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1.
Jack C. Vaughn Matthew T. Mason Ginger L. Sper-Whitis Peter Kuhlman Jeffrey D. Palmer 《Journal of molecular evolution》1995,41(5):563-572
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. Comparison to other coxI genes revealed a 966-bp group I intron, which, based on homology with the related yeast coxI intron aI4, potentially encodes a 279-amino-acid site-specific DNA endonuclease. This intron, which is believed to function as a ribozyme during its own splicing, is not present in any of 19 coxI genes examined from other diverse vascular plant species. Phylogenetic analysis of intron origin was carried out using three different tree-generating algorithms, and on a variety of nucleotide and amino acid data sets from the intron and its flanking exon sequences. These analyses show that the Peperomia coxI gene intron and exon sequences are of fundamentally different evolutionary origin. The Peperomia intron is more closely related to several fungal mitochondrial introns, two of which are located at identical positions in coxI, than to identically located coxI introns from the land plant Marchantia and the green alga Prototheca. Conversely, the exon sequence of this gene is, as expected, most closely related to other angiosperm coxI genes. These results, together with evidence suggestive of co-conversion of exonic markers immediately flanking the intron insertion site, lead us to conclude that the Peperomia coxI intron probably arose by horizontal transfer from a fungal donor, using the double-strand-break repair pathway. The donor species may have been one of the symbiotic mycorrhizal fungi that live in close obligate association with most plants.
Correspondence to: J.C. Vaughn 相似文献
2.
The nucleotide sequence of the 18S rDNA coding gene in the ascomycetes parasitic fungus Isaria japonica contains a group I intron with a length of 379 nucleotides. The identification of the DNA sequence as a group I intron is
based on its sequence homology to other fungal group I introns. Its group I intron contained the highly conserved sequence
elements P, Q, R, and S found in other group I introns. Surprisingly, the intron sequence of I. japonica is more similar to that of Ustilago maydis than to the one found in Sclerotinia sclerotiorum. This is in contrast to the sequence identity found on the neighboring rDNA. This is an interesting finding and suggests a
horizontal transfer of group I intron sequences.
Received: 19 September 1997 / Accepted: 10 September 1998 相似文献
3.
Yuji Inagaki Yasuko Hayashi-Ishimaru Megumi Ehara Ikuo Igarashi Takeshi Ohama 《Journal of molecular evolution》1997,45(3):295-300
The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired
during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have
been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase
subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan
protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and
algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The
COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes,
but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes
and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host
cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts
are remnants of endosymbiotic algae.
Received: 24 March 1997 / Accepted: 21 April 1997 相似文献
4.
The origins of fungal group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they
have never been reported in basal fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to
derived phyla (Ascomycota and Basidiomycota). Here we report group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales) and Coemansia mojavensis (Kickxellales). Secondary structure analyses predicted that both introns belong to the IC1 subgroup and that they are distantly
related to each other, which is also suggested by different insertion sites. Molecular phylogenetic analyses indicated that
the IC1 intron of Z. insidians is closely related to the IC1 intron inserted in the LSU rDNA of the basidiomycete fungus Clavicorona taxophila, which strongly suggests interphylum horizontal transfer. The IC1 intron of C. mojavensis has a low phylogenetic affinity to other fungal IC1 introns inserted into site 943 of nSSU rDNA (relative to E. coli 16S rDNA). It is noteworthy that this intron contains a putative ORF containing a His–Cys box motif in the antisense strand,
a hallmark for nuclear-encoded homing endonucleases. Overall, molecular phylogenetic analyses do not support the placement
of these two introns in basal fungal IC1 intron lineages. This result leads to the suggestion that fungal IC1 introns might
have invaded or been transferred laterally after the divergence of the four major fungal phyla.
Received: 8 February 2001 / Accepted: 1 November 2001 相似文献
5.
