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1.
Drosophila nuclear introns are commonly assumed to change according to a single rate of substitution, yet little is known about the
evolution of these non-coding sequences. The hypothesis of a uniform substitution rate for introns seems to be at odds with
recent findings that the nucleotide composition of introns varies at a scale unknown before, and that their base content variation
is correlated with that of the adjacent exons. However, no direct attempt at comparing substitution rates in introns seems
to have been addressed so far. We have studied the rate of nucleotide substitution over a region of the Xdh gene containing two adjacent short, constitutively spliced introns, in several species of Drosophila and related genera. The two introns differ significantly in base composition and substitution rate, with one intron evolving
at least twice as fast as the other. In addition, the substitution pattern of the introns is positively associated with that
of the surrounding coding regions, evidencing that the molecular evolution of these introns is impacted by the region in which
they are embedded. The observed differences cannot be attributed to selection acting differently at the level of the secondary
structure of the pre-mRNA. Rather, they are better accounted for by locally heterogeneous patterns of mutation.
Received: 26 July 1999 / Accepted: 21 August 1999 相似文献
2.
3.
The Nonrandom Location of Synonymous Codons Suggests That Reading Frame-Independent Forces Have Patterned Codon Preferences 总被引:6,自引:0,他引:6
Biased codon usage is common in eukaryotic and prokaryotic genes. Evidence from Escherichia, Saccharomyces, and Drosophila indicates that it favors translational efficiency and accuracy. However, to date no functional advantages have been identified
in the codon–anticodon interactions involving the most frequently used (preferred) codons. Here we present evidence that forces
not related to the individual codon–anticodon interaction may be involved in determining which synonymous codons are preferred
or avoided. We show that the ``off-frame' trinucleotide motif preferences inferrable from Drosophila coding regions are often in the same direction as Drosophila's ``in-frame' codon preferences, i.e., its codon usage. The off-frame preferences were inferred from the nonrandomness of
the location of confamilial synonymous codons along coding regions—a pattern often described as a context dependence of nucleotide
choice at synonymous positions or as codon-pair bias. We relied on randomizations of the location of confamilial codons that
do not alter, and cannot be influenced by, the encoded amino acid sequences, codon usage, or base composition of the genes
examined. The statistically significant congruency of in-frame and off-frame trinucleotide preferences suggests that the same
kind of reading-frame-independent force(s) may also influence synonymous codon choice. These forces may have produced biases
in codon usage that then led to the evolution of the translational advantages of these motifs as preferred codons. Under this
scenario, tRNA pool size differences between preferred and nonpreferred codons initially were evolved to track the default
overrepresentation of codons with preferred motifs. The motif preference hypothesis can explain the structuring of codon preferences
and the similarities in the codon usages of distantly related organisms.
Received: 10 November 1998 / Accepted: 23 February 1999 相似文献
4.
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
5.
The very high AT content of hymenopteran mtDNA has warranted speculation about nucleotide substitution processes in this
group. Here we investigate the pattern of honeybee, Apis mellifera, mtDNA nucleotide polymorphisms inferred from phylogeny in terms of differences between the ATPase6, COI, COII, COIII, cytochrome
b, and ND2 genes and strand asymmetry in mutation rates. The observed transition/transversion ratios and the distribution of
nonsynonymous substitutions between regions differed significantly. The pattern of differences between genes leading to these
heterogeneities (the ATPase6 and COIII genes group apart from the rest) differed markedly from that predicted on the basis
of long-term evolutionary change and may indicate differences between current and long-term dynamics of sequence evolution.
Also, there is strong strand asymmetry in substitutions, which probably results in a mutability of G and C sufficiently high
to account for the AT-richness of honeybee mtDNA.
Received: 21 October 1998 / Accepted: 27 January 1999 相似文献
6.
