Genome dynamics最新文献

{"title":"miRNAs in the Plant Genome: All Things Great and Small.","authors":"B C Meyers,&nbsp;P J Green,&nbsp;C Lu","doi":"10.1159/000126010","DOIUrl":"https://doi.org/10.1159/000126010","url":null,"abstract":"<p><p>Plants produce two major types of small RNAs that are 21 to 24 nucleotides in size. Small interfering RNAs (siRNAs) are typically involved in transcriptional gene silencing that results from the targeting of genomic DNA and triggering of histone modifications or DNA methylation. Deep sequencing experiments have demonstrated that thousands of loci, usually repetitive sequences, generate these siRNAs. In contrast, microRNAs (miRNAs) are encoded by perhaps just several hundred loci per genome that generate Pol II-derived single stranded precursors which are processed into specific miRNAs. miRNAs act in a post-transcriptional manner to regulate gene function. Recent work has focused on the identification and classification of small RNA-producing loci, as well as understanding small RNA targeting and function, and the evolution of this relatively recently discovered class of regulatory molecules.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"4 ","pages":"108-118"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000126010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27644108","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 rice genome structure as a trail from the past to beyond.","authors":"T Sasaki","doi":"10.1159/000126012","DOIUrl":"https://doi.org/10.1159/000126012","url":null,"abstract":"<p><p>Rice is the first cultivated plant species to be completely sequenced. Cultivation, in general, is a major factor that contributes to selection pressure of a target species resulting in accelerated changes in genome structure from an original wild species. The genome sequence of cultivated rice can now be used as a standard for comparison with many other cultivated rice species, its wild relatives and other grass species. Several indices define the dynamic nature of genome structure and function. Genome dynamics in rice is described here based on transposon, retrotransposon and polyploidy. Comparative studies with other related grass species based on the principle of synteny are expected to generate invaluable information that will clarify the trail that led to the present cultivated rice as well as the trail that will lead to its further improvement.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"4 ","pages":"131-142"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000126012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27644110","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":"Grass genome structure and evolution.","authors":"Joachim Messing,&nbsp;Jeffrey L Bennetzen","doi":"10.1159/000126005","DOIUrl":"https://doi.org/10.1159/000126005","url":null,"abstract":"<p><p>Advances in the construction of large insert libraries and physical maps have facilitated the sequencing of orthologous regions from related plant species that differ in genome size. This approach has been particularly productive for the Poaceae, including many important cereal crops. When the sequences of orthologous regions from closely related species are aligned, we can analyze the details of chromosomal evolution. The dynamics of chromosome structure appears to be driven by two types of rearrangement mechanisms, 'cut and paste' and 'copy and paste'. The latter mechanism has contributed to the expansion of orthologous regions, primarily by transposon amplification, while ongoing deletions by illegitimate and homologous recombination have at least partially counteracted or reversed this expansion in some regions. This review describes the current status of our understanding of the plasticity of plant genomes, emphasizing maize as a model for these studies.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"4 ","pages":"41-56"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000126005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27644158","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":"Recent insights into the evolution of genetic diversity of maize.","authors":"A Rafalski,&nbsp;S Tingey","doi":"10.1159/000126011","DOIUrl":"https://doi.org/10.1159/000126011","url":null,"abstract":"<p><p>Evolutionary changes that occur within the maize genome can be divided into two classes: In the protein-coding regions, mutations that survive selective pressure primarily consist of single nucleotide polymorphisms which evolve at a relatively slow rate (10-9 mutations/ bp/generation), and functionally detrimental insertions are strongly selected against. In intergenic regions rapidly evolving (10-4 10-8 mutations/bp/generation) transposon insertions and deletions predominate. While genic single nucleotide changes are expected in part to result in amino acid sequence variants leading to the modification of protein properties (catalytic properties of enzymes, binding constants, etc.), transposable elements and other large insertions and deletions, when functionally relevant, are predicted to be regulatory in nature and may affect gene expression at distances of up to 100 kb away. Here, we discuss recent experimental evidence for massive dynamic changes of maize intergenic regions and the predicted functional consequences of genome diversity within this species.