Genome-wide comparative analysis of pogo-like transposable elements in different Fusarium species.

Abstract:

:The recent availability of genome sequences of four different Fusarium species offers the opportunity to perform extensive comparative analyses, in particular of repeated sequences. In a recent work, the overall content of such sequences in the genomes of three phylogenetically related Fusarium species, F. graminearum, F. verticillioides, and F. oxysporum f. sp. lycopersici has been estimated. In this study, we present an exhaustive characterization of pogo-like elements, named Fots, in four Fusarium genomes. Overall 10 Fot and two Fot-related miniature inverted-repeat transposable element families were identified, revealing a diversification of multiple lineages of pogo-like elements, some of which accompanied by a gain of introns. This analysis also showed that such elements are present in an unusual high proportion in the genomes of F. oxysporum f. sp. lycopersici and Nectria haematococca (anamorph F. solani f. sp. pisi) in contrast with most other fungal genomes in which retroelements are the most represented. Interestingly, our analysis showed that the most numerous Fot families all contain potentially active or mobilisable copies, thus conferring a mutagenic potential of these transposable elements and consequently a role in strain adaptation and genome evolution. This role is strongly reinforced when examining their genomic distribution which is clearly biased with a high proportion (more than 80%) located on strain- or species-specific regions enriched in genes involved in pathogenicity and/or adaptation. Finally, the different reproductive characteristics of the four Fusarium species allowed us to investigate the impact of the process of repeat-induced point mutations on the expansion and diversification of Fot elements.

journal_name

J Mol Evol

authors

Dufresne M,Lespinet O,Daboussi MJ,Hua-Van A

doi

10.1007/s00239-011-9472-1

subject

Has Abstract

pub_date

2011-10-01 00:00:00

pages

230-43

issue

3-4

eissn

0022-2844

issn

1432-1432

journal_volume

73

pub_type

杂志文章
  • Radionuclide-induced evolution of DNA and the origin of life.

    abstract::Artesian groundwaters of high radionuclide concentration are ubiquitous and may have provided the large, sustained energy sources that were required to drive the multistage process of DNA and primordial cell evolution. The rapid, early development of the genetic code as well as its degeneracy can be attributed to exce...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00161172

    authors: Martell EA

    更新日期:1992-10-01 00:00:00

  • Insertion of an intermediate repetitive sequence into a sea urchin histone-gene spacer.

    abstract::A common polymorphism of the early embryonic histone-gene repeat of Strongylocentrotus purpuratus is a 195-bp insertion within the H4-H2B spacer. The sequence, found as an insert in histone-gene repeats of 6 of 22 individuals screened, is also found at approximately 50 sites elsewhere in the genome of every individual...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02134133

    authors: Yager LN,Kaumeyer JF,Lee I,Weinberg ES

    更新日期:1987-01-01 00:00:00

  • The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes.

    abstract::The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s002390010197

    authors: Farias IP,Ortí G,Sampaio I,Schneider H,Meyer A

    更新日期:2001-08-01 00:00:00

  • Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.

    abstract::Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We obs...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-018-9876-2

    authors: Runnels CM,Lanier KA,Williams JK,Bowman JC,Petrov AS,Hud NV,Williams LD

    更新日期:2018-12-01 00:00:00

  • Nucleotide sequence comparison of the Adh gene in three drosophilids.

    abstract::The alcohol dehydrogenase (Adh) gene has been isolated from Drosophila simulans and D. mauritiana by screening lambda clone libraries of each with a previously cloned Adh gene from D. melanogaster. The isolated lambda clones were subcloned and partially sequenced to determine the relatedness of these species and to ex...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02101983

    authors: Cohn VH,Thompson MA,Moore GP

    更新日期:1984-01-01 00:00:00

  • The implications and limitations of the findings of the Viking organic analysis experiment.

    abstract::The gas chromatograph mass spectrometer instrument of the Viking mission has demonstrated the absence of organic compounds in the immediate surface layer of the two landing sites. The demonstration of the successful operation of the instrument (comparison of ground-based test data with those obtained during interplane...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01732368

    authors: Biemann K

    更新日期:1979-12-01 00:00:00

  • Experimental indication in favor of the introns-late theory: the receptor tyrosine kinase gene from the sponge Geodia cydonium.

    abstract::We have analyzed the gene that encodes receptor tyrosine kinase (RTK) from the marine sponge Geodia cydonium, which belongs to the most ancient and simple metazoan groups, the Porifera. RTKs are enzymes found only in metazoa. The sponge gene contains two introns in the extracellular part of the protein. However, the r...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/pl00006141

    authors: Gamulin V,Skorokhod A,Kavsan V,Müller IM,Müller WE

    更新日期:1997-03-01 00:00:00

  • The "Origin-of-Life Reactor" and Reduction of CO2 by H2 in Inorganic Precipitates.

    abstract::It has been suggested that inorganic membranes were forerunners of organic membranes at the origin of life. Such membranes, interposed between alkaline fluid in submarine vents and the more acidic Hadean ocean, were thought to house inorganic molecular machines. H+ flowed down the pH gradient (ΔpH) from ocean to vent ...