Sílvia Atrian Luis Sánchez-Pulido Roser Gonzàlez-Duarte Alfonso Valencia 《Journal of molecular evolution》1998,47(2):211-221
Drosophilidae is a large, widely distributed family of Diptera including 61 genera, of which Drosophila is the most representative. Drosophila feeding is part of the saprophytic trophic chain, because of its dependence upon decomposing organic matter. Many species
have adapted to fermenting fruit feeding or to artificial (man-made) fermentation habitats, such as cellars and breweries.
Actually, the efficient exploitation of niches with alcohols is considered one of the reasons for the worldwide success of
this genus. Drosophila alcohol dehydrogenase (ADH), a member of the short-chain dehydrogenase/reductase family (SDR), is responsible for the oxidation
of alcohols, but its direct involvement in fitness, including alcohol tolerance and utilization, gives rise to much controversy.
Thus, it remains unclear whether ADH differentiation through evolution is somehow associated with natural adaptation to new
feeding niches, and thus maybe to Drosophila speciation, or if it is a simple reflection of neutral divergence correlated with time separation between species. To build
a hypothesis which could shed light on this dilemma, we analyzed the amino acid variability found in the 57 protein ADH sequences
reported up to now, identified the taxon-specific residues, and localized them in a three-dimensional ADH model. Our results
define three regions whose shaping has been crucial for ADH differentiation and would be compatible with a contribution of
ADH to Drosophila speciation.
Received: 11 August 1997 / Accepted: 30 December 1997 相似文献
7.
The Drosophila fat body protein 2 gene (Fbp2) is an ancient duplication of the alcohol dehydrogenase gene (Adh) which encodes a protein that differs substantially from ADH in its methionine content. In D. melanogaster, there is one methionine in ADH, while there are 51 (20% of all amino acids) in FBP2. Methionine is involved in 46% of amino
acid replacements when Fbp2 DNA sequences are compared between D. melanogaster and D. pseudoobscura. Methionine accumulation does not affect conserved residues of the ADH-ADHr-FBP2 multigene family. The multigene family has evolved by replacement of mildly hydrophobic amino acids by methionine with
no apparent reversion. Its short-term evolution was compared between two Drosophila species, while its long-term evolution was compared between two genera belonging respectively to acalyptrate and calyptrate
Diptera, Drosophila and Sarcophaga. The pattern of nucleotide substitution was consistent with an independent accumulation of methionines at the Fbp2 locus in each lineage. Under a steady-state model, the rate of methionine accumulation was constant in the lineage leading
to Drosophila, and was twice as fast as that in the calyptrate lineage. Substitution rates were consistent with a slight positive selective
advantage for each methionine change in about one-half of amino acid sites in Drosophila. This shows that selection can potentially account for a large proportion of amino acid replacements in the molecular evolution
of proteins.
Received: 12 December 1994 / Accepted: 15 April 1996 相似文献
8.
We analyzed the phylogenetic relationship between the species of Lordiphosa and other Drosophilidae using alcohol dehydrogenase (Adh) gene sequences. The phylogenetic trees consistently show that the four species Drosophila kurokawai, D. collinella, D. stackelbergi, and D. clarofinis, which include three species groups of Lordiphosa, form a monophyletic clade. This clade is placed as a sister group to the willistoni and saltans groups of Sophophora. On the other hand, three species of Lordiphosa, D. tenuicauda, D. pseudotenuicauda, and D. acutissima, all of which belong to the tenuicauda group, are not shown to be related to the major Lordiphosa lineage. In the phylogenetic trees, these species are included into the clade comprised of Drosophila and Hirtodrosophila, although it remains uncertain whether the tenuicauda group is a monophyletic group or not. These results indicate that Lordiphosa is polyphyletic and that most of the members of the subgenus have a close relationship to the neotropical groups of Sophophora. The above conclusion is compatible with the hypothesis of Okada (Mushi [1963] 37:79–100) and Lastovka and Máca (Acta Ent Bohemoslov [1978] 75:404–420) that Lordiphosa is most closely related to Sophophora; in contrast, our results contradict the hypothesis of Grimaldi (Bull Am Mus Nat Hist [1990] 197:1–139) that Lordiphosa is a sister group to the genus Scaptomyza.