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"4 ","pages":"119-130"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000126011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27644109","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":"Paleopolyploidy and its impact on the structure and function of modern plant genomes.","authors":"A H Paterson","doi":"10.1159/000125999","DOIUrl":"https://doi.org/10.1159/000125999","url":null,"abstract":"<p><p>Partial or complete genome duplication is a punctuational event in the evolutionary history of a lineage, with permanent consequences for all descendants. Careful analysis of burgeoning cDNA and genomic sequence data have underlined the importance of genome duplication in the evolution of biological diversity. Of singular importance among the consequences of paleopolyploidy is the extensive loss (or degradation beyond recognition) of duplicated genes. Gene loss complicates genome comparisons by fragmenting ancestral gene orders across multiple chromosomes, and may also link genome duplication to speciation. The recent discovery in angiosperms of gene functional groups that are 'duplicationresistant', i.e. which are preferentially returned to singleton status following genome duplications, adds a new dimension to classical views that focus on the potential advantages of genome duplication as a source of genes with new functions. The surprisingly conservative evolution of coding sequences that are preserved in duplicate, suggests still additional new dimensions in the spectrum of fates of duplicated genes. Looking forward, their many independent genome duplications, together with extensive sets of computational and experimental tools and resources, suggest that the angiosperms may play a major role in clarifying the structural, functional and evolutionary consequences of paleopolyploidy.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"4 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000125999","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27644155","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":"Plant transposable elements.","authors":"J M Deragon,&nbsp;J M Casacuberta,&nbsp;O Panaud","doi":"10.1159/000126007","DOIUrl":"https://doi.org/10.1159/000126007","url":null,"abstract":"<p><p>Genomic programs are yielding tremendous amounts of data about plant genomes and their expression. In order to exploit and understand this data it will be necessary to determine the mechanisms leading to natural variation of patterns of gene expression. The ability to understand how gene expression varies among populations (and not only within the population used in the genomics program) and following the exposure of plants to various stress conditions will be fundamental to progress in the post-genomics phase. Transposable elements (TEs) make up nearly half of the total amount of DNA in many plant genomes, so definition of their influence on genome structure and gene expression is of clear significance to the understanding of global genome regulation and phenotype variations. We describe here the different types of plant TEs and recent examples on how they contribute to structure, evolution and genetic control architecture of plant genomes.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"4 ","pages":"69-82"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000126007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27644160","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":"Evolution of gene function on the X chromosome versus the autosomes.","authors":"N D Singh,&nbsp;D A Petrov","doi":"10.1159/000107606","DOIUrl":"https://doi.org/10.1159/000107606","url":null,"abstract":"<p><p>Sex chromosomes have arisen from autosomes many times over the course of evolution. This process generates chromosomal heteromorphy between the sexes, which has important implications for the evolution of coding and noncoding sequences on the sex chromosomes versus the autosomes. The formation of sex chromosomes from autosomes involves a reduction in gene dosage, which can modify properties of selection pressure on sex-linked genes. This transition also generates differences in the effective population size and dominance characteristics of novel mutations on the sex chromosome versus the autosomes. All of these changes may affect both patterns of in situ gene evolution and the rates of interchromosomal gene duplication and movement. Here we present a synopsis of the current understanding of the origin of sex chromosomes, theoretical context for differences in rates and patterns of molecular evolution on the X chromosome versus the autosomes, as well as a summary of empirical molecular evolutionary data from Drosophila and mammalian genomes.