Genome dynamics最新文献

{"title":"Helicobacter pylori Sequences Reflect Past Human Migrations.","authors":"Y Moodley,&nbsp;B Linz","doi":"10.1159/000235763","DOIUrl":"https://doi.org/10.1159/000235763","url":null,"abstract":"<p><p>The long association between the stomach bacterium Helicobacter pylori and humans, in combination with its predominantly within-family transmission route and its exceptionally high DNA sequence diversity, make this bacterium a reliable marker for discerning both recent and ancient human population movements. As much of the diversity in H. pylori sequences is generated by recombination and mutation on a local scale, the partitioning of H. pylori sequences from a large globally distributed data set into six geographic populations enabled the detection of recent ( < 500 years) human population movements including the European colonial expansion and the slave trade. The further separation of bacterial populations into distinct sub-populations traced prehistoric population movements like the settlement of the Americas by Asians across the Bering Strait and the Bantu migrations in Africa. The ability to deduce ancestral population structure from modern sequences was a key development that allowed the detection of zones of admixture, such as Europe, and the inference of multiple migration waves into these zones. The significantly similar global population structure of both H. pylori and humans confirmed not only an evolutionary time-scale association between host and parasite, but also that humans had carried H. pylori in their stomachs on their migrations out of Africa.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"6 ","pages":"62-74"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000235763","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28353554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptation of Pathogenic E. coli to Various Niches: Genome Flexibility is the Key.","authors":"E Brzuszkiewicz,&nbsp;G Gottschalk,&nbsp;E Ron,&nbsp;J Hacker,&nbsp;U Dobrindt","doi":"10.1159/000235766","DOIUrl":"https://doi.org/10.1159/000235766","url":null,"abstract":"<p><p>It is a well-known observation and a long-standing hypothesis that pathogen genome dynamics are important in infectious disease processes. Recent achievements in large-scale genome sequencing, comparative genomics and molecular epidemiology help to unravel current challenges of E. coli pathogenomics, i.e. to gain insights into the in vivo relevance of genome dynamics. Data from comparative genomics support the hypothesis of widespread involvement of horizontal gene transfer in the evolution of E. coli, leading to the presence of distinct and variable 'genomic islands' within the conserved 'chromosomal backbone' in several bacterial lineages. Extensive gene acquisition and loss provide different lineages with distinct metabolic, pathogenic and other capabilities. Not only mobile genetic modules but also point mutations facilitate rapid adaptation of E. coli to changing environmental conditions and hence extend the spectrum of sites that can be infected. We report on recent research efforts to analyze pathoadaptive and other genomic alterations of the E. coli genome that affect disease severity and may have consequences for diagnostics and treatment of E. coli infections.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"6 ","pages":"110-125"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000235766","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28353557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meiosis in cereal crops: the grasses are back.","authors":"E Martinez-Perez","doi":"10.1159/000166617","DOIUrl":"https://doi.org/10.1159/000166617","url":null,"abstract":"<p><p>A major goal of breeding programs is to increase and manipulate the genetic diversity of crops. The incorporation of beneficial genes from wild relatives into crops is achieved by producing hybrid plants in which meiotic recombination events occur between the two genomes. Furthering our understanding of meiosis in the cereals could enable the manipulation of homolog pairing and recombination, significantly enhancing the efficiency of breeding programs. The main obstacle to the genetic analysis of meiosis in cereal crops has been the complex organization of most cereal genomes, many of which are polyploid. However, the recent sequencing of the rice genome, the use of insertional mutagenesis and reverse genetics approaches has opened the door for the genetic and genomic analysis of cereal meiosis. The goal of this review is to show how these new resources, as well as the use of three-dimensional microscopy, are rapidly providing insights into the mechanisms that control pairing, recombination and segregation of homologous chromosomes during meiosis in four major cereal crops: wheat, rice, maize and rye.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"26-42"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166617","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27815802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The meiotic recombination hotspots of Schizosaccharomyces pombe.","authors":"D W Pryce,&nbsp;R J McFarlane","doi":"10.1159/000166614","DOIUrl":"https://doi.org/10.1159/000166614","url":null,"abstract":"<p><p>Meiotic recombination predominantly occurs at genomic loci referred to as recombination hotspots. The fission yeast, Schizosaccharomyces pombe, has proved to be an excellent model organism in which to study details of the molecular basis of meiotic recombination hotspot activation. S. pombe has a number of different classes of meiotic hotspots, indicating that a single pathway does not confer hotspot activity throughout the genome. The M26-related hotspots are a particularly well characterised group of hotspots and details of the molecular activation of M26-related hotspots are now coming to light. Moreover, genome-wide DNA array analysis has been applied to the question of meiotic recombination in this organism and we are now starting to get a picture of recombination hotspot distribution on a genome-wide scale.