Received: 12 May 1999 / Accepted: 14 April 2000 相似文献
9.
Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require
divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3)
only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be
examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using
these methods, we found that mitochondrial genes have 1.7–3.4 times higher synonymous substitution rates than the fastest
nuclear genes or 4.5–9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was
2.7 (estimated from the melanogaster species subgroup) or 2.9 (estimated from the obscura group) times higher in mitochondrial genes than in nuclear genes. Synonymous transversions in mitochondrial genes occurred
at an approximately equivalent rate to those in the fastest nuclear genes. This last result is not consistent with the hypothesis
that the difference in turnover rates between mitochondrial and nuclear genomes is the major factor determining higher synonymous
substitution rates in mtDNA. We conclude that the difference in synonymous substitution rates is due to a combination of two
factors: a higher transitional mutation rate in mtDNA and constraints on nuclear genes due to selection for codon usage.
Received: 27 November 1996 / Accepted: 8 May 1997 相似文献
10.
Tatarenkov A Kwiatowski J Skarecky D Barrio E Ayala FJ 《Journal of molecular evolution》1999,48(4):445-462
We have sequenced most of the coding region of the gene Dopa decarboxylase (Ddc) in 24 fruitfly species. The Ddc gene is quite informative about Drosophila phylogeny. Several outstanding issues in Drosophila phylogeny are resolved by analysis of the Ddc sequences alone or in combination with three other genes, Sod, Adh, and Gpdh. The three species groups, melanogaster, obscura, and willistoni, are each monophyletic and all three combined form a monophyletic group, which corresponds to the subgenus Sophophora. The Sophophora subgenus is the sister group to all other Drosophila subgenera (including some named genera, previously considered outside the Drosophila genus, namely, Scaptomyza and Zaprionus, which are therefore downgraded to the category of subgenus). The Hawaiian Drosophila and Scaptomyza are a monophyletic group, which is the sister clade to the virilis and repleta groups of the subgenus Drosophila. The subgenus Drosophila appears to be paraphyletic, although this is not definitely resolved. The two genera Scaptodrosophila and Chymomyza are older than the genus Drosophila. The data favor the hypothesis that Chymomyza is older than Scaptodrosophila, although this issue is not definitely resolved. Molecular evolution is erratic. The rates of nucleotide substitution in 3rd
codon position relative to positions 1 + 2 vary from one species lineage to another and from gene to gene.
Received: 2 June 1998 / Accepted: 3 September 1998 相似文献
11.
Drosophila willistoni was the subject of intensive allozyme studies and the locus coding for alcohol dehydrogenase (Adh) was found to be virtually monomorphic. DNA sequence analysis of 18 alleles throughout the distribution of the species has
revealed six replacement polymorphisms. The ratio of replacement to silent polymorphisms is higher in D. willistoni than in any other Drosophila species studied for Adh nucleotide variation. Also in contrast to other species, the variation in introns and noncoding DNA is about the same as
in the coding region. We speculate that both these differences indicate D. willistoni has historically had a small population size possibly related to Pleistocene refugia in the Neotropics.
Received: 5 August 1996 / Accepted: 12 April 1997 相似文献
12.
