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1.
Analysis of DNA sequences of 132 introns and 140 exons from 42 pairs of orthologous genes of mouse and rat was used to compare
patterns of evolutionary change between introns and exons. The mean of the absolute difference in length (measured in base
pairs) between the two species was nearly five times as high in the case of introns as in the case of exons. The average rate
of nucleotide substitution in introns was very similar to the rate of synonymous substitution in exons, and both were about
three times the rate of substitution at nonsynonymous sites in exons. G+C content of introns and exons of the same gene were
correlated; but mean G+C content at the third positions of exons was significantly higher than that of introns or positions
1–2 of exons from the same gene. G+C content was conserved over evolutionary time, as indicated by strong correlations between
mouse and rat; but the change in G+C content was greatest at position 3 of exons, intermediate in introns, and lowest at positions
1–2 in introns.
Received: 23 December 1996 / Accepted: 1 April 1997 相似文献
2.
To study the evolution of human X-linked red and green opsin genes, genomic sequences in large regions of the two genes were
compared. The divergences in introns 3, 4, and 5 and the 3′ flanking sequence of the two genes are significantly lower than
those in exons 4 and 5. The homogenization mechanism of introns and the 3′ flanking sequence of human red and green opsin
genes is probably gene conversion, which also occurred in exons 1 and 6. At least one gene conversion event occurred in each
of three regions (1, 3, and 5) in the sequences compared. In conclusion, gene conversion has occurred frequently between human
red and green opsin genes, but exons 2, 3, 4, and 5 have been maintained distinct between the two genes by natural selection.
Received: 29 September 1997 / Accepted: 29 September 1997 相似文献
3.
Héctor Musto Héctor Romero Helena Rodríguez-Maseda 《Journal of molecular evolution》1998,46(2):159-167
Synonymous codon choices vary considerably among Schistosoma mansoni genes. Principal components analysis detects a single major trend among genes, which highly correlates with GC content in
third codon positions and exons, but does not discriminate among putatively highly and lowly expressed genes. The effective
number of codons used in each gene, and its distribution when plotted against GC3, suggests that codon usage is shaped mainly by mutational biases. The GC content of exons, GC3, 5′, 3′, and flanking (5′+ 3′+ introns) regions are all correlated among them, suggesting that variations in GC content may
exist among different regions of the S. mansoni genome. We propose that this genome structure might be among the most important factors shaping codon usage in this species,
although the action of selection on certain sequences cannot be excluded.
Received: 10 March 1997 / Accepted: 27 June 1997 相似文献
4.
de Miranda AB Alvarez-Valin F Jabbari K Degrave WM Bernardi G 《Journal of molecular evolution》2000,50(1):45-55
Mycobacterium tuberculosis and Mycobacterium leprae are the ethiological agents of tuberculosis and leprosy, respectively. After performing extensive comparisons between genes
from these two GC-rich bacterial species, we were able to construct a set of 275 homologous genes. Since these two bacterial
species also have a very low growth rate, translational selection could not be so determinant in their codon preferences as
it is in other fast-growing bacteria. Indeed, principal-components analysis of codon usage from this set of homologous genes
revealed that the codon choices in M. tuberculosis and M. leprae are correlated not only with compositional constraints and translational selection, but also with the degree of amino acid
conservation and the hydrophobicity of the encoded proteins. Finally, significant correlations were found between GC3 and synonymous distances as well as between synonymous and nonsynonymous distances.
Received: 30 October 1998 / Accepted: 16 August 1999 相似文献
5.
The extracellular hemoglobins of cladocerans derive from the aggregation of 12 two-domain globin subunits that are apparently
encoded by four genes. This study establishes that at least some of these genes occur as a tandem array in both Daphnia magna and Daphnia exilis. The genes share a uniform structure; a bridge intron separates two globin domains which each include three exons and two
introns. Introns are small, averaging just 77 bp, but a longer sequence (2.2–3.2 kb) separates adjacent globin genes. A survey
of structural diversity in globin genes from other daphniids revealed three independent cases of intron loss, but exon lengths
were identical, excepting a 3-bp insertion in exon 5 of Simocephalus. Heterogeneity in the extent of nucleotide divergence was marked among exons, largely as a result of the pronounced diversification
of the terminal exon. This variation reflected, in part, varying exposure to concerted evolution. Conversion events were frequent
in exons 1–4 but were absent from exons 5 and 6. Because of this difference, the results of phylogenetic analyses were strongly
affected by the sequences employed in this construction. Phylogenies based on total nucleotide divergence in exons 1–4 revealed
affinities among all genes isolated from a single species, reflecting the impact of gene conversion events. In contrast, phylogenies
based on total nucleotide divergence in exons 5 and 6 revealed affinities among orthologous genes from different taxa.
Received: 8 March 1999 / Accepted: 14 July 1999 相似文献
6.
7.
