Bestimmung des Schleimgehaltes myxospermer Diasporen verschiedener Angiospermenfamilien

The mucilage content of structurally differing myxospermatic diaspores from 49 species belonging to 19 families ofAngiospermae has been determined by applying various extraction procedures. The results demonstrate no obvious relationship between the size, mucilage quantity, and the swelling factor of the diaspores studied. Furthermore, mucilage producing structures and structural peculiarities of the mucilages themselves are elaborated.

     

Significance levels for biological sequence comparison using non-linear similarity functions

A class of non-linear similarity functionss ₁ has been proposed for comparing subalignments of biological sequences. The distribution of maximals ₁-similarities is well approximated by the extreme value distribution. The significance levels ofs ₁ are studied for a variety of nucleotide frequency distributions as well as for several matrices of amino acid substitution costs. Also, the significance levels ofs ₁ are explored for comparing three biological sequences. Several previously described subalignments of bovine proenkephalin and porcine prodynorphin are shown to be highly significant.     

Gypsy homologous sequences inDrosophila subobscura (gypsyDS)

Summary Characterization of sequences homologous to theDrosophila melanogaster gypsy transposable element was carried out inDrosophila subobscura (gypsyDS). They were found to be widely distributed among natural populations of this species. From Southern blot and in situ analyses, these sequences appear to be mobile in this species.GypsyDS sequences are located in both euchromatic and heterochromatic regions. A completegypsyDS sequence was isolated from aD. subobscura genomic library, and a 1.3-kb fragment which aligns with the ORF2 of theD. melanogaster gypsy element was sequenced. Comparisons of this sequence in three species (D. subobscura, D. melanogaster, and D. virilis) indicate that there is greater similarity between theD. subobscura-D. virilis sequences than betweenD. subobscura andD. melanogaster. Molecular divergence ofgypsy sequences betweenD. virilis andD. subobscura is estimated at 16 MY, whereas the most likely divergence time of these two species is more than 60 MY. These data strongly suggest thatgypsy sequences have been horizontally transferred between these species.Offprint requests to: T.M. Alberola     

Nucleotide sequence analysis of a variable region of the large subunit rRNA for identification of marine-occurring yeasts

A 230-nucleotide region of the large subunit (LSU) ribosomal RNA was examined to determine whether signature nucleotide sequences could be used for species identifications of basidiomycetous yeasts. Multiple strains of genetically defined heterothallic species ofRhodosporidium, Leucosporidium, Cystofilobasidium, andSporidiobolus demonstrated that nucleotide sequences within these species are homologous and that differences between species range from 1 to 20 or more bases. Also included in this study were several homothallic species of these teleomorphic genera and some anamorphs assigned toRhodotorula andCandida. Those results indicated close relationships among certain homothallic species, particularly in the genusMrakia, and potential relationships of homothallic and anamorphic strains to several teleomorphs. The data suggest that LSU sequences can be used for yeast identifications with the possible exception of closely related homothallic species.     

Phylogenetic relationship withinFusarium sambucinum Fuckel sensu lato,determined from ribosomal RNA sequences

Partial ribosomal RNA nucleotide sequences were determined for 11 strains ofFusarium sambucinum Fuckelsensu lato to assess by molecular genetic means, Nirenberg's recent morphotaxonomic interpretation which split the species into three distinct taxa:F. sambucinum sensu stricto, F. torulosum, and one other species, as yet unnamed (Fusarium species nova). Four sequence patterns were identified among the 11 strains. Two sequences that varied at one site were found among strains ofF. sambucinum, strains ofF. torulosum andFusarium sp. nov. showed no intraspecific variation. Interspecific comparisons revealed nucleotide sequence differences of 3–9 substitutions in the ca. 240 nucleotide rRNA segment examined. Although interspecific differences are not large in terms of percent nucleotide substitution, they are much larger than the observed intraspecific variation and support the morphological interpretation distinguishing three taxa. When the data were analysed using parsimony and bootstrapping, the three taxon tree was well supported. The phylogenetic arrangement of these strains is congruent with secondary metabolite profile similarities.     