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"3 ","pages":"101-118"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000107606","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27642855","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":"Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes.","authors":"J-N Volff,&nbsp;J Brosius","doi":"10.1159/000107611","DOIUrl":"https://doi.org/10.1159/000107611","url":null,"abstract":"<p><p>A fascinating evolutionary facet of retroposition is its ability to generate a dynamic reservoir of sequences for the formation of new genes within genomes. Retroelement genes, such as gag from retrotransposons or envelope genes from endogenous retroviruses, have been repeatedly exapted and domesticated during evolution. Such genes fulfill now useful novel functions in diverse aspects of host biology, for example placenta formation in mammals. New protein-coding genes can also be generated through the reverse transcription of mRNA from 'classical' genes by the enzymatic machinery of autonomous retroelements. Many of these retrogenes, which generally show a modified expression pattern compared to their molecular progenitor, have a testis-biased expression and a potential role in spermatogenesis in different animals. New non-protein-coding RNA genes have also been repeatedly generated through retroposition during evolution. A striking evolutionary parallel has been observed between two such RNA genes, the rodent BC1 and the primate BC200 genes. Although both genes are derived from different types of sequences (tRNA and Alu short interspersed element, respectively), they are both expressed almost specifically in neurons, transported into the dendrites and included in ribonucleoprotein complexes containing the poly(A)-binding protein PABP. Both BC1 and BC200 RNA are able to inhibit translation in vitro and are progenitors of new families of short interspersed elements. These genes, which might play a role in animal behavior, provide an astonishing example of evolutionary convergence in two distinct mammalian lineages, which is also observed for placenta genes derived from endogenous retroviruses. Finally, there are indications that genes for small nucleolar RNAs (snoRNAs) and possibly microRNAs (miRNAs) can also be duplicated via retroposition. Taken together, these observations definitely demonstrate the major role of retroposition as mediator of genomic plasticity and contributor to gene novelties. Therefore, the 'retro-look' of genomes is in fact indicative of their modernity.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"3 ","pages":"175-190"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000107611","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27642800","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":"Coevolution within and between genes.","authors":"N Galtier,&nbsp;J Dutheil","doi":"10.1159/000107599","DOIUrl":"https://doi.org/10.1159/000107599","url":null,"abstract":"<p><p>Interacting biological systems do not evolve independently, as exemplified many times at the cellular, organismal and ecosystem levels. Biological molecules interact tightly, and should therefore coevolve as well. Here we review the literature about molecular coevolution, between residues within RNAs or proteins, and between proteins. A panel of methodological and bioinformatic approaches have been developed to address this issue, yielding contrasting results: a strong coevolutionary signal is detected in RNA stems, whereas proteins show only moderate, uneasy to interpret departure from the independence hypothesis. The reasons for this discrepancy are discussed.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"3 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000107599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27642365","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":"Amino acid repeats and the structure and evolution of proteins.","authors":"M M Albà,&nbsp;P Tompa,&nbsp;R A Veitia","doi":"10.1159/000107607","DOIUrl":"https://doi.org/10.1159/000107607","url":null,"abstract":"<p><p>Many proteins have repeats or runs of single amino acids. The pathogenicity of some repeat expansions has fueled proteomic, genomic and structural explorations of homopolymeric runs not only in human but in a wide variety of other organisms. Other types of amino acid repetitive structures exhibit more complex patterns than homopeptides. Irrespective of their precise organization, repetitive sequences are defined as low complexity or simple sequences, as one or a few residues are particularly abundant. Prokaryotes show a relatively low frequency of simple sequences compared to eukaryotes. In the latter the percentage of proteins containing homopolymeric runs varies greatly from one group to another. For instance, within vertebrates, amino acid repeat frequency is much higher in mammals than in amphibians, birds or fishes. For some repeats, this is correlated with the GC-richness of the regions containing the corresponding genes. Homopeptides tend to occur in disordered regions of transcription factors or developmental proteins. They can trigger the formation of protein aggregates, particularly in 'disease' proteins. Simple sequences seem to evolve more rapidly than the rest of the protein/gene and may have a functional impact. Therefore, they are good candidates to promote rapid evolutionary changes. All these diverse facets of homopolymeric runs are explored in this review.</p>","PeriodicalId":87974,"journal":{"name":"Genome dynamics","volume":"3 ","pages":"119-130"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000107607","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27642856","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}