M.K. Tan 《Journal of molecular evolution》1997,44(6):637-645
Studies of the distribution of the three group I introns (intron A, intron T, and intron AT) in the 26S rDNA of Gaeumannomyces graminis had suggested that they were transferred to a common ancestor of G. graminis var. avenae and var. tritici after it had branched off from var. graminis. Intron AT and intron A exhibited vertical inheritance and coevolved in concert with their hosts. Intron loss could occur
after its acquisition. Loss of any one of the three introns could occur in var. tritici whereas only loss of intron T had been found in the majority of var. avenae isolates. The existence of isolates of var. tritici and var. avenae with three introns suggested that intron loss could be reversed by intron acquisition and that the whole process is a dynamic
one. This process of intron acquisition and intron loss reached different equilibrium points for different varieties and subgroups,
which explained the irregular distribution of these introns in G. graminis. Each of the three group I introns was more closely related to other intron sequences that share the same insertion point
in the 26S rDNA than to each other. These introns in distantly related organisms appeared to have a common ancestry. This
system had provided a good model for studies on both the lateral transfer and common ancestry of group I introns in the 26S
rRNA genes.
Received: 17 May 1996 / Accepted: 14 January 1997 相似文献
6.
Wang B 《Journal of molecular evolution》2001,53(3):244-250
Genes with atypical G+C content and pattern of codon usage in a certain genome are possibly of exotic origin, and this idea
has been applied to identify horizontal events. In this way, it was postulated that a total of 755 genes in the E. coli genome are relics of horizontal events after the divergence of E. coli from the Salmonella lineage 100 million years ago (Lawrence and Ochman, 1998). In this paper we propose a new way to study sequence composition
more thoroughly. We found that although the 755 genes differ in composition from other genes in the E. coli genome, the difference is minor. If we accepted that these genes are horizontally transferred, then (1) it would be more
likely that they were transferred from genomes evolutionarily closely related to E. coli; but (2) the dating method used by Lawrence and Ochman (1997, 1998) largely underestimated the average age of introduced sequences
in the E. coli genome, in particular, most of the 755 genes should be introduced into E. coli before, instead of after, the divergence of E. coli from the Salmonella lineage. Our study reveals that atypical G+C content and pattern of codon usage are not reliable indicators of horizontal
gene transfer events.
Received: 27 September 2000 / Accepted: 9 April 2001 相似文献
7.
Alexey Fedorov Larisa Fedorova Valery Starshenko Vadim Filatov Eugeni Grigor'ev 《Journal of molecular evolution》1998,46(3):263-271
Nonrandomness in the intron and exon phase distributions in a sample of 305 human genes has been found and analyzed. It was
shown that exon duplications had a significant effect on the exon phase nonrandomness. All of the nonrandomness is probably
due to both the processes of exon duplication and shuffling. A quantitative estimation of exon duplications in the human genome
and their influence on the intron and exon phase distributions has been analyzed. According to our estimation, the proportion
of duplicated exons in the human genome constitutes at least 6% of the total. Generalizing the particular case of exon duplication
to the more common event of exon shuffling, we modeled and analyzed the influence of exon shuffling on intron phase distribution.
Received: 28 March 1997 / Accepted: 9 July 1997 相似文献
8.
Hiroyuki Sawada Fumihiko Suzuki Izumi Matsuda Naruya Saitou 《Journal of molecular evolution》1999,49(5):627-644
Pseudomonas syringae are differentiated into approximately 50 pathovars with different plant pathogenicities and host specificities. To understand
its pathogenicity differentiation and the evolutionary mechanisms of pathogenicity-related genes, phylogenetic analyses were
conducted using 56 strains belonging to 19 pathovars. gyrB and rpoD were adopted as the index genes to determine the course of bacterial genome evolution, and hrpL and hrpS were selected as the representatives of the pathogenicity-related genes located on the genome (chromosome). Based on these
data, NJ, MP, and ML phylogenetic trees were constructed, and thus 3 trees for each gene and 12 gene trees in total were obtained,
all of which showed three distinct monophyletic groups: Groups 1, 2 and 3. The observation that the same set of OTUs constitute
each group in all four genes suggests that these genes had not experienced any intergroup horizontal gene transfer within
P. syringae but have been stable on and evolved along with the P. syringae genome. These four index genes were then compared with another pathogenicity-related gene, argK (the phaseolotoxin-resistant ornithine carbamoyltransferase gene, which exists within the argK–tox gene cluster). All 13 strains of pv. phaseolicola and pv. actinidiae used had been confirmed to produce phaseolotoxin and to have argK, whose sequences were completely identical, without a single synonymous substitution among the strains used (Sawada et al.
