Abstract：
:The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share similar morphologies and similar latent infection cycles. In fact, sequence comparisons show that the viruses have more than 60% of their genes in common. However, the order of genes is completely different in the two genomes, suggesting that extensive recombinational events in addition to several large deletions had occurred during the separate evolutionary routes from a common ancestor. We investigated genes encoding components of signal transduction pathways and genes encoding replicative functions in more detail. We found that the two genomes possess different, although overlapping, sets of genes in both classes, suggesting that different genes from each class were lost, perhaps randomly, after the separate evolution from an ancestral genome. Random loss would also account for the fact that more than one-third of the genes in one viral genome has no counterparts in the other genome. We speculate that the ancestral genome belonged to a cellular organism that had once invaded a primordial brown algal host.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Delaroque N,Boland W,Müller DG,Knippers Rdoi
10.1007/s00239-003-2501-ykeywords:
subject
Has Abstractpub_date
2003-12-01 00:00:00pages
613-22issue
6eissn
0022-2844issn
1432-1432journal_volume
57pub_type
杂志文章abstract：:We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Compar...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175814
更新日期：1995-11-01 00:00:00
abstract：:Actin is a highly conserved protein although many isoforms exist. In vertebrates and insects the different actin isoforms can be grouped by their amino acid sequence and tissue-specific gene expression into muscle and nonmuscle actins, suggesting that the different actins may have a functional significance. We ask her...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006125
更新日期：1997-01-01 00:00:00
abstract：:A long-standing hypothesis posits that morphological changes may be more likely to result from changes in regulation of gene expression than from changes in the protein coding sequences of genes. We have compared the expression pattern of the twisted gastrulation (tsg) gene among five Drosophila species: D. melanogast...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006293
更新日期：1998-02-01 00:00:00
abstract：:Runs of identical amino acids encoded by triplet repeats (homopolymers) are components of numerous proteins, yet their role is poorly understood. Large numbers of homopolymers are present in the Drosophila melanogaster mastermind (mam) protein surrounding several unique charged amino acid clusters. Comparison of mam s...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160429
更新日期：1993-11-01 00:00:00
abstract：:The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of biological entities. We investigated the amount and nature of this variation for the lichenized fun...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-013-9603-y
更新日期：2014-02-01 00:00:00
abstract：:The transposable element mariner occurs widely in the melanogaster species group of Drosophila. However, in drosophilids outside of the melanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genus Zaprionus. The mariner sequence obtained from Zaprionus tuberculatus is...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102804
更新日期：1991-12-01 00:00:00
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
更新日期：1997-03-01 00:00:00
abstract：:Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-squared-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 sp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0189-2
更新日期：2005-04-01 00:00:00
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
更新日期：2001-08-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0080-3
更新日期：2002-06-01 00:00:00
abstract：:Analysis of mitochondrial DNAs (mtDNAs) from parthenogenetic lizards of the Heteronotia binoei complex with restriction enzymes revealed an approximately 5-kb addition present in all 77 individuals. Cleavage site mapping suggested the presence of a direct tandem duplication spanning the 16S and 12S rRNA genes, the con...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02103135
更新日期：1991-11-01 00:00:00
abstract：:Previous studies have shown that pituitary growth hormone displays an episodic pattern of evolution, with a slow underlying evolutionary rate and occasional sustained bursts of rapid change. The present study establishes that pituitary prolactin shows a similar pattern. During much of tetrapod evolution the sequence o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010049
更新日期：2000-05-01 00:00:00
abstract：:The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9218-5
更新日期：2009-05-01 00:00:00
abstract：:Many eubacteria contain an ATP-dependent protease complex, which is built by multiple copies of the HslV and HslU proteins and is therefore called HslVU. HslU proteins are AAA + ATPases, while HslV proteins are proteases that show highly significant similarity to beta subunits of proteasomes. Therefore, the HslVU comp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0282-1
更新日期：2006-10-01 00:00:00
abstract：:Annotated, complete DNA sequences are available for 213 mitochondrial genomes from 132 species. These provide an extensive sample of evolutionary adjustment of codon usage and meaning spanning the history of this organelle. Because most known coding changes are mitochondrial, such data bear on the general mechanism of...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010220
