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1.
Isolation and mapping of the rabbit DM genes 总被引:2,自引:0,他引:2
Proper peptide presentation by major histocompatibility complex (MHC)-encoded class II antigens is dependent on the products
of the MHC DM loci. We identified the rabbit orthologues (RLA-DMA and -DMB) of human HLA-DMA and -DMB and found that they have 76.9% and 78.8% identity with HLA-DMA and -DMB, respectively. Like classical class II MHC genes, RLA-DM genes are more closely related to human HLA-DM genes than to mouse H2-DM. Among the DM family, there is a high degree of variability at the amino terminus of the DMa chains, and length variability in the cytoplasmic
tails of both DMα and DMβ. The rabbit DM genes are coexpressed with class II genes in lymphoid tissues, as are the DM genes of other mammals. The RLA-DM locus maps to the class II region of the rabbit MHC, and is flanked by the DP and DOB loci. Despite having some similarities to class II genes of bony fishes, the DM family represents a separate branch of the MHC class II family.
Received: 30 May 1998 / Revised: 28 July 1998 相似文献
2.
Analysis of the 18S rDNA sequences of five species of the family Dugesiidae (phylum Platyhelminthes, suborder Tricladida,
infraorder Paludicola) and eight species belonging to families Dendrocoelidae and Planaridae and to the infraorder Maricola
showed that members of the family Dugesiidae have two types of 18S rDNA genes, while the rest of the species have only one.
The duplication event also affected the ITS-1, 5.8S, ITS-2 region and probably the 28S gene. The mean divergence value between
the type I and the type II sequences is 9% and type II 18S rDNA genes are evolving 2.3 times more rapidly than type I. The
evolutionary rates of type I and type II genes were calibrated from biogeographical data, and an approximate date for the
duplication event of 80–120 million years ago was calculated. The type II gene was shown, by RT-PCR, to be transcribed in
adult individuals of Schmidtea polychroa, though at very low levels. This result, together with the fact that most of the functionally important positions for small-subunit
rRNA in prokaryotes have been conserved, indicates that the type II gene is probably functional.
Received: 24 March 1998 / Accepted: 17 March 1999 相似文献
3.
We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome
b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis
of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other
primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has
remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.
Received: 15 December 1997 / Accepted: 24 February 1998 相似文献
4.
We present an analysis of the evolutionary rates of the cytochrome c oxidase subunit I genes of primates and other mammals. Five primate genes were sequenced, and this information was combined
with published data from other species. The sequences from simian primates show approximately twofold increases in their nonsynonymous
substitution rate compared to those from other primates and other mammals. The species range and the overall magnitude of
this rate increase are similar to those previously identified for the cytochrome c oxidase subunit II and cytochrome b genes.
Received: 22 July 1999 / Accepted: 21 February 2000 相似文献
5.
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 mammalian class II major histocompatibility complex (Mhc) genes of the DRB family. Since the Mhc genes evolve under balancing selection and are believed to recombine or rearrange frequently, the evolution of their introns
could be expected to be particularly rapid and subject to scrambling. Sequences of intron 4 and 5 DRB genes were obtained from polymerase chain reaction-amplified fragments of genomic DNA from representatives of six eutherian
orders—Primates, Scandentia, Chiroptera, Dermoptera, Lagomorpha, and Insectivora. Although short stretches of the introns
have indeed proved to be unalignable, the bulk of the intron sequences from all six orders, spanning >85 million years (my)
of evolution, could be aligned and used in a study of the tempo and mode of intron evolution. The analysis has revealed the
Mhc introns to evolve at a rate similar to that of other genes and of synonymous sites of non-Mhc genes. No evidence of homogenization or large-scale scrambling of the intron sequences could be found. The Mhc introns apparently evolve largely by point mutations and insertions/deletions. The phylogenetic signals contained in the
intron sequences could be used to identify Scandentia as the sister group of Primates, to support the existence of the Archonta
superorder, and to confirm the monophyly of the Chiroptera.
Received: 26 October 1998 / Accepted: 21 December 1998 相似文献
6.
Characterization of Repetitive DNA Elements in Arabidopsis 总被引:1,自引:0,他引:1
We have applied computational methods to the available database and identified several families of repetitive DNA elements
in the Arabidopsis thaliana genome. While some of the elements have features expected of either miniature inverted-repeat transposable elements (MITEs)
or retrotransposons, the most abundant class of repetitive elements, the AthE1 family, is structurally related to neither. The AthE1 family members are defined by conserved 5′ and 3′ sequences, but these terminal sequences do not represent either inverted
or direct repeats. AthE1 family members with greater than 98% identity are easily identified on different Arabidopsis chromosomes. Similar to nonautonomous DNA-based transposon families, the AthE1 family contains members in which the conserved terminal domains flank unrelated sequences. The primary utility of characterizing
repetitive sequences is in defining, at least in part, the evolutionary architecture of specific Arabidopsis loci. The repetitive elements described here make up approximately 1% of the available Arabidopsis thaliana genomic sequence.