Multiple Origins of Cyclodiene Insecticide Resistance in Tribolium castaneum (Coleoptera: Tenebrionidae) 总被引:4,自引:0,他引:4
Andreev D Kreitman M Phillips TW Beeman RW ffrench-Constant RH 《Journal of molecular evolution》1999,48(5):615-624
The number of origins of pesticide resistance-associated mutations is important not only to our understanding of the evolution
of resistance but also in modeling its spread. Previous studies of amplified esterase genes in a highly dispersive Culex mosquito have suggested that insecticide resistance-associated mutations (specifically a single-gene duplication event) can
occur a single time and then spread throughout global populations. In order to provide data for resistance-associated point
mutations, which are more typical of pesticide mechanisms as a whole, we studied the number of independent origins of cyclodiene
insecticide resistance in the red flour beetle Tribolium castaneum. Target-site insensitivity to cyclodienes is conferred by single point mutations in the gene Resistance to dieldrin (Rdl), which codes for a subunit of a γ-aminobutyric acid (GABA) receptor. These point mutations are associated with replacements
of alanine 302 which render the receptor insensitive to block by the insecticide. We collected 141 strains of Tribolium worldwide and screened them for resistance. Twenty-four strains contained resistant individuals. After homozygosing 23 of
these resistance alleles we derived a nucleotide sequence phylogeny of the resistant strains from a 694-bp section of Rdl, encompassing exon 7 (which contains the resistance-associated mutation) and part of a flanking intron. The phylogeny also
included six susceptible alleles chosen at random from a range of geographical locations. Resistance alleles fell into six
clades and three clades contained both resistant and susceptible alleles. Although statistical analysis provided support at
only the 5–6% level, the pattern of variation in resistance alleles is more readily explained by multiple independent origins
of resistance than by spread of a single resistance-associated mutation. For example, two resistance alleles differed from
two susceptible alleles only by the resistance-associated mutation itself, suggesting that they form the susceptible ancestors
and that resistance arose independently in several susceptible backgrounds. This suggests that in Tribolium Rdl, de novo mutations for resistance have arisen independently in several populations. Identical alleles were found in geographically distant regions as well, also
implying that some Rdl alleles have been exported in stored grain. These differences from the Culex study may stem both from differences in the population genetics of Tribolium versus that of mosquitoes and differences in mutation rates associated with point mutations versus gene duplication events.
The Tribolium data therefore suggest that multiple origins of insecticide resistance (associated with specific point mutations) may be
more common than the spread of single events. These findings have implications for the way in which we model the evolution
and spread of insecticide resistance genes and also suggest that parallel adaptive substitutions may not be uncommon in phyletic
evolution.
Received: 14 October 1998 / Accepted: 4 January 1999 相似文献
13.
Carmichael AN Fridolfsson AK Halverson J Ellegren H 《Journal of molecular evolution》2000,50(5):443-447
Whether the mutation rate differs between sexes has been a matter of discussion for years. Molecular analyses of mammals
have indicated that males mutate more often than females, as manifested by the faster rate of neutral sequence evolution on
the Y chromosome than on the X chromosome. However, these observations can as well be interpreted as specific reduction of
the X chromosome mutation rate, which would be adaptive because of reducing the number of slightly deleterious recessive mutations
exposed in hemizygote males. Recently, data from birds have suggested that vertebrate mutation rates may indeed be male-biased.
In birds, females are the heterogametic sex (ZW), and analyses of the Z-linked CHD1Z gene have shown that it evolves faster
than its W-linked and thus female-specific homologue, CHD1W. We have now studied the second avian gene known to exist in a
copy on the nonrecombining regions of both the Z and the W chromosome, viz., the ATP synthase α-subunit (ATP5A1). In independent comparisons of three pairs of bird species from divergent lineages, intron
sequences of the Z-linked copy (ATP5A1Z) were consistently found to evolve faster than the W-linked copy (ATP5A1W). From these
data we calculated male-to-female mutation rate ratios (α) of 1.8, 2.3, and 5.0 in Galliform, Anseriform, and Ciconiiform
lineages, respectively. Therefore, this study provides independent support for a male-biased mutation rate in birds.
Received: 15 July 1999 / Accepted: 5 January 2000 相似文献
14.