1997a). On the other hand, argK were not present on the genomes of the other 43 strains used other than pv. actinidiae and pv. phaseolicola. Thus, the productivity of phaseolotoxin and the possession of the argK gene were shown at only two points on the phylogenetic tree: Group 1 (pv. actinidiae) and Group 3 (pv. phaseolicola). A t test between these two pathovars for the synonymous distances of argK and the tandemly combined sequence of the four index genes showed a high significance, suggesting that the argK gene (or argK–tox gene cluster) experienced horizontal gene transfer and expanded its distribution over two pathovars after the pathovars had
separated, thus showing a base substitution pattern extremely different from that of the noncluster region of the genome.
Received: 18 January 1999 / Accepted: 25 May 1999 相似文献
9.
10.
Evolution of Duplicated <Emphasis Type="BoldItalic">reggie</Emphasis> Genes in Zebrafish and Goldfish 总被引:1,自引:0,他引:1
Málaga-Trillo E Laessing U Lang DM Meyer A Stuermer CA 《Journal of molecular evolution》2002,54(2):235-245
Invertebrates, tetrapod vertebrates, and fish might be expected to differ in their number of gene copies, possibly due the
occurrence of genome duplication events during animal evolution. Reggie (flotillin) genes code for membrane-associated proteins involved in growth signaling in developing and regenerating axons. Until now,
there appeared to be only two reggie genes in fruitflies, mammals, and fish. The aim of this research was to search for additional copies of reggie genes in fishes, since a genome duplication might have increased the gene copy number in this group. We report the presence
of up to four distinct reggie genes (two reggie-1 and two reggie-2 genes) in the genomes of zebrafish and goldfish. Phylogenetic analyses show that the zebrafish and goldfish sequence pairs
are orthologous, and that the additional copies could have arisen through a genome duplication in a common ancestor of bony
fish. The presence of novel reggie mRNAs in fish embryos indicates that the newly discovered gene copies are transcribed and possibly expressed in the developing
and regenerating nervous system. The intron/exon boundaries of the new fish genes characterized here correspond with those
of human genes, both in location and phase. An evolutionary scenario for the evolution of reggie intron-exon structure, where loss of introns appears to be a distinctive trait in invertebrate reggie genes, is presented.
Received: 24 January 2001 / Accepted: 27 July 2001 相似文献
11.
The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to
pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A
phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the
mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla
paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present.
Received: 2 December 1997 / Accepted: 20 February 1998 相似文献
12.
A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA
gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly
within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is
likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA
gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely
to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
Received: 24 November 1997 / Accepted: 14 September 1998 相似文献
13.
Karen Miller Clare Lynch Joanne Martin Elisabeth Herniou Michael Tristem 《Journal of molecular evolution》1999,49(3):358-366
Gypsy LTR-retrotransposons have been identified in the genomes of many organisms, but only a small number of vertebrate examples
have been reported to date. Here we show that members of this family are likely to be widespread in many vertebrate classes
with the possible exceptions of mammals and birds. Phylogenetic analyses demonstrate that although there are several distinct
lineages of vertebrate gypsy LTR-retrotransposons, the majority clusters into one monophyletic clade. Groups of fungal, plant, and insect elements were
also observed, suggesting horizontal transfer between phyla may be infrequent. However, in contrast to this, there was little
evidence to support sister relationships between elements derived from vertebrate and insect hosts. In fact, the majority
of the vertebrate elements appeared to be most closely related to a group of gypsy LTR-retrotransposons present within fungi. This implies either that at least one horizontal transmission between these two
phyla has occurred previously or that a gypsy LTR-retrotransposon lineage has been lost from insect taxa.
Received: 22 December 1998 / Accepted: 6 April 1999 相似文献
14.