Cloning and characterization of thewhite andtopaz eye color genes from the sheep blowflylucilia cuprina

Summary Clones carrying thewhite andtopaz eye color genes have been isolated from genomic DNA libraries of the blowflyLucilia cuprina using cloned DNA from the homologouswhite andscarlet genes. respectively, ofDrosophila melanogaster as probes. On the basis of hybridization studies using adjacent restriction fragments, homologous fragments were found to be colinear between the genes from the two species. The nucleotide sequence of a short region of thewhite gene ofL. cuprina has been determined, and the homology to the corresponding region ofD. melanogaster is 72%; at the derived amino acid level the homology is greater (84%) due to a marked difference in codon usage between the species. A major difference in genome organization between the two species is that whereas the DNA encompassing theD. melanogaster genes is free of repeated sequences. that encompassing theirL. cuprina counterparts contains substantial amounts of repeated sequences. This suggests that the genome ofL. cuprina is organized on the short period interspersion pattern. Repeated sequence DNA elements, which appear generally to be short (less than 1 kb) and which vary in repetitive frequency in the genome from greater than 10⁴ copies to less than 10² copies, are found in at least two different locations in the clones carrying these genes. One type of repeat structure, found by sequencing, consists of tandemly repeating short sequences. Restriction site and restriction fragment length polymorphisms involving both thewhite andtopaz gene regions are found within and between populations ofL. cuprina.     

Variation within and among the chloroplast genomes ofMelaleuca alternifolia andM. linariifolia (Myrtaceae)

Melaleuca alternifolia andM. linariifolia are commercially important Australian species harvested for their essential oils. Both species have relatively narrow and disjunct distributions on the central coast of eastern Australia. Variation in the chloroplast genome was assessed for eight individuals from each of twelve populations, representing the species' geographic range. Low nucleotide diversity withinM. alternifolia contrasted with high nucleotide diversity inM. linariifolia. CpDNA data are consistent with the southern population ofM. alternifolia being a hybrid population withM. linariifolia. The two species are sympatric in this region. Variation inM. linariifolia was geographically structured, with northern populations differing from southern populations by seven restriction site mutations, five length mutations and an inversion. There was no evidence of hybridisation of the cp genome of northernM. linariifolia with the partially sympatric speciesM. trichostachya. Intra- and interspecific variation in the chloroplast genomes ofM. alternifolia, M. linariifolia, andM. trichostachya indicate considerable potential for the use of intraspecific cpDNA studies in examining phylogenetic relationships in melaleucas.     

Sedum surculosum andS. jaccardianum (Crassulaceae) share a unique 70 bp deletion in the chloroplast DNA trnL (UAA)-trnF (GAA) intergenic spacer

TrnL (UAA)-trnF (GAA) chloroplast DNA spacer sequences of three species ofMonanthes, Sedum surculosum (=Monanthes atlanticum) andS. jaccardianum were compared.S. surculosum, the systematic position of which has been disputed ever since its discovery, shares a phylogenetically highly significant 70 bp deletion withS. jaccardianum. In addition to this large deletion the two Moroccan species ofS. ser.Monanthoidea differ in three more indels as well as in four nucleotide substitutions from the species ofMonanthes. These data render strong support for the monophyly ofS. ser.Monanthoidea andMonanthes. Spacer length in seven species and one subspecies ofMonanthes is relatively uniform.     

Gene segments encoding membrane domains of the human immunoglobulin gamma 3 and alpha chains

The carboxyterminal region of the heavy chains, according to its hydrophilic or hydrophobic properties, determines whether the immunoglobulin will be secreted or membrane-bound. We have determined the nucleotide sequences of the human IGHG3, IGHA1, and IGHA2 membrane exons isolated from genomic DNA libraries. The IGHG3 M1 and M2 exons are separated by a long intron of 2.1 kilobases (kb) containing an highly repeated motif of 34 base pairs (bp). The IGHA1 and IGHA2 genes, like the mouse Igh-A gene, have a single exon encoding the extracellular, transmembrane, and cytoplasmic regions. For each class of immunoglobulins, the sequences of membrane exons are highly conserved between human and mouse, but no alignment is possible for the flanking regions. In contrast, for a same species, the sequences of the heavy chain membrane exons differ from one class to another. While the hydrophobic profile of the membrane core is well conserved, the cytoplasmic region differs in length and in composition. None of the intracellular domains presents the sequence implied in signal transduction, implying that membrane immunoglobulins need other proteins, which probably interact with the constant or membrane domain, to transmit signals leading to B-cell activation.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers M35288-91. Address correspondence and offprint requests to: M.-P. Lefranc.     

