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Annual review of genetics最新文献

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Prevalence and Adaptive Impact of Introgression. 渗透的普遍性及其适应性影响。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-27 DOI: 10.1146/annurev-genet-021821-020805
Nathaniel B Edelman, James Mallet
{"title":"Prevalence and Adaptive Impact of Introgression.","authors":"Nathaniel B Edelman,&nbsp;James Mallet","doi":"10.1146/annurev-genet-021821-020805","DOIUrl":"https://doi.org/10.1146/annurev-genet-021821-020805","url":null,"abstract":"<p><p>Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"265-283"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39464831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 63
Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria. 细菌中应激信号核苷酸警报素(p)ppGpp的调控主题和变化。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 DOI: 10.1146/annurev-genet-021821-025827
Brent W Anderson, Danny K Fung, Jue D Wang
{"title":"Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria.","authors":"Brent W Anderson,&nbsp;Danny K Fung,&nbsp;Jue D Wang","doi":"10.1146/annurev-genet-021821-025827","DOIUrl":"https://doi.org/10.1146/annurev-genet-021821-025827","url":null,"abstract":"<p><p>Bacterial stress-signaling alarmones are important components of a protective network against diverse stresses such as nutrient starvation and antibiotic assault. pppGpp and ppGpp, collectively (p)ppGpp, have well-documented regulatory roles in gene expression and protein translation. Recent work has highlighted another key function of (p)ppGpp: inducing rapid and coordinated changes in cellular metabolism by regulating enzymatic activities, especially those involved in purine nucleotide synthesis. Failure of metabolic regulation by (p)ppGpp results in the loss of coordination between metabolic and macromolecular processes, leading to cellular toxicity. In this review, we document how (p)ppGpp and newly characterized nucleotides pGpp and (p)ppApp directly regulate these enzymatic targets for metabolic remodeling. We examine targets' common determinants for alarmone interaction as well as their evolutionary diversification. We highlight classical and emerging themes in nucleotide signaling, including oligomerization and allostery along with metabolic interconversion and crosstalk, illustrating how they allow optimized bacterial adaptation to their environmental niches.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"55 ","pages":"115-133"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10209448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 39
Variation and Evolution of Human Centromeres: A Field Guide and Perspective. 人类着丝粒的变异和进化:野外指南和展望。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 DOI: 10.1146/annurev-genet-071719-020519
Karen H Miga, Ivan A Alexandrov
{"title":"Variation and Evolution of Human Centromeres: A Field Guide and Perspective.","authors":"Karen H Miga,&nbsp;Ivan A Alexandrov","doi":"10.1146/annurev-genet-071719-020519","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020519","url":null,"abstract":"<p><p>We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"583-602"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9549924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39651663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 26
Genomic and Epigenetic Foundations of Neocentromere Formation. 新着丝粒形成的基因组和表观遗传学基础。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-08 DOI: 10.1146/annurev-genet-071719-020924
Evon M DeBose-Scarlett, Beth A Sullivan
{"title":"Genomic and Epigenetic Foundations of Neocentromere Formation.","authors":"Evon M DeBose-Scarlett,&nbsp;Beth A Sullivan","doi":"10.1146/annurev-genet-071719-020924","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020924","url":null,"abstract":"<p><p>Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Normally, centromeres are assembled and maintained at the same chromosomal location. However, ectopic centromeres form spontaneously at new genomic locations and contribute to genome instability and developmental defects as well as to acquired and congenital human disease. Studies in model organisms have suggested that certain regions of the genome, including pericentromeres, heterochromatin, and regions of open chromatin or active transcription, support neocentromere activation. However, there is no universal mechanism that explains neocentromere formation. This review focuses on recent technological and intellectual advances in neocentromere research and proposes future areas of study. Understanding neocentromere biology will provide a better perspective on chromosome and genome organization and functional context for information generated from the Human Genome Project, ENCODE, and other large genomics consortia.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"331-348"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39395731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 12
Green Algal Models for Multicellularity. 多细胞绿藻模型。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-21 DOI: 10.1146/annurev-genet-032321-091533
James Umen, Matthew D Herron
{"title":"Green Algal Models for Multicellularity.","authors":"James Umen,&nbsp;Matthew D Herron","doi":"10.1146/annurev-genet-032321-091533","DOIUrl":"https://doi.org/10.1146/annurev-genet-032321-091533","url":null,"abstract":"<p><p>The repeated evolution of multicellularity across the tree of life has profoundly affected the ecology and evolution of nearly all life on Earth. Many of these origins were in different groups of photosynthetic eukaryotes, or algae. Here, we review the evolution and genetics of multicellularity in several groups of green algae, which include the closest relatives of land plants. These include millimeter-scale, motile spheroids of up to 50,000 cells in the volvocine algae; decimeter-scale seaweeds in the genus <i>Ulva</i> (sea lettuce); and very plantlike, meter-scale freshwater algae in the genus <i>Chara</i> (stoneworts). We also describe algae in the genus <i>Caulerpa</i>, which are giant, multinucleate, morphologically complex single cells. In each case, we review the life cycle, phylogeny, and genetics of traits relevant to the evolution of multicellularity, and genetic and genomic resources available for the group in question. Finally, we suggest routes toward developing these groups as model organisms for the evolution of multicellularity.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"603-632"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39435901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 15
