Sequence analysis of Vicia faba highly repeated DNA: the BamHI repeated sequence families

Cleavage of Vicia faba nuclear DNA with the restriction endonuclease BamHI yielded discrete size classes of 250, 850, 900, 990, 1 150, 1 500 and 1 750 bp of highly repetitive DNA. Each of these sequence families comprised about 3% of the total genomic DNA. Some sequence members from each sequence family were cloned in pBR322 and their primary structures determined. Computer analyses of nucleotide sequences suggested the existence of about 60 bp sequence periodicity within the repeating unit of the 990 bp sequence family, though the extent of homology among the surmised shorter subrepeat units was very low. With other BamHI sequence families, however, the data did not show any clear internal sequence periodicity. The repeat units of the 850 bp and 1 750 bp sequence families contained nucleotide sequences homologous to the 250 bp family sequence. No sequence relationship between or among other sequence families was observed. There was 13–25% sequence variation among 6 cloned members of the 250 bp family and probably also among those of other BamHI repeat families. DNA sequences homologous to these V. faba BamHI repeat families were detected in Pisum sativum DNA by Southern blot hybridization. Furthermore, very weak cross-hybridization was observed with plant DNAs from Phaseolus vulgaris, Triticum aestivum, Cucumis sativus and Trillium kamtschaticum.     

DPB1 * BR: an Mhc class II DPB1 allele (DPB1 * 6601) of negroid origin

The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number X96986. The nameDPB1 ^* 6601 was officially assigned by the WHO Nomenclature Committee in May 1996. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1995), names will be assigned to new sequences as they are identified. Lists of such sequences will be published in the following WHO Nomenclature Report     

基于5.8S rDNA-ITS序列的我国浙江沿海铜藻群体遗传多样性分析

为了调查我国浙江沿海铜藻(Sargassum horneri)群体遗传多样性,对浙江省南麂岛火焜岙、洞头岛、枸杞岛的野生群体和南麂岛马祖岙养殖群体的铜藻44个样品的5.8S rDNA-ITS序列进行了PCR扩增和序列分析,获得DNA片段长度为1485 bp,包括部分ITS1、完整的5.8S rDNA和部分ITS2序列。序列分析表明仅有1个变异位点,说明群体间没有明显的遗传分化,遗传多样性较低。另外,将包含这一变异位点的基因型与GenBank公共数据库中另外2株铜藻的5.8S rDNA-ITS区序列进行比对,共有31个变异位点,其中插入/缺失位点10个。因此,建议加快人工铜藻场的建设以及野生铜藻场的恢复,保持铜藻场的生态平衡。     

Sequence variation in the cytochrome oxidase I, internal transcribed spacer 1, and Ts14 diagnostic antigen sequences of Taenia solium isolates from South and Central America, India, and Asia

We examined the genetic variability in the pig–human tapeworm, Taenia solium, by sequencing the genes for cytochrome oxidase I, internal transcribed spacer 1, and a diagnostic antigen, Ts14, from individual cysts isolated from Peru, Colombia, Mexico, India, China, and the Philippines. For these genes, the rate of nucleotide variation was minimal. Isolates from these countries can be distinguished based on one to eight nucleotide differences in the 396 nucleotide cytochrome oxidase I (COI) sequence. However, all of the 15 isolates from within Peru had identical COI sequences. The Ts14 sequences from India and China were identical and differed from the Peru sequence by three nucleotides in 333. These data indicate that there is minimal genetic variability within the species T. solium. Minimal variability was also seen in the ITS1 sequence, but this variation was observed within the individual. Twenty-two cloned sequences from six isolates sorted into 13 unique sequences. The variability observed within the sequences from individual cysts was as great as the variability between the isolates.     

The sheep CD1 gene family contains at least four CD1B homologues

We identified four cDNA sequences encoding sheep homologues of the CD1 molecule. The sheep sequences were selected from λgt11 thymocyte cDNA libraries by hybridization with a humanCD1C probe and a homologous sheep probe. TheSCD1B-42 andSCD1A25 sequences encode complete CD1 molecules. The third sequence,SCD1B-52, which is closely related toSCD1B-42 and may be an allele, has the sequence encoding the α3 region precisely deleted. The fourth sequence,SCD1T10, is truncated at the 5′ end. All four sequences are related to the humanCD1B and domestic rabbitCD1B-like sequences at both nucleotide and amino acid level. Comparison of the derivedCD1 amino acid sequences with the sequence of major histocompatibility complex class I molecules showed that the sheep CD1 molecules, like human CD1 molecules, lack most of the conserved class I residues known to be involved in interaction with 132-microglobulin and the CD8 molecule. They do not contain the peptide docking residues involved in anchoring peptides in the peptide binding groove of class I molecules. Southern hybridization of sheep DNA with a sheepCD1 exon 4/ga3 probe showed that the sheep genome encodes at least sevenCD1 genes. The implications of these analyses for CD1 function are discussed. The nucleotide sequence data reported in this paper have been submitted to the EMBL/GenBank nucleotide sequence databases and have been assigned the accession numbers Z36890 (SCD1A25), Z36891 (SCD1B-42), Z36892 (SCD1B-52), and X90567 (SCDIT10)     