Sun L Li Y McCullough AK Wood TG Lloyd RS Adams B Gurnon JR Van Etten JL 《Journal of molecular evolution》2000,50(1):82-92
Large dsDNA-containing chlorella viruses encode a pyrimidine dimer-specific glycosylase (PDG) that initiates repair of UV-induced
pyrimidine dimers. The PDG enzyme is a homologue of the bacteriophage T4-encoded endonuclease V. The pdg gene was cloned and sequenced from 42 chlorella viruses isolated over a 12-year period from diverse geographic regions. Surprisingly,
the pdg gene from 15 of these 42 viruses contain a 98-nucleotide intron that is 100% conserved among the viruses and another 4 viruses
contain an 81-nucleotide intron, in the same position, that is nearly 100% identical (one virus differed by one base). In
contrast, the nucleotides in the pdg coding regions (exons) from the intron-containing viruses are 84 to 100% identical. The introns in the pdg gene have 5′-AG/GTATGT and 3′-TTGCAG/AA splice site sequences which are characteristic of nuclear-located, spliceosomal processed
pre-mRNA introns. The 100% identity of the 98-nucleotide intron sequence in the 15 viruses and the near-perfect identity of
an 81-nucleotide intron sequence in another 4 viruses imply strong selective pressure to maintain the DNA sequence of the
intron when it is in the pdg gene. However, the ability of intron-plus and intron-minus viruses to repair UV-damaged DNA in the dark was nearly identical.
These findings contradict the widely accepted dogma that intron sequences are more variable than exon sequences.
Received: 13 May 1999 / Accepted: 20 August 1999 相似文献
15.
Mathieu Blanchette Takashi Kunisawa David Sankoff 《Journal of molecular evolution》1999,49(2):193-203
Multiple genome rearrangement methodology facilitates the inference of animal phylogeny from gene orders on the mitochondrial
genome. The breakpoint distance is preferable to other, highly correlated but computationally more difficult, genomic distances when applied to these data.
A number of theories of metazoan evolution are compared to phylogenies reconstructed by ancestral genome optimization, using
a minimal total breakpoints criterion. The notion of unambiguously reconstructed segments is introduced as a way of extracting the invariant aspects of multiple solutions for a given ancestral genome; this enables
a detailed reconstruction of the evolution of non-tRNA mitochondrial gene order.
Received: 15 July 1998 / Accepted: 5 March 1999 相似文献
16.
The Path from the RNA World 总被引:1,自引:0,他引:1
We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through
to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the
RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome
we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that
incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis
is transferred from RNA → RNP → protein, the first proteins in the ``breakthrough organism' (the first to have encoded protein
synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date
protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular
introns are older than the exons surrounding them, the ``introns-first' theory. Many features of the model for the genome
organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic
genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like' genome
organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism
RNA genome → eukaryotic-like DNA genome → prokaryotic-like DNA genome are all relatively straightforward, whereas the transition
prokaryotic-like genome → eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption
of the transition RNA → RNP → protein. A likely molecular mechanism, ``plasmid transfer,' is available for the origin of
prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and
derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection
for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.
Received: 14 January 1997 / Accepted: 19 May 1997 相似文献
17.
Wei Wu Morris Goodman Margaret I. Lomax Lawrence I. Grossman 《Journal of molecular evolution》1997,44(5):477-491
Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory
chain on the mitochondrial inner membrane. Up to 13 subunits encoded by both the mitochondrial (subunits I, II, and III) and
nuclear genomes occur in eukaryotic organisms ranging from yeast to human. Previously, we observed a high number of amino
acid replacements in the human COX IV subunit compared to mouse, rat, and cow orthologues. Here we examined COX IV evolution
in the two groups of anthropoid primates, the catarrhines (hominoids, cercopithecoids) and platyrrhines (ceboids), as well
as one prosimian primate (lorisiform), by sequencing PCR-amplified portions of functional COX4 genes from genomic DNAs. Phylogenetic analysis of the COX4 sequence data revealed that accelerated nonsynonymous substitution rates were evident in the early evolution of both catarrhines
and, to a lesser extent, platyrrhines. These accelerated rates were followed later by decelerated rates, suggesting that positive
selection for adaptive amino acid replacement became purifying selection, preserving replacements that had occurred. The evidence
for positive selection was especially pronounced along the catarrhine lineage to hominoids in which the nonsynonymous rate
was first faster than the synonymous rate, then later much slower. The rates of three types of ``neutral DNA' nucleotide
substitutions (synonymous substitutions, pseudogene nucleotide substitutions, and intron nucleotide substitutions) are similar
and are consistent with previous observations of a slower rate of such substitutions in the nuclear genomes of hominoids than
in the nuclear genomes of other primate and mammalian lineages.
