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1.
In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging
to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of
the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin:
The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles
and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor
BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont
algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded
by the well-supported successive divergence of labyrinthulomycetes and bicosoecids.
On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching
order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae,
and several smaller groups of organisms remains largely unresolved.
When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution
rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving
sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic
grouping in most distance trees.
Received: 11 June 1997 / Accepted: 21 July 1997 相似文献
2.
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
3.
Julius Lukeš Milan Jirků David Doležel Ivica Kral'ová Laura Hollar Dmitri A. Maslov 《Journal of molecular evolution》1997,44(5):521-527
To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU)
and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome,
Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new
taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of
the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there
is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal
paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade
of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission.
This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the
adaptation to vertebrate hosts.
Received: 5 July 1996 / Accepted: 26 September 1996 相似文献
4.
The complete nucleotide sequence of the 18S subunit of ribosomal DNA (rDNA) was determined for the venerid clams Callista chione (Pitarinae) and Venus verrucosa (Venerinae). Comparison of the new sequences with the published sequences of 1 annelid, 2 gastropods, 2 polyplacophorans,
and 19 bivalves showed that when the annelids are used as outgroup the gastropods diverge from the bivalves, which form a
cluster including the polyplacophorans. When the gastropods alone were compared with the bivalves, the latter split in two
groups corresponding to the two subclasses of Heterodonta and Pteriomorpha. The former include two taxa that diverged early,
Galeomma and Tridacna, while the Veneridae and Mactridae form two sister groups. In contrast to previous reports and in line with morphological
data, the Ostreidae are included in the Pteriomorphia and form a monophyletic group.
Received: 16 May 1998 / Accepted: 11 August 1998 相似文献
5.
The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid
protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this
organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal
genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes
for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI
cDNAs from E. gracilis possess short 5′ and 3′ untranslated transcribed sequences and lack a 3′ poly[A] tail.
The COI gene does not require uridine insertion/deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional,
and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [α-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3′ end structures of mRNAs, phylogenetic
analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes
of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using
nuclear ribosomal RNA sequences.
Received: 5 March 1996 / Accepted: 31 July 1996 相似文献
6.
The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu 总被引:4,自引:0,他引:4
Ken-ichiro Ishida Ying Cao Masami Hasegawa Norihiro Okada Yoshiaki Hara 《Journal of molecular evolution》1997,45(6):682-687
A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify
the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic
eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that
contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial
EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods.
The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic
trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the
chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at
least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
Received: 10 March 1997 / Accepted: 28 July 1997 相似文献
7.
Bocchetta M Gribaldo S Sanangelantoni A Cammarano P 《Journal of molecular evolution》2000,50(4):366-380
The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in
the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1α) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase β- and β′-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade
in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum
parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1α) and EF-G(2) data sets, which lack both resolution
and statistical robustness. In the EF analysis MP outperforms ML in discriminating (at the 0.05 level) trees having A. pyrophilus and T. maritima as the most basal lineages from competing alternatives that have (i) mesophiles, or the Thermus genus, as the deepest bacterial radiation and (ii) a monophyletic A. pyrophilus–T. maritima cluster situated at the base of the bacterial clade. RNAP-based phylogenies are equivocal with respect to the Aquifex and Thermotoga placements. The two hyperthermophiles fall basal to all other bacterial phyla when potential artifacts contributed by the
compositionally biased and fast-evolving Mycoplasma genitalium and Mycoplasma pneumoniae sequences are eschewed. However, the branching order of the phyla is tenuously supported in ML trees inferred by the exhaustive
search method and is unresolved in ML trees inferred by the quartet puzzling algorithm. A rooting of the RNA polymerase-subunit
tree at the mycoplasma level seen in both the MP trees and the ML trees reconstructed with suboptimal amino acid substitution
models is not supported by the EF-based phylogenies which robustly affiliate mycoplasmas with low-G+C gram-positives and,
most probably, reflects a ``long branch attraction' artifact.
Received: 22 September 1999 / Accepted: 11 January 2000 相似文献
8.
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all.
Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate
variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of
Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate
chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot
be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae
by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA
trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast
phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora)
have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
Received: 27 December 1999 / Accepted: 24 March 2000 相似文献
9.