Taxonomic reappraisal on<Emphasis Type="Italic">Suaeda australis</Emphasis> (Chenopodiaceae) in korea based on the morphological and molecular characteristics

We used morphological and molecular characteristics to perform a taxonomic reappraisal ofSuaeda australis (Brown) Moquin-Tandon from Korea. Populations of this species are dispersed at the bottoms of sand zones, and usually exhibit a depressed habit. Except for their total heights and leaf lengths, the morphology of these plants does not differ from that ofS. maritima. Molecular traits were examined based on ITS and psbB-psbH spacer region sequences. The former region included ITS-1, 5.8S, and ITS-2, which were 629 nucleotide bases long. Pair-wise distances (p-distance) among KoreanSuaeda species ranged from 1.12 to 17.84. The psbB-psbH spacer region sequences were 618 nucleotide bases long, and were conserved in the alignment of KoreanSuaeda species. In our ML and MrBayesian analysis of ITS sequences aligned with other sequences from GenBank, the plants of KoreanSuaeda made three clades: 1)S. japonica;S. australis, andS. maritima;2)S. malacosperma; and 3) S.glauca. However, the psbB-psbH region sequences could not be resolved amongS. japonica, S. maritima, andS. australis from Korea. Molecular and vegetative characteristics indicated that the plants now classified asS. australis from Korea should instead be named as S.maritima (L.) Dumont.     

Reconstruction of ancestral sequences by the inferential method,a tool for protein engineering studies

This paper describes the inferential method, an approach for reconstructing protein and nucleotide sequences of ancestral species, starting from known, homologous, contemporary sequences. The method requires knowledge of the topology of the phylogenetic tree, whose nodes are the species to whom the reconstructed sequences belong.The method has been tested by computer simulation of speciation and nucleotide substitutions, starting from a single ancestral sequence, and by subsequent reconstruction of nodal sequences. Results have shown that reconstructions obtained by the inferential method are affected by limited error frequencies, which (1) are proportional to the squares of nucleotide substitution rates and of internodal distances, and (2) are little influenced by non-uniformity of transformation rates of nucleotides.Furthermore, good agreement of the results has been obtained by comparing protein-sequence reconstructions carried out with the inferential method with those obtained using the maximum parsimony method in two different cases: e.g., a reconstruction of simulated sequences and a reconstruction of mammalian ribonuclease sequences.Abbreviations used MP maximum parsimony method - ML maximum likelihood method - IM inferential method - MY millions of years - N-tree natural-like phylogenetic tree - E-tree equibranched phylogenetic tree - EA percentage number of erroneous amino acids in a reconstructed sequence - EC percentage number of erroneous codons in a reconstructed sequence - t _n time interval between a P- and its - F-sequence nucleotides and amino acids are indicated by their I.U.B. codes (N.C.-I.U.B., 1985) Correspondence to: A. Di Donato     

Nonhomologous Recombination Between the Large Unassigned Region of the Male and Female Mitochondrial Genomes in the Mussel, Mytilus trossulus

Doubly uniparental inheritance of mtDNA (DUI) is commonly observed in several genera of bivalves. Under DUI, female offspring inherit mtDNA from their mothers, while male offspring inherit mtDNA from both parents but preferentially transmit the paternally inherited mtDNA to their sons. Several studies have shown that the female- and male-specific mtDNA lineages in blue mussels, Mytilus spp., vary by upward of 20% at the nucleotide level. In addition to high levels of nucleotide substitution, the present study observed substantial gender-based length polymorphism in the presumptive mitochondrial control region (=large unassigned region; LUR) of North American M. trossulus. In this species, female lineage LUR haplotypes are over 2 kb larger than male lineage LUR haplotypes. Analysis of sequence data for these length variants indicates that the F LUR haplotypes of North American M. trossulus contain sequences similar to the F lineage control region in the congeners M. edulis and M. galloprovincialis. Relative to the F LUR in the latter two species, however, the F lineage LUR haplotypes in M. trossulus contain two large sequence insertions, each nearly 1 kb in size. One of these insertions has high sequence similarity to the male lineage LUR of M. trossulus. The tandem arrangement of F and M control region sequences in the F lineage LUR of M. trossulus is most likely the result of nonhomologous recombination between the male and the female mitochondrial genomes in M. trossulus, a finding that has important implications regarding the transmission and evolution of blue mussel mitochondrial genomes. [Reviewing Editor: Dr. Martin Kreitman]     