Museum Genomics. 博物馆基因组学。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-23 DOI: 10.1146/annurev-genet-071719-020506
Daren C Card, Beth Shapiro, Gonzalo Giribet, Craig Moritz, Scott V Edwards
{"title":"Museum Genomics.","authors":"Daren C Card,&nbsp;Beth Shapiro,&nbsp;Gonzalo Giribet,&nbsp;Craig Moritz,&nbsp;Scott V Edwards","doi":"10.1146/annurev-genet-071719-020506","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020506","url":null,"abstract":"<p><p>Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"633-659"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39464476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 35
DREAM On: Cell Cycle Control in Development and Disease. DREAM On:发育和疾病中的细胞周期控制。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-08 DOI: 10.1146/annurev-genet-071819-103836
Hayley Walston, Audra N Iness, Larisa Litovchick
{"title":"DREAM On: Cell Cycle Control in Development and Disease.","authors":"Hayley Walston,&nbsp;Audra N Iness,&nbsp;Larisa Litovchick","doi":"10.1146/annurev-genet-071819-103836","DOIUrl":"https://doi.org/10.1146/annurev-genet-071819-103836","url":null,"abstract":"<p><p>Perfectly orchestrated periodic gene expression during cell cycle progression is essential for maintaining genome integrity and ensuring that cell proliferation can be stopped by environmental signals. Genetic and proteomic studies during the past two decades revealed remarkable evolutionary conservation of the key mechanisms that control cell cycle-regulated gene expression, including multisubunit DNA-binding DREAM complexes. DREAM complexes containing a retinoblastoma family member, an E2F transcription factor and its dimerization partner, and five proteins related to products of <i>Caenorhabditis elegans</i> multivulva (Muv) class B genes <i>lin-9</i>, <i>lin-37</i>, <i>lin-52</i>, <i>lin-53</i>, and <i>lin-54</i> (comprising the MuvB core) have been described in diverse organisms, from worms to humans. This review summarizes the current knowledge of the structure, function, and regulation of DREAM complexes in different organisms, as well as the role of DREAM in human disease.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"309-329"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39395730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 20
RAD51 Gene Family Structure and Function. RAD51基因家族结构与功能。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-07-14 DOI: 10.1146/annurev-genet-021920-092410
Braulio Bonilla, Sarah R Hengel, McKenzie K Grundy, Kara A Bernstein
{"title":"<i>RAD51</i> Gene Family Structure and Function.","authors":"Braulio Bonilla,&nbsp;Sarah R Hengel,&nbsp;McKenzie K Grundy,&nbsp;Kara A Bernstein","doi":"10.1146/annurev-genet-021920-092410","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-092410","url":null,"abstract":"<p><p>Accurate DNA repair and replication are critical for genomic stability and cancer prevention. <i>RAD51</i> and its gene family are key regulators of DNA fidelity through diverse roles in double-strand break repair, replication stress, and meiosis. RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable accurate and timely DNA repair. Its paralogs, which arose from ancient gene duplications of <i>RAD51</i>, have evolved to regulate and promote RAD51 function. Underscoring its importance, misregulation of RAD51, and its paralogs, is associated with diseases such as cancer and Fanconi anemia. In this review, we focus on the mammalian RAD51 structure and function and highlight the use of model systems to enable mechanistic understanding of RAD51 cellular roles. We also discuss how misregulation of the <i>RAD51</i> gene family members contributes to disease and consider new approaches to pharmacologically inhibit RAD51.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"25-46"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-092410","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38157713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 92
Linking Genes to Shape in Plants Using Morphometrics. 利用形态计量学将植物的基因与形状联系起来。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-04 DOI: 10.1146/annurev-genet-022620-094553
Hao Xu, George W Bassel
{"title":"Linking Genes to Shape in Plants Using Morphometrics.","authors":"Hao Xu,&nbsp;George W Bassel","doi":"10.1146/annurev-genet-022620-094553","DOIUrl":"https://doi.org/10.1146/annurev-genet-022620-094553","url":null,"abstract":"<p><p>A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"417-437"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022620-094553","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 8
Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms. 线粒体是后生动物出现的基础:新陈代谢、基因组调控和复杂生物的诞生。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-28 DOI: 10.1146/annurev-genet-021920-105545
Hadar Medini, Tal Cohen, Dan Mishmar
{"title":"Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms.","authors":"Hadar Medini,&nbsp;Tal Cohen,&nbsp;Dan Mishmar","doi":"10.1146/annurev-genet-021920-105545","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-105545","url":null,"abstract":"<p><p>Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (<i>a</i>) Differentiation and embryogenesis rely on mitochondrial function; (<i>b</i>) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (<i>c</i>) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"151-166"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-105545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38319653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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: 9
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