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166614","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27816391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Helicobacter pylori Genome Plasticity.","authors":"D A Baltrus,&nbsp;M J Blaser,&nbsp;K Guillemin","doi":"10.1159/000235764","DOIUrl":"https://doi.org/10.1159/000235764","url":null,"abstract":"<p><p>Helicobacter pylori, a Gram-negative pathogen associated with ulcers, chronic gastritis, and gastric cancers, has been a resident of the human stomach since early human history [1]. This association has only recently begun to erode with the advent of antibiotics and modern lifestyles, but even today H. pylori colonizes approximately half the world's population. To have remained a successful colonizer of humans during thousands of years of association, populations of H. pylori must have been able to survive and adapt to countless evolutionary challenges within and between hosts. As a species, H. pylori possesses one of the most fluid genomes within the prokaryotic kingdom [2], a characteristic that has likely aided its continued success. H. pylori exhibits exceptionally high rates of DNA point mutations, intragenomic recombination (facilitated by repetitive elements common in H. pylori genomes), and intergenomic recombination (mediated by natural transformation), all of which contribute to the high genomic variability between isolates. Previous reviews have focused on these processes as agents of evolutionary change within H. pylori [2-8]. The mechanisms of both mutation and natural transformation, and the evolutionary processes that retain genetic variation generated by these mechanisms, dictate the extent to which each contributes to genomic diversity in the context of different bacterial population structures [9-13]. Unlike well-studied evolutionary systems, such as Salmonella and Escherichia coli, H. pylori is notable in its lack of an environmental reservoir outside of human and other primate stomachs, suggesting that between-host survival is a relatively weak determinant of selection pressures [14, 15]. Given that H. pylori exist largely as distinct host-associated populations, it is possible to begin to model the evolutionary mechanisms that affect the long-term persistence of this species. In this chapter, we consider how the attributes of H. pylori's natural history as a long-term resident of the human stomach and the specific mechanisms of mutation and genetic exchange in this organism have shaped the H. pylori genome. We begin with a survey of genome plasticity in H. pylori. We then discuss mechanisms of mutation and natural transformation in H. pylori and examine experimental evidence for the generation of genomic changes within populations. Finally, we consider how different models of H. pylori population structure affect the relative contributions of mutation and recombination to the evolutionary success of this organism. By bridging evolutionary studies with investigations of pathogenesis from a molecular perspective, we hope to shed new light on how H. pylori has and continues to evolve with its human hosts.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"6 ","pages":"75-90"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000235764","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28353555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of Horizontal Gene Transfer in the Evolution of Pseudomonas aeruginosa Virulence.","authors":"X Qiu,&nbsp;B R Kulasekara,&nbsp;S Lory","doi":"10.1159/000235767","DOIUrl":"https://doi.org/10.1159/000235767","url":null,"abstract":"<p><p>The opportunistic pathogen Pseudomonas aeruginosa causes serious infections in immunocompromised patients and individuals with cystic fibrosis (CF). It is one of the most versatile organisms as illustrated by its ability to occupy a wide range of environmental niches. Comparative genomic analysis suggests that horizontal gene transfer (HGT) plays a significant role in determining the genetic repertoire of each strain. Genomic diversity is, in part, due to the acquisition of genetic material that has integrated into the chromosome at a relatively limited number of sites. The resulting genomic islands (GIs) contain genes specifying virulence traits as well as genes that may enhance fitness in a specific environmental niche. Several islands are integrative and conjugative elements (ICEs) that may have evolved from ancestral self-transmissible conjugative plasmids. For some genomic islands, the mechanism of acquisition is not apparent suggesting that the mechanisms utlized are either transformation or bacteriophage-mediated generalized transduction. It appears that HGT takes place primarily in the natural environment of P. aeruginosa and, conceivably, an uncharacterized host-pathogen interaction provides the selective pressures for acquisition and maintenance of the observed virulence phenotypes.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"6 ","pages":"126-139"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000235767","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28353558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homolog pairing and segregation in Drosophila meiosis.","authors":"B D McKee","doi":"10.1159/000166619","DOIUrl":"https://doi.org/10.1159/000166619","url":null,"abstract":"<p><p>Pairing of homologous chromosomes is fundamental to their reliable segregation during meiosis I and thus underlies sexual reproduction. In most eukaryotes homolog pairing is confined to prophase of meiosis I and is accompanied by frequent exchanges, known as crossovers, between homologous chromatids. Crossovers give rise to chiasmata, stable interhomolog connectors that are required for bipolar orientation (orientation to opposite poles) of homologs during meiosis I. Drosophila is unique among model eukaryotes in exhibiting regular