Substitution Model of Sequence Evolution for the Human Immunodeficiency Virus Type 1 Subtype B gp120 Gene over the C2-V5 Region

Phylogenetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution rates, nucleotide frequencies, and site-to-site rate heterogeneity. These models can influence hypothesis testing and can affect the accuracy of phylogenetic inferences. Maximum likelihood methods of simultaneously constructing phylogenetic tree topologies and estimating model parameters are computationally intensive, and are not feasible for sample sizes of 25 or greater using personal computers. Techniques that initially construct a tree topology and then use this non-maximized topology to estimate ML substitution rates, however, can quickly arrive at a model of sequence evolution. The accuracy of this two-step estimation technique was tested using simulated data sets with known model parameters. The results showed that for a star-like topology, as is often seen in human immunodeficiency virus type 1 (HIV-1) subtype B sequences, a random starting topology could produce nucleotide substitution rates that were not statistically different than the true rates. Samples were isolated from 100 HIV-1 subtype B infected individuals from the United States and a 620 nt region of the env gene was sequenced for each sample. The sequence data were used to obtain a substitution model of sequence evolution specific for HIV-1 subtype B env by estimating nucleotide substitution rates and the site-to-site heterogeneity in 100 individuals from the United States. The method of estimating the model should provide users of large data sets with a way to quickly compute a model of sequence evolution, while the nucleotide substitution model we identified should prove useful in the phylogenetic analysis of HIV-1 subtype B env sequences. Received: 4 October 2000 / Accepted: 1 March 2001     

Analysis of nucleotide sequence polymorphism of internal transcribed spacers of ribosomal genes in diploid <Emphasis Type="Italic">Aegilops</Emphasis> (L.) species

The nucleotide sequence of the fragment of the internal transcribed spacer (ITS) of rDNA comprising the full-length ITS1, the gene encoding 5.8S rRNA, and part of the ITS2 sequence was determined in 22 samples of five diploid Aegilops species. The full alignment length of compared sequences was 524 bp. Species-specific substitutions were found in the ITS nucleotide sequence of rDNA of different Aegilops species. Intraspecific differences in ITS structure in diploid Aegilops species were detected for the first time. Polymorphism of the ITS nucleotide sequence within the same sample was revealed, which might be due either to differences between the genomes of individual plants comprising the sample or to the presence of several types of ribosomal genes in the genome of one plant. In general, both interspecific and intraspecific variability of the ITS nucleotide sequences of rDNA is extremely low. In total, 26 variable sites, twelve of which were informative, were identified.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 2, 2005, pp. 193–197.Original Russian Text Copyright © 2005 by Goryunova, Chikida, Gori, Kochieva.     

Sequence and diversity of variable gene segments coding for rabbit T-cell receptor beta chains

The nucleotide sequences of 11 variable gene segments coding for rabbit T-cell receptor beta (Tcrb-V) chains were determined by directly sequencing fragments amplified by the cassette-ligation mediated polymerase chain reaction (CLM-PCR) and by modified anchor PCR without the cloning procedure. The nucleotide sequences in two of these 11 rabbit Tcrb-V gene segments coincided with those in two of the four rabbit Tcrb-V gene segments previously reported; the others have not been described. The percentage similarity of each nucleotide sequence of the 11 rabbit Tcrb-V gene segments was analyzed and the segments were divided into nine families, which were homologous to nine human families (Vb 2, 3, 4, 5, 7, 8, 10, 18, and 22), respectively.The nucleotide sequence data reported in this paper have been submitted to the DDBJ, EMBL, and GenBank nucleotide sequence databases and have been assigned the accession numbers D17416-D17426.     