Compositional compartmentalization and compositional patterns in the nuclear genomes of plants. 总被引:14,自引:5,他引:9
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We report here results which indicate (i) that the nuclear genomes of angiosperms is characterized by a compositional compartmentalization and an isochore structure; and (ii) that the nuclear genomes of some Gramineae exhibit strikingly different compositional patterns compared to those of many dicots. Indeed, the compositional distribution of nuclear DNA molecules (in the 50-100 Kb size range) from three dicots (pea, sunflower and tobacco) and three monocots (maize, rice and wheat) were found to be centered around lower (41%) and higher (45% for rice, 48% for maize and wheat) GC levels, respectively (and to trail towards even higher GC values in maize and wheat). Experiments on gene localization in density gradient fractions showed a remarkable compositional homogeneity in vast (greater than 100-200 Kb) regions surrounding the genes. On the other hand, the compositional distribution of coding sequences (GenBank and literature data) from dicots (several orders) was found to be narrow, symmetrical and centered around 46% GC, that from monocots (essentially barley, maize and wheat) to be broad, asymmetrical and characterized by an upward trend towards high GC values, with the majority of sequences between 60 and 70% GC. Introns exhibited a similar compositional distribution, but lower GC levels, compared to exons from the same genes. 相似文献
8.
The isochore organization and the compositional distribution of homologous coding sequences in the nuclear genome of plants. 总被引:11,自引:7,他引:4
The isochore structure of the nuclear genome of angiosperms described by Salinas et al. (1) was confirmed by using a different experimental approach, namely by showing that the levels of coding sequences from both dicots and Gramineae are linearly correlated with GC levels of the corresponding flanking sequences. The compositional distribution of homologous coding sequences from several orders of dicots and from Gramineae were also studied and shown to mimick the compositional distributions previously seen (1) for coding sequences in general, most coding sequences from Gramineae being much higher than those of the dicots explored. These differences were even stronger for third codon positions and led to striking codon usages for many coding sequences especially in the case of Gramineae. 相似文献
9.
The intron positions of ten different protein families were examined to determine (the statistical likelihood of) whether
spliceosomal introns are the result of random insertion events into previously intronless genes, on the one hand, or the result
of random loss from common ancestral introns, on the other. The number of expected matches for the alternative scenarios was
calculated for a binomial distribution by considering currently observed introns relative to all possible locations for insertion
or loss. Introns occurring at approximately the same location (hereafter called a ``match') were tallied for each of the
paired proteins. Matches were identified by their positions in the multiple alignment and were defined as any two introns
occurring within a window of 11 possible nucleotide positions, thereby allowing for possible alignment errors and ``intron
sliding.' Matches were tallied from the raw data and compared with the expected number of matches for the two different scenarios.
The results suggest that the distribution of introns in genes encoding proteins is due to random insertion and not random
loss.
Received: 8 September 1996 / Accepted: 24 January 1997 相似文献
10.
Jean-Luc Da Lage Maurice Wegnez Marie-Louise Cariou 《Journal of molecular evolution》1996,43(4):334-347
While the two amylase genes of Drosophila melanogaster are intronless, the three genes of D. pseudoobscura harbor a short intron. This raises the question of the common structure of the Amy gene in Drosophila species. We have investigated the presence or absence of an intron in the amylase genes of 150 species
of Drosophilids. Using polymerase chain reaction (PCR), we have amplified a region that surrounds the intron site reported
in D. pseudoobscura and a few other species. The results revealed that most species contain an intron, with a variable size ranging from 50 to
750 bp, although the very majoritary size was around 60–80 bp. Several species belonging to different lineages were found
to lack an intron. This loss of intervening sequence was likely due to evolutionarily independent and rather frequent events.
Some other species had both types of genes: In the obscura group, and to a lesser extent in the ananassae subgroup, intronless copies had much diverged from intron-containing genes. Base composition of short introns was found to
be variable and correlated with that of the surrounding exons, whereas long introns were all A-T rich. We have extended our
study to non-Drosophilid insects. In species from other orders of Holometaboles, Lepidoptera and Hymenoptera, an intron was
found at an identical position in the Amy gene, suggesting that the intron was ancestral.
Received: 23 October 1995 / Accepted: 5 March 1996 相似文献
11.
12.
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
13.
Ferritin, a protein widespread in nature, concentrates iron ∼1011–1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor
(based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin
gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants
but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals
and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization
in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning
of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals
but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the
absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In
plant ferritin genes, the number of introns (n= 7) is higher than in animals (n= 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin
gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary
protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin
genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding
sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional
constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin
gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid,
the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
Received: 25 July 1995 / Accepted: 3 October 1995 相似文献
14.