Received: 13 October 1998 / Accepted: 30 December 1998 相似文献
7.
Fernando Alvarez-Valin Kamel Jabbari Nicolas Carels Giorgio Bernardi 《Journal of molecular evolution》1999,49(3):330-342
In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding
sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide
divergence, both synonymous and nonsynonymous, are, to some extent, dependent on each other and on the base composition. In
the first place, the variation in nonsynonymous rate is related to the GC level at the second codon position (the higher the
GC2 level, the higher the amino acid replacement rate). The correlation is especially strong with T2, the coefficients being significant in the three data sets analyzed. This correlation between nonsynonymous rate and base
composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend
to increase the intergenic variance in nonsynonymous rates also affect the intragenic variance. On the other hand, we have
shown that the synonymous rate is strongly correlated with the GC3 level. This correlation is observed both across genes and at the intragenic level. Similarly, the nonsynonymous rate is also
affected at the intragenic level by GC3 level, like the silent rate. In fact, synonymous and nonsynonymous rates exhibit a parallel behavior in relation to GC3 level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar
way by the intragenic variation of GC3. This result, taken together with the fact that the number of genes displaying intragenic correlation coefficients between
synonymous and nonsynonymous rates is not very high, but higher than random expectation (in the three data sets analyzed),
strongly suggests that the processes of silent and amino acid replacement divergence are, at least in part, driven by common
evolutionary forces in genes from Gramineae.
Received: 2 July 1998 / Accepted: 18 April 1999 相似文献
8.
9.
Thomas J.S. Merritt Siana LaForest Glenn D. Prestwich Joseph M. Quattro Richard G. Vogt 《Journal of molecular evolution》1998,46(3):272-276
We have isolated and characterized cDNAs representing two distinct pheromone binding proteins (PBPs) from the gypsy moth,
Lymantria dispar. We use the L. dispar protein sequences, along with other published lepidopteran PBPs, to investigate the evolutionary relationships among genes
within the PBP multigene family. Our analyses suggest that the presence of two distinct PBPs in genera representing separate
moth superfamilies is the result of relatively recent, independent, gene duplication events rather than a single, ancient,
duplication. We discuss this result with respect to the biochemical diversification of moth PBPs.
Received: 19 March 1997 / Accepted: 11 July 1997 相似文献
10.
Partial sequences of two mitochondrial genes, the 12S ribosomal gene (739 bp) and the cytochrome b gene (672 bp), were analyzed in hopes of reconstructing the evolutionary relationships of 11 leporid species, representative
of seven genera. However, partial cytochrome b sequences were of little phylogenetic value in this study. A suite of pairwise comparisons between taxa revealed that at
the intergeneric level, the cytochrome b gene is saturated at synonymous coding positions due to multiple substitution events. Furthermore, variation at the nonsynonymous
positions is limited, rendering the cytochrome b gene of little phylogenetic value for assessing the relationships between leporid genera. If the cytochrome b data are analyzed without accounting for these two classes of nucleotides (i.e., synonymous and nonsynonymous sites), one
may incorrectly conclude that signal exists in the cytochrome b data. The mitochondrial 12S rRNA gene, on the other hand, has not experienced excessive saturation at either stem or loop
positions. Phylogenies reconstructed from the 12S rDNA data support hypotheses based on fossil evidence that African rock
rabbits (Pronolagus) are outside of the main leporid stock and that leporids experienced a rapid radiation. However, the molecular data suggest
that this radiation event occurred in the mid-Miocene several millions of years earlier than the Pleistocene dates suggested
by paleontological evidence.
Received: 23 April 1998 / Accepted: 14 May 1998 相似文献
11.
The φ29-like phage genus of Podoviridae family contains phages B103, BS32, GA-1, M2, Nf, φ15, φ29, and PZA that all infect
Bacillus subtilis. They have very similar morphology and their genomes consist of linear double-stranded DNA of approximately 20 kb. The nucleotide
sequences of individual genomes or their parts determined thus far show that these phages evolved from a common ancestor.