Linguistic Measure of Taxonomic and Functional Relatedness of Nucleotide Sequences

Abstract

The frequencies of “words”, oligonucleotides within nucleotide sequences, reflect the genetic information contained in the sequence “texts”. Nucleotide sequences are characteristically represented by their contrast word vocabularies. Comparison of the sequences by correlating their contrast vocabularies is shown to reflect well the relatedness (unrelatedness) between the sequences. A single value, the linguistic similarity between the sequences, is suggested asa measure of sequence relatedness. Sequences as short as 1000 bases can be characterized and quantitatively related to other sequences by this technique. The linguistic sequence similarity value is used for analysis of taxonomically and functionally diverse nucleotide sequences. The similarity value is shown to be very sensitive to the relatedness of the source species, thus providing a convenient tool for taxonomic classification of species by their sequence vocabularies. Functionally diverse sequences appear distinct by their linguistic similarity values. This can be a basis for a quick screening technique for functional characterization of the sequences and for mapping functionally distinct regions in long sequences.     

Evolution of the noncoding regions inDrosophila mitochondrial DNA: Two intergenic regions

The sequences of the mitochondrial DNA (mtDNA) segment containing the two intergenic regions were determined for six species belonging to theDrosophila immigrans species group and compared to the corresponding segments ofDrosophila species which had been studied previously. We found remarkable differences in the evolutionary rates of the two intergenic regions. The Intergenic I region, which lies between thetRNA ^gln and thetRNA ^ile genes, was found to be highly conserved in terms of both size (30 ntp) and nucleotide sequence among the species studied. In contrast, the sequences of the Intergenic II region, which lies between thetRNA ^f-met and thetRNA ^ile genes, showed considerable variation. The size of the Intergenic II region ranged from 0 to 88 ntp, and accurate alignment was possible only among sequences from geographical strains or very closely related species in thenasuta species subgroup. The observed differences in conservation of the two mtDNA intergenic regions are discussed in light of functional constraints on mtDNA sequences.     

Molecular phylogenetic analysis ofChrysosplenium (Saxifragaceae) in Japan

The phylogeny of Japanese species ofChrysosplenium (Saxifragaceae) was examined using variation in DNA sequences. Sequences ofrbcL andmatK genes were compared for their feasibility for reconstructing the phylogeny ofChrysosplenium, and thematK sequences was found to give greater resolution. All but one of the 17 Japanese species have been examined formatK gene sequences and phylogenetic analysis of these data resulted in eight most parsimonious trees of 390 steps and a consistency index (Cl) of 0.823. The molecular phylogeny obtained was generally in agreement with Hara's (1957) classification based upon phenotypic similarity, although a conclusion needs extensive examination of the genus on a world-wide level. Using the phylogenetic data, character evolution was examined, especially in the characters traditionally used for grouping infrageneric taxa. Differentiation of opposite and alternate phyllotaxis appears to have occurred only once in the course of evolution ofChrysosplenium.     

Lengths and nucleotide sequences of the internal spacers of nuclear ribosomal DNA in gymnosperms and pteridophytes

The nucleotide sequences of the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal DNA were analyzed in species belonging to gymnosperms and pteridophytes. The lengths of the ITSs of sixteen species of gymnosperms and seven species of pteridophytes were estimated. The gymnosperms have ITS1 regions larger than those observed in the pteridophytes and angiosperms (ca. 610–3100 bp versus 159–360 bp). On the other hand, the ITS2 regions appear to be of a conserved length (182–370 bp). We have determined the complete nucleotide sequences of ITS regions from four gymnosperm species and five pteridophyte species by cloning the PCR products. Sequence analysis showed the presence of three short tandem arranged subrepeats of about 70 bp in the 1112 bp ITS1 ofEphedra fragilis. Pyrimidine rich (about 90%) DNA segments of 40–50 bp were observed in the ITS1 ofGinkgo biloba. A highly conserved 16 bp long sequence known to be present in the ITS1 of the angiosperm species has been also found in the ITS1 ofCycas revoluta, Taxus baccata andEphedra fragilis. Dedicated to Prof.Emilio Battaglia.     