更新日期：2001-10-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00174042
更新日期：1995-07-01 00:00:00
abstract：:The Pten gene was initially identified in humans as a tumor suppressor. It has since been shown to play important roles in the control of cell size, cell motility, apoptosis, and organ size, and it has also been implicated in aging. Pten is highly conserved among organisms as diverse as nematodes, insects, and vertebr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0002-x
更新日期：2006-06-01 00:00:00
abstract：:We have performed a genome-wide analysis of the mimp family of miniature inverted-repeat transposable elements, taking advantage of the recent release of the F. oxysporum genome sequence. Using different approaches, we detected 103 mimp elements, corresponding to 75 nonredundant copies, half of which are located on a ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9164-7
更新日期：2008-12-01 00:00:00
abstract：:Hydrophobins are small proteins, characterised by the presence of eight positionally conserved cysteine residues, and are present in all filamentous asco- and basidiomycetes. They are found on the outer surfaces of cell walls of hyphae and conidia, where they mediate interactions between the fungus and the environment...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9438-3
更新日期：2011-04-01 00:00:00
abstract：:DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9441-8
更新日期：2011-04-01 00:00:00
abstract：:In this work detailed statistics on ancestral gene duplication and gene conservation in completely sequenced cellular genomes are presented. Analysis of open reading frame (ORF) products having simultaneous matches in several distinct organisms showed a significant correlation between duplication and conservation. Sys...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006580
更新日期：1999-11-01 00:00:00
abstract：:Previous observations have indicated that Drosophila DNA contains a component that evolves so rapidly that it fails to hybridize between the DNAs of sibling species. To establish the reality of this component and study its properties, the fraction (about 20%) of Drosophila simulans (Dsim) DNA that fails to hybridize t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099998
更新日期：1990-03-01 00:00:00
abstract：:The local stability of unbranched biosynthetic pathways is examined by mathematical analysis and computer simulation using a novel nonlinear formalism that appears to accurately describe biochemical systems. Four factors affecting the stability are examined: strength of feedback inhibition, equalization of the values...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01741242
更新日期：1975-08-05 00:00:00
abstract：:Copia is a retrotransposon that appears to be distributed widely among the Drosophilidae subfamily. Evolutionary analyses of regulatory regions have indicated that the Copia retrotransposon evolved through both positive and purifying selection, and that horizontal transfer (HT) could also explain its patchy distributi...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9435-6
更新日期：2011-03-01 00:00:00
abstract：:We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationshi...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00176084
更新日期：1994-03-01 00:00:00
abstract：:The LMP7 and PSMB5 genes were created through an ancient gene duplication event of their ancestral locus. These proteins contain an active site of proteolysis, and LMP7 replaces PSMB5 as a component of the 20S proteasome after stimulation of cells by interferon-gamma. Replacement of PSMB5 by LMP7 changes the profile o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0120-x
更新日期：2005-02-01 00:00:00
abstract：:Response regulators of bacterial sensory transduction systems generally consist of receiver module domains covalently linked to effector domains. The effector domains include DNA binding and/or catalytic units that are regulated by sensor kinase-catalyzed aspartyl phosphorylation within their receiver modules. Most re...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00167109
更新日期：1995-02-01 00:00:00
abstract：:Introns are generally believed to evolve too rapidly and too erratically to be of much use in phylogenetic reconstructions. Few phylogenetically informative intron sequences are available, however, to ascertain the validity of this supposition. In the present study the supposition was tested on the example of the mamm...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006510
更新日期：1999-06-01 00:00:00
abstract：:We provide here evidence for a conserved regulatory element for transcription of the β-family globin genes based on a comparative study of 32 genes from 16 mammals. The element is characterized by the appearance of AA or TT dinucleotides in the A + T-rich region located 200-400 bp upstream of the cap sites. G-tracts 3...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9459-y
更新日期：2011-10-01 00:00:00
abstract：:The mutation and selection of regulatory DNA sequences are presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we construct an explicit model for the evolution of regulatory sequences, making use ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2335-z
更新日期：2002-10-01 00:00:00