A terminal protein (TP) that is covalently bound to the DNA 5′-end primes DNA replication of these phages. The same mechanism
of DNA replication is used by the Cp-1 related phages (also members of the Podoviridae family) and by the phage PRD1 (member
of the Tectoviridae family). Based on the complete or partial genomic sequence data of these phages it was possible to analyze
the evolutionary relationship within the φ29-like phage genus as well as to other protein-primed replicating phages. Noncoding
regions containing origins of replication were used in the analysis, as well as amino acid sequences of DNA polymerases, and
with the φ29-like phages also amino acid sequences of the terminal proteins and of the gene 17 protein product, an accessory
component of bacteriophage DNA replicating machinery. Included in the analysis are also results of a comparison of these phage
DNAs with the prophages present in the Bacillus subtilis genome. Based on this complex analysis we define and describe in more detail the evolutionary branches of φ29-like phages,
one branch consisting of phages BS32, φ15, φ29, and PZA, the second branch composed of phages B103, M2, and Nf, and the third
branch having phage GA-1 as its sole member. In addition, amino acid sequences of holins, proteins involved in phage lysis
were used to extend the evolutionary study to other phages infecting Gram-positive bacteria. The analysis based on the amino
acid sequences of holins showed several weak points in present bacteriophage classification.
Received: 14 April 1998 / Accepted: 31 July 1998 相似文献
12.
Edward L. Braun Seogchan Kang Mary Anne Nelson Donald O. Natvig 《Journal of molecular evolution》1998,47(5):531-543
Annexin homologues have been found in animals, plants, and distinct protist lineages. We report the identification of the
first fungal annexin, encoded by the anx14 gene of the filamentous ascomycete Neurospora crassa. Annexins have a complex evolutionary history and exhibit a large number of gene duplications and gene losses in various taxa,
including the complete loss of annexin sequences from another ascomycete, the budding yeast Saccharomyces cerevisiae. Surprisingly, the N. crassa annexin homologue is most closely related to the annexin homologue of the slime mold Dictyostelium discoideum, suggesting a phylogenetic link between cellular slime molds and true fungi. Both of these annexin homologues are closely
related to the family of annexin homologues present in animals, an observation consistent with the existence of the animal–fungal
clade. These data further suggest that the gene duplications that generated the family of annexin sequences present in animals,
fungi, and slime molds began prior to the divergence of these taxa.
Received: 10 December 1997 / Accepted: 17 April 1998 相似文献
13.
Evolutionary Relationship of the Ligand-Gated Ion Channels and the Avermectin-Sensitive,Glutamate-Gated Chloride Channels 总被引:4,自引:0,他引:4
Demetrios K. Vassilatis Keith O. Elliston Philip S. Paress Michel Hamelin Joseph P. Arena James M. Schaeffer Lex H.T. Van der Ploeg Doris F. Cully 《Journal of molecular evolution》1997,44(5):501-508
Two cDNAs, GluClα and GluClβ, encoding glutamate-gated chloride channel subunits that represent targets of the avermectin
class of antiparasitic compounds, have recently been cloned from Caenorhabditis elegans (Cully et al., Nature, 371, 707–711, 1994). Expression studies in Xenopus oocytes showed that GluClα and GluClβ have pharmacological profiles distinct from the glutamate-gated cation channels as
well as the γ-aminobutyric acid (GABA)- and glycine-gated chloride channels. Establishing the evolutionary relationship of
related proteins can clarify properties and lead to predictions about their structure and function. We have cloned and determined
the nucleotide sequence of the GluClα and GluClβ genes. In an attempt to understand the evolutionary relationship of these
channels with the members of the ligand-gated ion channel superfamily, we have performed gene structure comparisons and phylogenetic
analyses of their nucleotide and predicted amino acid sequences. Gene structure comparisons reveal the presence of several
intron positions that are not found in the ligand-gated ion channel superfamily, outlining their distinct evolutionary position.
Phylogenetic analyses indicate that GluClα and GluClβ form a monophyletic subbranch in the ligand-gated ion channel superfamily
and are related to vertebrate glycine channels/receptors. Glutamate-gated chloride channels, with electrophysiological properties
similar to GluClα and GluClβ, have been described in insects and crustaceans, suggesting that the glutamate-gated chloride
channel family may be conserved in other invertebrate species. The gene structure and phylogenetic analyses in combination
with the distinct pharmacological properties demonstrate that GluClα and GluClβ belong to a discrete ligand-gated ion channel
family that may represent genes orthologous to the vertebrate glycine channels.
Received: 30 September 1996 / Accepted: 15 November 1996 相似文献
14.