D. Casane S. Boissinot B.H.-J. Chang L.C. Shimmin W.-H. Li 《Journal of molecular evolution》1997,45(3):216-226
We sequenced three argininosuccinate-synthetase-processed pseudogenes (ΨAS-A1, ΨAS-A3, ΨAS-3) and their noncoding flanking
sequences in human, orangutan, baboon, and colobus. Our data showed that these pseudogenes were incorporated into the genome
of the Old World monkeys after the divergence of the Old World and New World monkey lineages. These pseudogene flanking regions
show variable mutation rates and patterns. The variation in the G/C to A/T mutation rate (u) can account for the unequal GC contents at equilibrium: 34.9, 36.9, and 41.7% in the pseudogene ΨAS-A1, ΨAS-A3, and ΨAS-3
flanking regions, respectively. The A/T to G/C mutation rate (v) seems stable and the u/v ratios equal 1.9, 1.7, and 1.4 in the flanking regions of ΨAS-A1, ΨAS-A3, and ΨAS-3, respectively. These ``regional' variations
of the mutation rate affect the evolution of the pseudogenes, too. The ratio u/v being greater than 1.0 in each case, the overall mutation rate in the GC-rich pseudogenes is, as expected, higher than in
their GC-poor flanking regions. Moreover, a ``sequence effect' has been found. In the three cases examined u and v are higher (at least 20%) in the pseudogene than in its flanking region—i.e., the pseudogene appears as mutation ``hot'
spots embedded in ``cold' regions. This observation could be partly linked to the fact that the pseudogene flanking regions
are long-standing unconstrained DNA sequences, whereas the pseudogenes were relieved of selection on their coding functions
only around 30–40 million years ago. We suspect that relatively more mutable sites maintained unchanged during the evolution
of the argininosuccinate gene are able to change in the pseudogenes, such sites being eliminated or rare in the flanking regions
which have been void of strong selective constraints over a much longer period. Our results shed light on (1) the multiplicity
of factors that tune the spontaneous mutation rate and (2) the impact of the genomic position of a sequence on its evolution.
Received: 10 February 1997 / Accepted: 21 April 1997 相似文献
15.
Ballard JW 《Journal of molecular evolution》2000,51(1):48-63
In this study, a comparative genomics approach is employed to investigate the forces that shape evolutionary change in the
mitochondrial DNA (mtDNA) of members of the Drosophila melanogaster subgroup. This approach facilitates differentiation of the patterns of variation resulting from processes acting at a higher
level from those acting on a single gene. The mitochondrial genomes of three isofemale lines of D. simulans (siI, -II, and -III), two of D. melanogaster (Oregon R and a line from Zimbabwe), and D. mauritiana (maI and -II), and one of D. sechellia were sequenced and compared with that derived from D. yakuba. Data presented here indicate that at least three broad mechanisms shape the evolutionary dynamics of mtDNA in these taxa.
The first set of mechanisms is intrinsic to the molecule. Dominant processes may be interpreted as selection for an increased
rate of replication of the mtDNA molecule, biases in DNA repair, and differences in the pattern of nucleotide substitution
among strands. In the genes encoded on the major strand (62% of the coding DNA) changes to or from C predominate, whereas
on the minor changes to or from G predominate. The second set of mechanisms affects distinct lineages. There are evolutionary
rate differences among lineages, possibly owing to population demographic changes or changes in mutational biases. This is
supported by the heterogeneity found in synonymous, nonsynonymous, and silent substitutions. The third set of mechanisms differentially
affects distinct genes. A maximum-likelihood sliding-window analysis detected four disjunct regions that have a significantly
different nucleotide substitution process from that derived from the complete sequence. These data show the potential for
comparative genomics to tease apart subtle forces that shape the evolution of DNA.
Received: 30 July 1999 / Accepted: 16 March 2000 相似文献
16.