Received: 22 May 1996 / Accepted: 24 November 1996 相似文献
18.
Johannes A. Jehle Antje Nickel Just M. Vlak Horst Backhaus 《Journal of molecular evolution》1998,46(2):215-224
We characterized an insertion mutant of the baculovirus Cydia pomonella granulovirus (CpGV), which contained a transposable element of 3.2 kb. This transposon, termed TCp3.2, has unusually long
inverted terminal repeats (ITRs) of 756 bp and encodes a defective gene for a putative transposase. Amino acid sequence comparison
of the defective transposase gene revealed a distant relationship to a putative transposon in Caenorhabditis elegans which also shares some similarity of the ITRs. Maximum parsimony analysis of the predicted amino acid sequences of Tc1- and
mariner-like transposases available from the GenBank data base grouped TCp3.2 within the superfamily of Tc1-like transposons.
DNA hybridization indicated that TCp3.2 originated from the genome of Cydia pomonella, which is the natural host of CpGV, and is present in less than 10 copies in the C. pomonella genome. The transposon TCp3.2 most likely was inserted into the viral genome during infection of host larvae. TCp3.2 and
the recently characterized Tc1-like transposon TC14.7 (Jehle et al. 1995), which was also found in a CpGV mutant, represent
a new family of transposons found in baculovirus genomes. The occasional horizontal escape of different types of host transposons
into baculovirus genomes evokes the question about the possible role of baculoviruses as an interspecies vector in the horizontal
transmission of insect transposons.
Received: 27 February 1997 / Accepted: 16 May 1997 相似文献
19.
The 22,704-bp circular mitochondrial DNA (mtDNA) of the chlamydomonad alga Chlorogonium elongatum was completely cloned and sequenced. The genome encodes seven proteins of the respiratory electron transport chain, subunit
1 of the cytochrome oxidase complex (cox1), apocytochrome b (cob), five subunits of the NADH dehydrogenase complex (nad1, nad2, nad4, nad5, and nad6), a set of three tRNAs (Q, W, M), and the large (LSU)- and small (SSU)-subunit ribosomal RNAs. Six group-I introns were found,
two each in the cox1, cob, and nad5 genes. In each intron an open reading frame (ORF) related to maturases or endonucleases was identified. Both the LSU and
the SSU rRNA genes are split into fragments intermingled with each other and with other genes. Although the average A + T
content is 62.2%, GC-rich clusters were detected in intergenic regions, in variable domains of the rRNA genes, and in introns
and intron-encoded ORFs. A comparison of the genome maps reveals that C. elongatum and Chlamydomonas eugametos mtDNAs are more closely related to one another than either is to Chlamydomonas reinhardtii mtDNA.
Received: 3 November 1997 / Accepted: 12 January 1998 相似文献
20.
Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria 总被引:11,自引:0,他引:11
Kenji V. P. Nagashima Akira Hiraishi Keizo Shimada Katsumi Matsuura 《Journal of molecular evolution》1997,45(2):131-136
Phylogenetic trees were drawn and analyzed based on the nucleotide sequences of the 1.5-kb gene fragment coding for the L
and M subunits of the photochemical reaction center of various purple photosynthetic bacteria. These trees are mostly consistent
with phylogenetic trees based on 16S rRNA and soluble cytochrome c, but differ in some significant details. This inconsistency implies horizontal transfer of the genes that code for the photosynthetic
apparatus in purple bacteria. Possibilities of similar transfers of photosynthesis genes during the evolution of photosynthesis
are discussed especially for the establishment of oxygenic photosynthesis.
Received: 8 July 1996 / Accepted: 12 March 1997 相似文献