona pellucida protein-rich precuticle aECMs alternately coat external epithelia across the molt cycle and play many important roles in the worm's development, behavior, and physiology. Both these types of aECMs contain many matrix proteins related to those in vertebrates, as well as some that are nematode-specific. Extensive differences observed among tissues and life stages demonstrate that aECMs are a major feature of epithelial cell identity. In addition to forming discrete layers, some cuticle components assemble into complex substructures such as ridges, furrows, and nanoscale pillars. The epidermis and cuticle are mechanically linked, allowing the epidermis to sense cuticle damage and induce protective innate immune and stress responses. The C. elegans model, with its optical transparency, facilitates the study of aECM cell biology and structure/function relationships and all the myriad ways by which aECM can influence an organism.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141601988","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

Estimating genetic variance contributed by a quantitative trait locus: removing nuisance parameters. 估算数量性状基因座贡献的遗传变异：去除干扰参数

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae095

Shizhong Xu

{"title":"Estimating genetic variance contributed by a quantitative trait locus: removing nuisance parameters.","authors":"Shizhong Xu","doi":"10.1093/genetics/iyae095","DOIUrl":"10.1093/genetics/iyae095","url":null,"abstract":"The main objective of mapping quantitative trait loci (QTL) and genome-wide association studies (GWAS) is to identify and locate QTLs on the genome. Estimating the sizes of QTL is equally important as identifying the QTLs. The size of a QTL is often measured by the QTL variance, or the proportion of phenotypic variance explained by the QTL, known as the QTL heritability. The reported QTL heritability is biased upward for small-sized QTLs estimated from small samples, especially in GWAS with a very small P-value threshold accommodating to Bonferroni correction for multiple tests. The phenomenon is called the Beavis effect. Methods of correcting the Beavis effect have been developed for additive effect models. Corresponding methods are not available for QTLs with more than one effect, such as QTLs including dominance and other genetic effects. In this study, we developed explicit formulas for estimating the variances and heritability for QTL with multiple effects. We also developed a method to remove nuisance parameters via an annihilator matrix. Finally, biases in estimated QTL variances caused by the Beavis effect are investigated and corrected. The new method is demonstrated by analyzing the 1000 grain weight (KGW) trait in a hybrid rice population.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307235","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

Extracellular vesicles. 细胞外囊泡

IF 3.3 3区生物学

Genetics Pub Date : 2024-08-07 DOI: 10.1093/genetics/iyae088

Juan Wang, Maureen M Barr, Ann M Wehman

{"title":"Extracellular vesicles.","authors":"Juan Wang, Maureen M Barr, Ann M Wehman","doi":"10.1093/genetics/iyae088","DOIUrl":"10.1093/genetics/iyae088","url":null,"abstract":"Extracellular vesicles (EVs) encompass a diverse array of membrane-bound organelles released outside cells in response to developmental and physiological cell needs. EVs play important roles in remodeling the shape and content of differentiating cells and can rescue damaged cells from toxic or dysfunctional content. EVs can send signals and transfer metabolites between tissues and organisms to regulate development, respond to stress or tissue damage, or alter mating behaviors. While many EV functions have been uncovered by characterizing ex vivo EVs isolated from body fluids and cultured cells, research using the nematode Caenorhabditis elegans has provided insights into the in vivo functions, biogenesis, and uptake pathways. The C. elegans EV field has also developed methods to analyze endogenous EVs within the organismal context of development and adult physiology in free-living, behaving animals. In this review, we summarize major themes that have emerged for C. elegans EVs and their relevance to human health and disease. We also highlight the diversity of biogenesis mechanisms, locations, and functions of worm EVs and discuss open questions and unexplored topics tenable in C. elegans, given the nematode model is ideal for light and electron microscopy, genetic screens, genome engineering, and high-throughput omics.","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332329","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