Alessandra Gambacurta Maria Cristina Piro Franca Ascoli 《Journal of molecular evolution》1998,47(2):167-171
Vertebrate and many invertebrate globin genes have a three-exon/two-intron organization, with introns in highly conserved
positions. According to the ``intron early' hypothesis, introns are the vestigial segments which flank previously independent
coding sequences, thus providing evidence for the assembly of the ancient proteins by ``exon shuffling.' In this paper, we
report the analysis of the genes of the bivalve mollusk Scapharca inaequivalvis tetrameric hemoglobin (HbII), which support this hypothesis, at least for the hemoglobin genes. We show the existence of
``minigenes' in the IIA and IIB globin genes, spanning part of the first and second introns, ``in frame' with the heme-binding
domain coded by the second exon. Further support for the exon shuffling hypothesis can be found in the degree of identity
of the ``new' translated sequences with those flanking the central protein domain of some invertebrate hemoglobins.
Received: 31 July 1997 / Accepted: 12 December 1997 相似文献
15.
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
16.
17.
Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria 总被引:16,自引:0,他引:16
We show that in animal mitochondria homologous genes that differ in guanine plus cytosine (G + C) content code for proteins
differing in amino acid content in a manner that relates to the G + C content of the codons. DNA sequences were analyzed using
square plots, a new method that combines graphical visualization and statistical analysis of compositional differences in
both DNA and protein. Square plots divide codons into four groups based on first and second position A + T (adenine plus thymine)
and G + C content and indicate differences in amino acid content when comparing sequences that differ in G + C content. When
sequences are compared using these plots, the amino acid content is shown to correlate with the nucleotide bias of the genes.
This amino acid effect is shown in all protein-coding genes in the mitochondrial genome, including cox I, cox II, and cyt b, mitochondrial genes which are commonly used for phylogenetic studies. Furthermore, nucleotide content differences are shown
to affect the content of all amino acids with A + T- and G + C-rich codons. We speculate that phylogenetic analysis of genes
so affected may tend erroneously to indicate relatedness (or lack thereof) based only on amino acid content.
Received: 3 July 1996 / Accepted: 6 November 1996 相似文献
18.
The protein-coding sequences of the major histocompatibility complex (MHC) genes are characterized by extraordinarily high
polymorphism, apparently maintained by balancing selection, which favors diversity in the peptide-binding domains of the MHC
glycoproteins. Here we report that the introns flanking the polymorphic exons of the human MHC class I loci HLA-A, -B, and -C genes have been relatively conserved and have become locus-specific apparently as a result of recombination and subsequent
genetic drift, leading to homogenization within loci over evolutionary time. Thus, HLA class I genes have been shaped by contrasting evolutionary forces maintaining polymorphism in the exons and leading to conservation
in the introns. This study provides the first extensive analysis of the introns of a highly polymorphic gene family.
Received: 10 April 1997 / Revised: 15 July 1997 相似文献
19.
Two classes of genes in plants 总被引:19,自引:0,他引:19
Two classes of genes were identified in three Gramineae (maize, rice, barley) and six dicots (Arabidopsis, soybean, pea, tobacco, tomato, potato). One class, the GC-rich class, contained genes with no, or few, short introns. In contrast, the GC-poor class contained genes with numerous, long introns. The similarity of the properties of each class, as present in the genomes of maize and Arabidopsis, is particularly remarkable in view of the fact that these plants exhibit large differences in genome size, average intron size, and DNA base composition. The functional relevance of the two classes of genes is stressed by (1) the conservation in homologous genes from maize and Arabidopsis not only of the number of introns and of their positions, but also of the relative size of concatenated introns; and (2) the existence of two similar classes of genes in vertebrates; interestingly, the differences in intron sizes and numbers in genes from the GC-poor and GC-rich classes are much more striking in plants than in vertebrates. 相似文献
20.
A.D. Shutov H. Braun Yu.V. Chesnokov Ch. Horstmann I.A. Kakhovskaya H. Bäumlein 《Journal of molecular evolution》1998,47(4):486-492
The development of seeds as a specialized organ for the nutrition, protection, and dispersal of the next generation was an
important step in the evolution of land plants. Seed maturation is accompanied by massive synthesis of storage compounds such
as proteins, starch, and lipids. To study the processes of seed storage protein evolution we have partially sequenced storage
proteins from maturing seeds of representatives from the gymnosperm genera Gnetum, Ephedra, and Welwitschia—morphologically diverse and unusual taxa that are grouped in most formal systems into the common order Gnetales. Based on
partial N-terminal amino acid sequences, oligonucleotide primers were derived and used for PCR amplification and cloning of
the corresponding cDNAs. We also describe the structure of the nuclear gene for legumin of Welwitschia mirabilis. This first gnetalean nuclear gene structure contains introns in only two of the four conserved positions previously characterized
in other spermatophyte legumin genes. The distinct phylogenetic status of the gnetalean taxa is also reflected in a sequence
peculiarity of their legumin genes. A comparative analysis of exon/intron sequences leads to the hypothesis that legumin genes
from Gnetales belong to a monophyletic evolutionary branch clearly distinct from that of legumin genes of extant Ginkgoales
and Coniferales as well as from all angiosperms.
Received: 5 June 1997 / Accepted: 31 March 1998 相似文献