    journal_title:Journal of molecular evolution

    pub_type: 信件,评审

    doi:10.1007/s00239-017-9805-9

    authors: Jackson JB

    更新日期:2017-08-01 00:00:00

  • Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans.

    abstract::In this paper we present a new method for detecting block duplications in a genome. It is more stringent than previous ones in that it requires a more rigorous definition of paralogous genes and that it requires the paralogous proteins on the two blocks to be contiguous. In addition, it provides three criterion choice...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-002-2377-2

    authors: Cavalcanti AR,Ferreira R,Gu Z,Li WH

    更新日期:2003-01-01 00:00:00

  • Organization and evolution of the mitochondrial genome of yeast.

    abstract::The mitochondrial genome of yeast (S. cerevisiae or S. carlsbergensis) appears to be formed by 60-70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01796120

    authors: Bernardi G

    更新日期:1976-12-31 00:00:00

  • Molecular evolution of prolactin in primates.

    abstract::Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked seque...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-004-0239-9

    authors: Wallis OC,Mac-Kwashie AO,Makri G,Wallis M

    更新日期:2005-05-01 00:00:00

  • Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes.

    abstract::Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al. analyzed release factors and identified the amino acids therein that recognize stop codons. ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-002-2435-9

    authors: Ozawa Y,Saito R,Washio T,Tomita M

    更新日期:2003-06-01 00:00:00

  • TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes.

    abstract::Bacterial lipoproteins, characterized by the N-terminal N-acyl S-diacylglyceryl Cysteine, are key membrane proteins in bacterial homeostasis. It is generally thought that during the modification lipoprotein precursors are translocated via the Sec-machinery in an unfolded state. The recent discovery of twin-arginine tr...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-010-9334-2

    authors: Shruthi H,Babu MM,Sankaran K

    更新日期:2010-04-01 00:00:00

  • Molecular evidence from the nuclear genome for the time frame of human evolution.

    abstract::Evolutionary divergence times can be inferred from molecular distances if a molecular clock can be assumed and if the substitution rate can be estimated. We present new evidence from relative rate tests that the rate of substitution at fourfold degenerate sites of nuclear genome-coding DNA is uniform in primate and ro...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/pl00000066

    authors: Easteal S,Herbert G

    更新日期:1997-01-01 00:00:00

  • Exchanges of short polymorphic DNA segments predating speciation in feline major histocompatibility complex class I genes.

    abstract::Sequence comparisons of 14 distinct MHC class I cDNA clones isolated from species representing the three major taxonomic lineages of Felidae (domestic cat lineage, ocelot lineage, and pantherine lineage) revealed that feline MHC class I alleles have highly mosaic structures with short polymorphic sequence motifs that ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00178246

    authors: Yuhki N,O'Brien SJ

    更新日期:1994-07-01 00:00:00

  • Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred.

    abstract::Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-018-9836-x

    authors: Paquola ACM,Asif H,Pereira CAB,Feltes BC,Bonatto D,Lima WC,Menck CFM

    更新日期:2018-04-01 00:00:00

  • The Semi-Enzymatic Origin of Metabolic Pathways: Inferring a Very Early Stage of the Evolution of Life.

    abstract::The early evolution of life is a period with many important events with a lot of big and open questions. One of them is the evolution of metabolic pathways, which means the origin and assembly of enzymes that act together. The retrograde hypothesis was the first attempt to explain the origin and evolutionary history o...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-021-09994-0

    authors: Becerra A

    更新日期:2021-01-28 00:00:00

  • Hemoglobin Vancouver [alpha2beta2(73)(E17) Asp replaced by Tyr]: its structure and function.

    abstract::Hemoglobin Vancouver is a new abnormal hemoglobin with an amino acid substitution of the normal aspartyl residue 73 of the beta chain by a tyrosyl residue. It was discovered in a man of Chinese descent in association with beta thalassemia. It was subsequently detected in a sister in association with normal Hb A. The o...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01796121

    authors: Jones RT,Brimhall B,Pootrakul S,Gray G

    更新日期:1976-12-31 00:00:00

  • Reduced polymorphism in the chimpanzee semen coagulating protein, semenogelin I.

    abstract::The semen of many primate species coagulates into a mating plug believed to prevent the sperm of subsequent mating events from accessing the ova. The texture of the coagulum varies among species: from a semisoft mass in humans to a firm plug in chimpanzees. In humans, a component of the coagulum, semenogelin I, also i...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-002-2463-0

    authors: Kingan SB,Tatar M,Rand DM

    更新日期:2003-08-01 00:00:00

  • A new member of a secretory protein gene family in the dipteran Chironomus tentans has a variant repeat structure.

    abstract::We describe the structure of a gene expressed in the salivary gland cells of the dipteran Chironomus tentans and show that it encodes 1 of the approximately 15 secretory proteins exported by the gland cells. This sp115,140 gene consists of approximately 65 copies of a 42-bp sequence in a central uninterrupted core blo...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02101791

    authors: Galli J,Lendahl U,Paulsson G,Ericsson C,Bergman T,Carlquist M,Wieslander L