Because avian females are heterogametic, the reverse of mammals, avian sex chromosomes undergo significantly different patterns
and numbers of DNA replications than do those in mammals. This makes the W (female-specific) and the Z chromosomes an excellent
model system for the study of the replicative division hypothesis, which purports that DNA substitution rate is determined
by the number of germline replications. The sex-specific chromosome in birds (the W) is predicted to change at the slowest
rate of all avian chromosomes because it undergoes the fewest rounds of replication per unit of evolutionary time. Using published
data on gametogenesis from a variety of sources, we estimated the ratio of male-to-female germline replications (c) in galliforms and anseriforms to be approximately 4.4. The value of c should predict the value of the ratio of male-to-female mutation rates (αm) if the replicative division hypothesis is true. Homologous DNA sequences including an intron and parts of two exons of the
CHD gene were obtained from the W and the Z chromosomes in ostrich, sage grouse, canvasback duck, tundra swan, and snow goose.
The exons show significantly different nucleotide composition from the introns, and the W-linked exons show evidence of relaxed
constraint. The Z-linked intron is diverging ≈ 3.1 times faster than the W-linked intron. From this, αm was calculated to be approximately 4.1, with a confidence interval of 3.1 to 5.1. The data support the idea that the number
of replicative divisions is a major determinant of substitution rate in the Eoavian genome.
Received: 19 January 1999 / Accepted: 8 June 1999 相似文献
17.
In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent
biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we
consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In
particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered.
Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary
conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that
strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably
between genomes.
Received: 6 May 1999 / Accepted: 29 October 1999 相似文献
18.
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
19.
In human populations, a null allele having several nucleotide differences from the wild-type allele is segregating at the
FUT2 locus (the ABO-Secretor locus) encoding α(1,2)fucosyltransferase. To estimate the age of the most recent common ancestor
(MRCA) of these two alleles, we sequenced FUT2 homologues from chimpanzee, gorilla, orangutan, and green monkey. Since we did not detect acceleration or any heterogeneity
in the substitution rate at this locus among these species, the age of the MRCA was estimated to be around 3 MYA, assuming
the divergence time of human and chimpanzee to be 5 MYA. We developed a simple test to examine whether or not the old age
of the MRCA of the FUT2 is consistent with that expected for two divergent neutral alleles sampled from a random mating population. An application
of the test to the data at FUT2 indicated that the age of the MRCA is too old to be explained by the simple neutral assumptions, although our test depends
on accurate estimation of the divergence time of human and chimpanzee in units of twice the human population size. Various
possibilities including balancing selection are discussed to explain this old age of the MRCA.
Received: 9 May 1999 / Accepted: 20 September 1999 相似文献
20.
The complete nucleotide sequence of the SSU rRNA gene from the soil bug, Armadillidium vulgare (Crustacea, Isopoda), was determined. It is 3214 bp long, with a GC content of 56.3%. It is not only the longest SSU rRNA
gene among Crustacea but also longer than any other SSU rRNA gene except that of the strepsipteran insect, Xenos vesparum (3316 bp). The unusually long sequence of this species is explained by the long sequences of variable regions V4 and V7,
which make up more than half of the total length. RT-PCR analysis of these two regions showed that the long sequences also
exist in the mature rRNA and sequence simplicity analysis revealed the presence of slippage motifs in these two regions. The
putative secondary structure of the rRNA is typical for eukaryotes except for the length and shape variations of the V2, V4,
V7, and V9 regions. Each of the V2, V4, and V7 regions was elongated, while the V9 region was shortened. In V2, two bulges,
located between helix 8 and helix 9 and between helix 9 and helix 10, were elongated. In V4, stem E23-3 was dramatically expanded,
with several small branched stems. In V7, stem 43 was branched and expanded. Comparisons with the unusually long SSU rRNAs
of other organisms imply that the increase in total length of SSU rRNA is due mainly to expansion in the V4 and V7 regions.
Received: 2 March 1999 / Accepted: 22 July 1999 相似文献