An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes

The 655 bp cytochrome c oxidase subunit I barcode region of single specimens of 388 species of fishes (four Holocephali, 61 Elasmobranchii and 323 Actinopterygii) was examined. All but two (Urolophus cruciatus and Urolophus sufflavus) showed different cox1 nucleotide sequences (99.5% species discrimination); the two that could not be resolved are suspected to hybridize. Most of the power of cox1 nucleotide sequence analysis for species identification comes from the degenerate nature of the genetic code and the highly variable nature of the third codon position of amino acids. Variation at the third codon position is bimodally distributed, and the more variable mode is dominated by amino acids with four or six codons, while the less variable mode is dominated by amino acids with two codons. The ratio of nonsynonymous to synomymous changes is much less than one, indicating that this gene is subject to strong purifying selection. Consequently, cox1 amino acid sequence diversity is much less than nucleotide sequence diversity and has very poor species resolution power. Fourteen of the 16 amino acid residues recognized as having important functions in the region of cox1 sequenced were completely conserved over all 388 species (and the bovine cox1 sequence), with one fish species varying at one of these sites, and three fish at another site. No significant differences in amino acid conservation were observed between residues in helices, strands and turns. Patterns of nucleotide and amino acid variability were very similar between elasmobranchs and actinopterygians.     

Molecular diagnosis of ochratoxinogenicAspergillus species

Toxigenic and non-toxigenic black aspergilli belonging to theAspergillus niger aggregate and toA. carbonarius were compared to each other and to strains of other species by DNA fingerprinting. AFLPs showed a clear separation ofA. niger andA. carbonarius. However, no clear correlation between the genetic similarity of the strains and the ability to produce ochratoxin A (OTA) was detected. Based on AFLP, marker sequences were chosen for the construction of SCAR-PCR primers for the detection ofA. carbonarius. A similar approach was used forA. ochraceus, another fungus of concern regarding ochratoxin A contamination of coffee. Cluster analysis ofA. ochraceus isolates mainly from Brazilian coffee showed a very close genetic similarity. Three species specific primer pairs were developed and one of these was used for the PCR and realtime PCR (RT-PCR) based detection of the mould in green coffee.A. ochraceus was specifically and rapidly detected and quantified in green coffee. A positive correlation between the amount of DNA and OTA content was established.     

Highly repeated DNA sequences and systematics of malagasy primates

We have analyzed highly repeated DNA sequences of Malagasy lemurs with restriction enzymes, Southern blotting and nucleotide sequencing to assess relatedness among repeated DNA fragments from different species. We have focused our studies on two prosimian families:Lemuridae andCheirogaleidae. Our results have allowed us to draw the following conclusions: confirmation of the separation based on molecular biology data ofEulemur species from theLemur catta/Hapalemur group; classification ofVarecia in a genus clearly separated from the otherLemuridae genera; confirmation of the specific status ofHapalemur aureus; confirmation of cytogenetic data in favour of the subdivision of the familyCheirogaleidae into two subfamilies:Cheirogaleinae andPhanerinae. Finally a cladogram has been constructed by numbering all the highly repeated DNA fragments (obtained by Southern blotting) and analyzing the inferred systematic relationships between the Lemuridae and Cheirogaleidae species.     

Evolution ofMHC polymorphism: Extensive sharing of polymorphic sequence motifs between human and bovine DRB alleles

The evolution ofMHC polymorphism has been studied by comparing the amino acid and nucleotide sequences of 14 bovine and 32 humanDRB alleles. The comparison revealed an extensive sharing of polymorphic sequence motifs in the two species. Almost identical sets of residues were found at several highly polymorphic amino acid positions in the putative antigen recognition site. Consequently, certain bovine alleles were found to be more similar to certain human alleles than to other bovine alleles. In contrast, the frequencies of silent nucleotide substitutions were found to be much higher in comparisons between species than within species implying that none of the human or bovine DRB alleles originated before the divergence of these distantly related species. The results suggest that the observed similarity inDRB polymorphism is due to convergent evolution and possibly the sharing of short ancestral sequence motifs. However, the relative role of the latter mechanism is difficult to assess due to the biased base composition in the first domain exon of polymorphic class 11 genes. The frequency of silent substitutions betweenDRB alleles was markedly lower in cattle than in man suggesting that theDRB diversity has evolved more rapidly in the former species.