New copies of the mammalian retrotransposon L1 arise in the germline at an undetermined rate. Each new L1 copy appears at
a specific evolutionary time point that can be estimated by phylogenetic analysis. In humans, the active L1 sequence L1.2
resides at the genomic locus LRE1. Here we analyzed the region surrounding the LRE1 locus in humans and gorillas to determine the evolutionary history of the region and to estimate the age of L1.2. We found
that the region was composed of an ancient L1, L1Hs-Lrg, which was significantly divergent from all other L1 sequences available
in the databases. We also determined that L1.2 was absent from the gorilla genome and arose in humans after the divergence
of gorilla and human lineages. In the gorilla LRE1 region, we discovered a different full-length L1 element, L1Gg-1, which
was allelic and present at a high gene frequency in gorillas but absent from other primates. We determined the nucleotide
sequence of L1Gg-1 and found that it was 98% identical to L1.2, suggesting a close relationship between active L1s in gorillas
and humans.
Received: 28 December 1997 / Accepted: 20 March 1998 相似文献
15.
The ascomycetous fungus Cryptendoxyla hypophloia contains an insertion of 433 base pairs in the genes encoding nuclear small subunit ribosomal RNA. Secondary structure analyses
of the insert reveal characteristics indicative of a Group I intron, including elements P, Q, R, and S; however, the sequences
of these conserved regions deviate significantly from recognized consensus sequences for Group I introns. Principal-components
analysis, based on 79 nucleotide positions from the conserved core sequences of 93 Group I introns, identified 17 introns
similar to that of C. hypophloia. This grouping, which includes inserts from phylogenetically diverse organisms, cannot readily be classified in any previously
recognized major group of Group I introns. We propose the creation of a new group, IE, to accommodate these sequences, and
discuss the evolutionary relationships between group IE and other major groups of Group I introns.
Received: 11 January 1998 / Accepted: 12 October 1998 相似文献
16.
In the unicellular green alga, Chlamydomonas reinhardtii, cytochrome oxidase subunit 2 (cox2) and 3 (cox3) genes are missing from the mitochondrial genome. We isolated and sequenced a BAC clone that carries the whole cox3 gene and its corresponding cDNA. Almost the entire cox2 gene and its cDNA were also determined. Comparison of the genomic and the corresponding cDNA sequences revealed that the
cox3 gene contains as many as nine spliceosomal introns and that cox2 bears six introns. Putative mitochondria targeting signals were predicted at each N terminal of the cox genes. These spliceosomal introns were typical GT–AG-type introns, which are very common not only in Chlamydomonas nuclear genes but also in diverse eukaryotic taxa. We found no particular distinguishing features in the cox introns. Comparative analysis of these genes with the various mitochondrial genes showed that 8 of the 15 introns were interrupting
the conserved mature protein coding segments, while the other 7 introns were located in the N-terminal target peptide regions.
Phylogenetic analysis of the evolutionary position of C. reinhardtii in Chlorophyta was carried out and the existence of the cox2 and cox3 genes in the mitochondrial genome was superimposed in the tree. This analysis clearly shows that these cox genes were relocated during the evolution of Chlorophyceae. It is apparent that long before the estimated period of relocation
of these mitochondrial genes, the cytosol had lost the splicing ability for group II introns. Therefore, at least eight introns
located in the mature protein coding region cannot be the direct descendant of group II introns. Here, we conclude that the
presence of these introns is due to the invasion of spliceosomal introns, which occurred during the evolution of Chlorophyceae.
This finding provides concrete evidence supporting the ``intron-late' model, which rests largely on the mobility of spliceosomal
introns.
Received: 22 August 2000 / Accepted: 28 February 2001 相似文献
17.
Thomas A. Gorr Barbara K. Mable Traute Kleinschmidt 《Journal of molecular evolution》1998,47(4):471-485
Phylogenetic relationships among reptiles were examined using previously published and newly determined hemoglobin sequences.
Trees reconstructed from these sequences using maximum-parsimony, neighbor-joining, and maximum-likelihood algorithms were
compared with a phylogenetic tree of Amniota, which was assembled on the basis of published morphological data. All analyses differentiated α chains into αA and αD types, which are present in all reptiles except crocodiles, where only αA chains are expressed. The occurrence of the αD chain in squamates (lizards and snakes only in this study) appears to be a general characteristic of these species. Lizards
and snakes also express two types of β chains (βI and βII), while only one type of β chain is present in birds and crocodiles.