    更新日期:1990-07-01 00:00:00

  • Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes).

    abstract::The gene content of a mitochondrial (mt) genome, i.e., 37 genes and a large noncoding region (LNR), is usually conserved in Metazoa. The arrangement of these genes and the LNR is generally conserved at low taxonomic levels but varies substantially at high levels. We report here a variation in mt gene content and gene ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-005-0196-y

    authors: Shao R,Barker SC,Mitani H,Takahashi M,Fukunaga M

    更新日期:2006-08-01 00:00:00

  • Identification of three distinct phylogenetic groups of CAX cation/proton antiporters.

    abstract::Ca(2+)/cation antiporter (CaCA) proteins are integral membrane proteins that transport Ca(2+) or other cations using the H(+) or Na(+) gradient generated by primary transporters. The CAX (for CAtion eXchanger) family is one of the five families that make up the CaCA superfamily. CAX genes have been found in bacteria, ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-006-0048-4

    authors: Shigaki T,Rees I,Nakhleh L,Hirschi KD

    更新日期:2006-12-01 00:00:00

  • Evolutionary distances in Hawaiian Drosophila measured by DNA reassociation.

    abstract::Comparisons of the sequence divergence of three species of Hawaiian Drosophila have been made by hybridization of single-copy tracer DNA of each of the species with driver DNA from each species, and measurement of the average melting temperature (Tma) in a chaotropic solvent (2.4 M tetraethylammonium chloride) which m...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF01734358

    authors: Hunt JA,Hall TJ,Britten RJ

    更新日期:1981-01-01 00:00:00

  • Molecular evolution of the odorant and gustatory receptor genes in lepidopteran insects: implications for their adaptation and speciation.

    abstract::Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecul...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-014-9633-0

    authors: Engsontia P,Sangket U,Chotigeat W,Satasook C

    更新日期:2014-08-01 00:00:00

  • Microsatellite allelic homoplasy due to variable flanking sequences.

    abstract::Microsatellite DNA sequences have become the dominant source of nuclear genetic markers for most applications. It is important to investigate the basis of variation between alleles and to know if current assumptions about the mechanisms of microsatellite mutation (that is to say, variations involving simple changes in...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/pl00006151

    authors: Grimaldi MC,Crouau-Roy B

    更新日期:1997-03-01 00:00:00

  • Combinations of ancestral modules in proteins.

    abstract::Twenty-seven protein sequence elements, six to nine amino acids long, were extracted from 15 phylogenetically diverse complete prokaryotic proteomes. The elements are present in all of these proteomes, with at least one copy each (omnipresent elements), and have presumably been conserved since the last universal commo...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-007-9032-x

    authors: Sobolevsky Y,Frenkel ZM,Trifonov EN

    更新日期:2007-12-01 00:00:00

  • Mutation rates and evolution of multiple coding in RNA-based protocells.

    abstract::RNA has a myriad of biological roles in contemporary life. We use the RNA paradigm for genotype-phenotype mappings to study the evolution of multiple coding in dependence to mutation rates. We study three different one-to-many genotype-phenotype mappings which have the potential to encode the information for multiple ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/s00239-014-9648-6

    authors: de Boer FK,Hogeweg P

    更新日期:2014-12-01 00:00:00

  • Different evolutionary histories of kringle and protease domains in serine proteases: a typical example of domain evolution.

    abstract::With the aim of elucidating the evolutionary processes of the kringle and protease domains in serine proteases which are involved with the system of blood coagulation and fibrinolysis, we constructed phylogenetic trees for the kringle and protease domains, separately, by use of amino acid sequence data. The phylogenet...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00163238

    authors: Ikeo K,Takahashi K,Gojobori T

    更新日期:1995-03-01 00:00:00

  • The paradox of MHC-DRB exon/intron evolution: alpha-helix and beta-sheet encoding regions diverge while hypervariable intronic simple repeats coevolve with beta-sheet codons.

    abstract::Twenty-one different caprine and 13 ovine MHC-DRB exon 2 sequences were determined including part of the adjacent introns containing simple repetitive (gt)n(ga)m elements. The positions for highly polymorphic DRB amino acids vary slightly among ungulates and other mammals. From man and mouse to ungulates the basic (gt...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF00175503

    authors: Schwaiger FW,Weyers E,Epplen C,Brün J,Ruff G,Crawford A,Epplen JT

    更新日期:1993-09-01 00:00:00

  • Molecular genetics and evolution of stomach and nonstomach lysozymes in the hoatzin.

    abstract::Multiple genes of the hoatzin encoding stomach lysozyme c and closely related members of this calcium-binding lysozyme c group were cloned from a genomic DNA library and sequenced. There are a minimum of five genes represented among these sequences that encode two distinct groups of protein sequences. One group of thr...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章

    doi:10.1007/BF02338801

    authors: Kornegay JR

    更新日期:1996-06-01 00:00:00