The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides 总被引:1,自引:0,他引:1
Van der Auwera G; De Baere R; Van de Peer Y; De Rijk P; Van den Broeck I; De Wachter R 《Molecular biology and evolution》1995,12(4):671-678
Based on biochemical and ultrastructural data, hyphochytriomycetes are
believed to share an ancestor with oomycetes and heterokont algae. In order
to study the phylogeny of the hyphochytriomycetes, we determined both the
small- and large-subunit ribosomal RNA sequence of Hyphochytrium
catenoides. Phylogenetic trees were constructed using the neighbor-joining
and maximum-parsimony method and include representatives of Chlorobionta,
Fungi, Metazoa, Alveolata, and all known Heterokonta. Our main conclusion
is that the hyphochytriomycetes form a monophyletic group with the
oomycetes and heterokont algae and that they are probably the closest
relatives of the oomycetes. However, the order of divergence between the
various heterokont algal phyla and the oomycete-hyphochytriomycete cluster
remains uncertain.
相似文献
10.
Nuclear ribosomal small subunit and chloroplast rbcL sequence data for heterokont algae and potential outgroup taxa were analyzed separately and together using maximum parsimony. A series of taxon sampling and character weighting experiments was performed. Traditional classes (e.g. diatoms, Phaeophyceae, etc.) were monophyletic in most analyses of either data set and in analyses of combined data. Relationships among classes and of heterokont algae to outgroup taxa were sensitive to taxon sampling. Bootstrap (BS) values were not always predictive of stability of nodes in taxon sampling experiments or between analyses of different data sets. Reweighting sites by the rescaled consistency index artificially inflates BS values in the analysis of rbcL data. Inclusion of the third codon position from rbcL enhanced signal despite the superficial appearance of mutational saturation. Incongruence between data sets was largely due to placement of a few problematic taxa, and so data were combined. BS values for the combined analysis were much higher than for analyses of each data set alone, although combining data did not improve support for heterokont monophyly. 相似文献
11.
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
12.
Miyuki Noro Ryuichi Masuda Irena A. Dubrovo Michihiro C. Yoshida Makoto Kato 《Journal of molecular evolution》1998,46(3):314-326
Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth
(Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed
by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the ``Mammuthus-Loxodonta' clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
Received: 8 April 1997 / Accepted: 23 July 1997 相似文献
13.
Steinhauser S Beckert S Capesius I Malek O Knoop V 《Journal of molecular evolution》1999,48(3):303-312
RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine
bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing
has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required
extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene
(1104 nt) was analyzed in a large collection of bryophytes and green algae (Charales). The genomic nad5 sequences predict
editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required
in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae,
on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic
sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes
the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by
cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants.
Received: 2 April 1998 / Accepted: 4 August 1998 相似文献
14.
Carolyn J. Lawrence Russell L. Malmberg Michael G. Muszynski R. Kelly Dawe 《Journal of molecular evolution》2002,54(1):42-53
We have reconstructed the evolution of the anciently derived kinesin superfamily using various alignment and tree-building
methods. In addition to classifying previously described kinesins from protists, fungi, and animals, we analyzed a variety
of kinesin sequences from the plant kingdom including 12 from Zea mays and 29 from Arabidopsis thaliana. Also included in our data set were four sequences from the anciently diverged amitochondriate protist Giardia lamblia. The overall topology of the best tree we found is more likely than previously reported topologies and allows us to make the
following new observations: (1) kinesins involved in chromosome movement including MCAK, chromokinesin, and CENP-E may be
descended from a single ancestor; (2) kinesins that form complex oligomers are limited to a monophyletic group of families;
(3) kinesins that crosslink antiparallel microtubules at the spindle midzone including BIMC, MKLP, and CENP-E are closely
related; (4) Drosophila NOD and human KID group with other characterized chromokinesins; and (5) Saccharomyces SMY1 groups with kinesin-I sequences, forming a family of kinesins capable of class V myosin interactions. In addition, we
found that one monophyletic clade composed exclusively of sequences with a C-terminal motor domain contains all known minus
end-directed kinesins.
Received: 20 February 2001 / Accepted: 5 June 2001 相似文献
15.
16.