homolog pairing in mitotic as well as meiotic cells. I review the results of recent molecular studies of pairing in both mitosis and meiosis in Drosophila. These studies show that homolog pairing is continuous between pre-meiotic mitosis and meiosis but that pairing frequencies and patterns are altered during the mitotic-meiotic transition. They also show that, with the exception of X-Y pairing in male meiosis, which is mediated specifically by the 240-bp rDNA spacer repeats, chromosome pairing is not restricted to specific sites in either mitosis or meiosis. Instead, virtually all chromosome regions, both heterochromatic and euchromatic, exhibit autonomous pairing capacity. Mutations that reduce the frequencies of both mitotic and meiotic pairing have been recently described, but no mutations that abolish pairing completely have been discovered, and the genetic control of pairing in Drosophila remains to be elucidated.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"56-68"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166619","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27815804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cohesin complexes and sister chromatid cohesion in mammalian meiosis.","authors":"J A Suja, J L Barbero","doi":"10.1159/000166622","DOIUrl":"10.1159/000166622","url":null,"abstract":"<p><p>Maintenance and precise regulation of sister chromatid cohesion is essential to ensure correct attachment of chromosomes to the spindle, thus preserving genome integrity by correct chromosome segregation. Errors in these processes often lead to aneuploidy, frequently implicated in cell death and/or tumor development. The so-called cohesin complexes are essential in sister chromatid cohesion during both mitosis and meiosis; they are responsible for maintaining sister chromatids together physically until their segregation during the metaphase/anaphase transition. The recent identification of new molecules involved in the control of sister chromatid cohesion, and the characterization of mouse loss-of-function models, have improved our understanding of the variety of cohesin complexes and their chromatin binding and removal regulation. This review will focus basically on the distribution and function of cohesin complexes during mammalian meiosis.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"94-116"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166622","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27815807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomics of host-restricted pathogens of the genus bartonella.","authors":"P Engel,&nbsp;C Dehio","doi":"10.1159/000235769","DOIUrl":"https://doi.org/10.1159/000235769","url":null,"abstract":"<p><p>The alpha-proteobacterial genus Bartonella comprises numerous arthropod-borne pathogens that share a common host-restricted life-style, which is characterized by long-lasting intraerythrocytic infections in their specific mammalian reservoirs and transmission by blood-sucking arthropods. Infection of an incidental host (e.g. humans by a zoonotic species) may cause disease in the absence of intra-erythrocytic infection. The genome sequences of four Bartonella species are known, i.e. those of the human-specific pathogens Bartonella bacilliformis and Bartonella quintana, the feline-specific Bartonella henselae also causing incidental human infections, and the rat-specific species Bartonella tribocorum. The circular chromosomes of these bartonellae range in size from 1.44 Mb (encoding1,283 genes) to 2.62 Mb (encoding 2,136 genes). They share a mostly synthenic core genome of 959 genes that features characteristics of a host-integrated metabolism. The diverse accessory genomes highlight dynamic genome evolution at the species level, ranging from significant genome expansion in B. tribocorum due to gene duplication and lateral acquisition of prophages and genomic islands (such as type IV secretion systems that adopted prominent roles in host adaptation and specificity) to massive secondary genome reduction in B. quintana. Moreover, analysis of natural populations of B. henselae revealed genomic rearrangements, deletions and amplifications, evidencing marked genome dynamics at the strain level.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"6 ","pages":"158-169"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000235769","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28352918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inverted meiosis: the true bugs as a model to study.","authors":"A Viera,&nbsp;J Page,&nbsp;J S Rufas","doi":"10.1159/000166639","DOIUrl":"https://doi.org/10.1159/000166639","url":null,"abstract":"<p><p>Most of the meiotic literature is based on species with monocentric chromosomes, however meiosis in protoctist, plant and animal species with holocentric chromosomes is less characterized. In some cases, an inverted meiotic sequence is claimed to occur, in which segregation of homologs is postponed until the second meiotic division. Additionally, other features also deserve interest, namely: (i) the different behavior of sex chromosomes if compared to that of the autosomes; (ii) the absence of a canonical kinetochore structure; (iii) the restriction of the kinetic activity to the chromosomal ends; (iv) the variations in the orientation of bivalents at the division plate, and (v) the possible occurrence of chiasma terminalization. Here we summarize the current knowledge on these topics in the meiosis of Hemiptera (Heteroptera) and present novel results that illustrate some of the special features mentioned above. We also point out the necessity of reviewing the term 'inverted meiosis' and propose some future prospects to study this peculiar meiosis.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"5 ","pages":"137-156"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000166639","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27816235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}