Analysis of the sequence variations in the Mhc DRB1-like gene of the endangered Humboldt penguin (Spheniscus humboldti)

The Major Histocompatibility Complex (Mhc) genomic region of many vertebrates is known to contain at least one highly polymorphic class II gene that is homologous in sequence to one or other of the human Mhc DRB1 class II genes. The diversity of the avian Mhc class II gene sequences have been extensively studied in chickens, quails, and some songbirds, but have been largely ignored in the oceanic birds, including the flightless penguins. We have previously reported that several penguin species have a high degree of polymorphism on exon 2 of the Mhc class II DRB1-like gene. In this study, we present for the first time the complete nucleotide sequences of exon 2, intron 2, and exon 3 of the DRB1-like gene of 20 Humboldt penguins, a species that is presently vulnerable to the dangers of extinction. The Humboldt DRB1-like nucleotide and amino acid sequences reveal at least eight unique alleles. Phylogenetic analysis of all the available avian DRB-like sequences showed that, of five penguin species and nine other bird species, the sequences of the Humboldt penguins grouped most closely to the Little penguin and the mallard, respectively. The present analysis confirms that the sequence variations of the Mhc class II gene, DRB1, are useful for discriminating among individuals within the same penguin population as well those within different penguin population groups and species.The nucleotide sequence and amino acid sequence data reported in this paper have been submitted to the DDBJ database and have been assigned the accession numbers AB088371–AB088374, AB089199, AB154393–AB154399, and AB162144.     

Analysis in Neisseria meningitidis and other Neisseria species of genes homologous to the FKBP immunophilin family

The immunophilin family of FK506-binding proteins (FKBPs), involved in eukaryotic protein folding and cell regulation, have recently been found to have prokaryotic homologues. Genes with sequences homologous to those encoding human FKBPs were examined in Neisseria species. An FKBP DNA sequence was present, as shown by the polymerase chain reaction and Southern blotting experiments, in the chromosome of Neisseria meningitidis (14 strains) and in all 11 different commensal Neisseria spp. studied, but was not found in Neisseria gonorrhoeae (11 strains tested) or in Moraxella catarrhalis. The nucleotide and predicted protein sequences of the FKBP-encoding domain from five of the meningococcal strains were highly conserved (e.g. ≥97% homologous). The meningococcal nucleotide sequence was ≥93% homologous and the consensus meningococcal protein sequence was ≥97% homologous to FKBP sequences found in seven different commensal Neisseria spp. The meningococcal nucleotide and predicted protein sequences were ≥59% homologous to the conserved C-terminus of the human FKBP gene family. The FKBP nucleotide sequence was present as a single copy in the chromosome of commensal Neisseria spp. and in most strains of N. meningitidis. The FKBP gene was linked to the silent pilin locus, pilS, in class II-piliated meningococcal strains. In meningococcal strains expressing class I pili, the FKBP gene was linked to one of several pilS loci but not the pilE locus present in these strains. FKBP genes found in commensal Neisseria spp. were not linked to known pilin loci.     

Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon

Polymorphism of the nucleotide sequences encoding 149 amino acids of linked major histocompatibility complex (Mhc) class II 131 and 132 peptides, and of the intervening intron (548–773 base pairs), was examined within and among seven Pacific salmon (Oncorhynchus) species. Levels of nucleotide diversity were higher for theB1 sequence than forB2 or the intron in comparisons both within and between species. For the codons of the peptide binding region of the BI sequence, the level of nonsynonymous nucleotide substitution (d_N) exceeded the level of synonymous substitution (d_S) by a factor of ten for within-species comparisons, and by a factor of four for between-species comparisons. The excess of d_N indicates that balancing selection maintains diversity at this salmonidMhc class II locus, as is common forMhc loci in other vertebrates. Levels of nucleotide diversity for both the exon and intron sequences were greater among than within species, and there were numerous species-specific nucleotides present in both the coding and noncoding regions. Thus, neighbor-joining analysis of both the intron and exon regions provided phylogenies in which the sequences clustered strongly by species. There was little evidence of shared ancestral (trans-species) polymorphism in the exon phylogeny, and the intron phylogeny depicted standard relationships among the Pacific salmon species. The lack of shared allelicB1 lineages in these closely related species may result from severe bottlenecks that occurred during speciation or during the ice ages that glaciated the rim of the north Pacific Ocean approximately every 100 000 years in the Pleistocene.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers U34692-U34720     

Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison

Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genusDiplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA inD. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred inD. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA. Published: March 4, 2003     

A method for estimating rates of nucleotide substitution using DNA sequence data

An estimate of the average number of evolutionarily acceptable substitutions per nucleotide since the most recent common ancestor of a pair of homologous sequences is found which uses nucleotide sequence data. The estimate is derived assuming a Poisson-like model for the evolutionary process. A method is also suggested for analyzing nucleotide sequence data in M homologous sequences (M 3). A simulation study is reported showing that the estimates are satisfactory providing there is sufficient homology between the sequences. To demonstrate the methods a numerical example using some β-globin data is presented.     

Gene Transfer of a Part of a β-Lactamase Gene?