In order to study the phylogenetic relationships within the stramenopiles, and particularly among the heterokont algae, we have determined complete or nearly complete large-subunit ribosomal RNA sequences for different species of raphidophytes, phaeophytes, xanthophytes, chrysophytes, synurophytes and pinguiophytes. With the small- and large-subunit ribosomal RNA sequences of representatives for nearly all known groups of heterokont algae, phylogenetic trees were constructed from a concatenated alignment of both ribosomal RNAs, including more than 5,000 positions. By using different tree construction methods, inferred phylogenies showed phaeophytes and xanthophytes as sister taxa, as well as the pelagophytes and dictyochophytes, and the chrysophytes/synurophytes and eustigmatophytes. All these relationships are highly supported by bootstrap analysis. However, apart from these sister group relationships, very few other internodes are well resolved and most groups of heterokont algae seem to have diverged within a relatively short time frame. 相似文献
17.
Wytze T. Stam Jaap J. Beintema Rossana D’Avino Maurizio Tamburrini Guido di Prisco 《Journal of molecular evolution》1997,45(4):437-445
Amino acid sequences of α- and β-chains of human hemoglobin and of hemoglobins of coelacanth and 24 teleost fish species,
including 11 antarctic and two temperate Notothenioidei, were analyzed using maximum parsimony. Trees were derived for the
α- and β-chains separately and for tandemly arranged sequences, using the human and coelacanth sequences as outgroups in all
analyses. The topologies of the trees of the α-and β-chains are highly congruent and indicate a specific pattern of gene duplications
and gene expression of teleost hemoglobins which has not yet been investigated into more detail. The Notothenioid fish generally
contain a single major hemoglobin and often a second minor component. The α- and β-chains of the major components form a monophyletic
group in all investigated trees, with the nonantarctic Pseudaphritis as their sister taxon. The minor chains also are a monophyletic group and form an unresolved cluster with the major chains
and the hemoglobins of tuna and red gurnard. The Notothenioid families Nototheniidae and Bathydraconidae appear to be paraphyletic.
Received: 26 March 1997 / Accepted: 7 May 1997 相似文献
18.
Megumi Ehara Yasuko Hayashi-Ishimaru Yuji Inagaki Takeshi Ohama 《Journal of molecular evolution》1997,45(2):119-124
Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new
phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However,
due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can
be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather
slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae,
on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla.
We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code
where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two,
Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In
addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap
value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest
that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination
of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms,
especially when it is considered with the results obtained through a molecular phylogenetic tree.
Received: 14 December 1996 / Accepted: 3 April 1997 相似文献
19.
Marie Claude Leclerc Véronique Barriel Guillaume Lecointre Bruno de Reviers 《Journal of molecular evolution》1998,46(1):115-120
Sequences from the two ribosomal DNA internal transcribed spacers (ITS1 and ITS2) were compared among five species of Fucus. Based on the present taxon sampling, parsimony analysis showed that Fucus serratus is the sister-group of the remaining Fucus species when Ascophyllum nodosum was used as an outgroup. The topology of the tree was (Fucus serratus (F. lutarius (F. vesiculosus (F. spiralis+F. ceranoides)))). The extremely low variation observed suggests a very recent radiation of the genus which supports the view widely accepted
that the Fucales are among the most evolutionarily advanced of the brown algae. We further note that sequence differences
between Fucus and Ascophyllum were 28%: this does not rule out the utility of ITS sequences within the Fucaceae. The very low number of informative positions
allows to demonstrate empirically that distance matrix methods group on the basis of symplesiomorphies.
Received: 17 February 1997 / Accepted: 17 April 1997 相似文献
20.
Sakai H Imamura C Osada Y Saito R Washio T Tomita M 《Journal of molecular evolution》2001,52(2):164-170
In this study, we analyzed the correlation between codon usage bias and Shine–Dalgarno (SD) sequence conservation, using
complete genome sequences of nine prokaryotes. For codon usage bias, we adopted the codon adaptation index (CAI), which is
based on the codon usage preference of genes encoding ribosomal proteins, elongation factors, heat shock proteins, outer membrane
proteins, and RNA polymerase subunit proteins. To compute SD sequence conservation, we used SD motif sequences predicted by
Tompa and systematically aligned them with 5′UTR sequences. We found that there exists a clear correlation between the CAI
values and SD sequence conservation in the genomes of Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii, and no relationship is found in M. genitalium, M. pneumoniae, and Synechocystis. That is, genes with higher CAI values tend to have more conserved SD sequences than do genes with lower CAI values in these
organisms. Some organisms, such as M. thermoautotrophicum, do not clearly show the correlation. The biological significance of these results is discussed in the context of the translation
initiation process and translation efficiency.
Received: 22 June 2000 / Accepted: 18 October 2000 相似文献