Reconstructed hemoglobin trees for both α and β sequences did not yield the monophyletic Archosauria (i.e., crocodilians + birds) and Lepidosauria (i.e., Sphenodon+ squamates) groups defined by the morphology tree. This discrepancy, as well as some other poorly resolved nodes, might be
due to substantial heterogeneity in evolutionary rates among single hemoglobin lineages. Estimation of branch lengths based
on uncorrected amino acid substitutions and on distances corrected for multiple substitutions (PAM distances) revealed that
relative rates for squamate αA and αD chains and crocodilian β chains are at least twice as high as those of the rest of the chains considered. In contrast to
these rate inequalities between reptilian orders, little variation was found within squamates, which allowed determination
of absolute evolutionary rates for this subset of hemoglobins. Rate estimates for hemoglobins of lizards and snakes yielded
1.7 (αA) and 3.3 (β) million years/PAM when calibrated with published divergence time vs. PAM distance correlates for several speciation
events within snakes and for the squamate ↔ sphenodontid split. This suggests that hemoglobin chains of squamate reptiles
evolved ∼3.5 (αA) or ∼1.7 times (β) faster than their mammalian equivalents. These data also were used to obtain a first estimate of some
intrasquamate divergence times.
Received: 15 September 1997 / Accepted: 4 February 1998 相似文献
18.
Bacterial family C DNA polymerases (DNA pol IIIs), the major chromosomal replicative enzymes, have been provisionally classified
based on primary sequences and domain structures into three classes: class I (Escherichia coli DNA pol C-type), class II (Bacillus subtilis DNA pol C-type), and class III (cyanobacterial DNA pol C-type), respectively. We have sequenced the structural gene encoding
the DNA pol C catalytic subunit of the thermophilic bacterium Thermus aquaticus. This gene, designated the Taq DNA pol C gene, contains a 3660-bp open reading frame which specifies a polypeptide of molecular
weight of 137,388 daltons. Comparative sequence analyses revealed that Taq DNA pol C is a class I family C DNA polymerase.
The Taq DNA pol C is most closely related to the Deinococcus radiodurans DNA pol C. Although a phylogenetic tree based on the class I family C DNA pols is still in the provisional stage, some important
conclusion can be drawn. First, the high-G+C and the low-G+C Gram-positive bacteria are not monophyletic. Second, the low-G+C
Gram-positive bacteria contain multigenes of family C DNA pols (classes I and II). Third, the cyanobacterial family C DNA
pol, classified as class III because it is encoded by a split gene, forms a group with the high-G+C Gram-positive bacteria.
Received: 7 October 1998 / Accepted: 12 January 1999 相似文献
19.
A+T content, phylogenetic relationships, codon usage, evolutionary rates, and ratio of synonymous versus non-synonymous substitutions
have been studied in partial sequences of the atpD and aroQ/pheA genes of primary (Buchnera) and secondary symbionts of aphids and a set of selected non-symbiotic bacteria, belonging to the five subdivisions of the
Proteobacteria. Compared to the homologous genes of the last group, both genes belonging to Buchnera behave in a similar way, showing a higher A+T content, forming a monophyletic group, a loss in codon bias, especially in
third base position, an evolutionary acceleration and an increase in the number of non-synonymous substitutions, confirming
previous results reported elsewhere for other genes. When available, these properties have been partly observed with the secondary
symbionts, but with values that are intermediate between Buchnera and free living Proteobacteria. They show high A+T content, but not as high as Buchnera, a non-solved phylogenetic position between Buchnera, and the other γ-Proteobacteria, a loss in codon bias, again not as high as in Buchnera and a significant evolutionary acceleration in the case of the three atpD genes, but not when considering aroQ/pheA genes. These results give support to the hypothesis that they are symbionts at different stages of the symbiotic accommodation
to the host. 相似文献
20.
Phylogenetic relationships among the Japanese papilionid butterflies were analyzed by comparing 783 nucleotide sequences
of the mitochondrial gene encoding NADH dehydrogenase subunit 5 (ND5). Phylogenetic trees of the representative species from each family in the superfamily Papilionoidea revealed that the species
of the family Papilionidae and those of all other families formed distinct clusters, with a few species of the family Hesperiidae
(Hesperioidea) as an outgroup. In the phylogenetic trees of most Japanese species of the family Papilionidae with Nymphalis xanthomelas (Nymphalidae) as an outgroup, the tribe Parnassiini (Parnassiinae) formed a cluster, and the rest formed the other cluster
in which the tribe Zerynthiini (Parnassiinae) and the subfamily Papilioninae formed different subclusters. In the Papilioninae
cluster, the tribes Troidini and Graphiini formed a subcluster, and the tribe Papilionini formed the other subcluster. These
results generally agree with the traditional classification of the papilionid butterflies based on their morphological characteristics
and support the proposed evolutionary genealogy of the butterflies based on their morphology, behavior, and larval host plants,
except that the tribes Parnasiini and Zerynthiini (both Parnassiinae) are not in the same cluster.
Received: 16 March 1998 / Accepted: 28 April 1998 相似文献