β-Lactamase is an enzyme which catalyzes the hydrolysis of the β-lactam ring of penicillins and cephalosporins. By similarity analysis of amino acid sequences in a database, the amino acid sequence deduced from the nucleotide sequence of the upstream region of cytochrome c oxidase subunit II from Paracoccus denitrificans was found to have an unusually high score of homology to that of a portion of β-lactamases from Gram-negative bacteria. Furthermore, the nucleotide sequences corresponding only to this region had a very high score of similarity among them. The phylogenetic tree constructed on the basis of the amino acid sequences was in accord with that constituted on the 5S rRNA's. Moreover, the molar G + C contents and the codon usage were similar to those in their respective bacteria. It is suggested, therefore, that the nucleotide sequence in P. denitrificans was positioned by a transfer of a part of a β-lactamase gene formed as a result of gene duplication or it was formed by a deletion of the essential region of the β-lactamase gene, although no β-lactamase gene has been yet detected in P. denitrificans.     

Evolutionary Process of the Genomic Sequence Around the 100 Map Unit of Chromosome 1 in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Comparative analysis of nucleotide sequences of the genomic region located around 100 map unit of chromosome 1 using two accessions, Columbia (Col) and Landsberg erecta (Ler), of Arabidopsis thaliana was performed. High divergence was detected between them, and the length of the Ler sequence was half of corresponding sequence of Col. This divergence occurred by tandem duplication, deletion of large regions, and insertion of unrelated sequences. These events led to the high polymorphism of plant disease resistant genes, which are located in the analyzed region. It is highly probable that two-round duplication occurred, and the insertion sequences are transposable elements. The data suggest that the analyzed region had been evolving until quite recently.     

Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny

The nucleotide sequences of the gorilla and orangutan myc loci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence.The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining.Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan. Correspondence to: F. Galibert     

Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences

Summary The potential of variation in repeated nucleotide sequences as a tool for phylogenetic studies was examined by investigating the phylogeny of 13 diploid species of the genus Triticum L. sensu Bowden. Low intraspecific variation in repeated nucleotide sequence families in Triticum indicated that restriction fragment profiles of repeated nucleotide sequences in Southern blots are reliable and uniform characteristics of each species. Cloned repeated nucleotide sequences were hybridized with Southern blots of DNAs of the Triticum species and the outgroup, Lophopyrum elongatum (Host) Á. Löve. The presence or absence of bands in the Southern blot autoradiograms was considered to be a character for phylogenetic analysis. A most parsimonious tree was resolved with the PAUP version 3.0L computer package. The tree was consistent with cytotaxonomic and evolutionary data available on the species.     

Absence of short period interspersion of repetitive and non-repetitive sequences in the DNA of Drosophila melanogaster

A sensitive search has been made in Drosophila melanogaster DNA for short repetitive sequences interspersed with single copy sequences. Five kinds of measurements all yield the conclusion that there are few short repetitive sequences in this genome: 1) Comparison of the kinetics of reassociation of short (360 nucleotide) and long (1,830 nucleotide) fragments of DNA; 2) reassociation kinetics of long fragments (2,200 nucleotide) with an excess of short (390 short nucleotide) fragments; 3) measurement of the size of S1 nuclease resistant reassociated repeated sequences; 4) measurement of the hyperchromicity of reassociated repetitive fragments as a function of length; 5) direct assay by kinetics of reassociation of the amount of single copy sequence present on 1,200 nucleotide long fragments which also contain repetitive sequences.     

Polymorphism of the IGHA gene in sheep

Genetic variation in immunoglobulin A, the most abundant immunoglobulin in mammalian cells, has not been reported in ruminants. In this study, variation in the immunoglobulin heavy alpha chain constant gene (IGHA) of sheep was investigated by amplification of a fragment that included the hinge coding sequence, followed by single-strand conformational polymorphism (SSCP) analysis and DNA sequencing. Three novel sequences, each characterized by unique SSCP banding patterns, were identified. One or two sequences were detected in individual sheep and all the sequences identified shared high homology to the published ovine and bovine IGHA sequences, suggesting that these sequences represent allelic variants of the IGHA gene in sheep. Sequence alignment showed that these sequences differed mainly in the 3′ end of exon 1 and in the coding sequence of the hinge region. There was either a deletion or an insertion of two codons in the hinge coding region in these allelic variants. Codon usage in the hinge coding region was quite different from that in the non-hinge coding regions of the gene, suggesting different evolution of the IGHA hinge sequence. Three novel amino acid sequences of ovine IGHA were also predicted, and variation in these sequences might not only affect antigen recognition but also susceptibility to cleavage by bacterial or parasitic proteases. Nucleotide sequence data reported in this paper have been submitted to the NCBI GenBank nucleotide sequence database and have been assigned the accession nos. AY956424–AY956426.