Intragenomic Variation Research Articles

The role of recombination and mutation in 16S-23S rDNA spacer rearrangements.

The intragenomic heterogeneity of the bacterial intergenic (16S-23S rDNA) spacer region (ISR) was analysed from the following species in which sequences for the complete rRNA operon (rrn) set have been determined (rrn number): Enterococcus faecalis (6) and E. faecium (6), Bacillus subtilis (10), Staphylococcus aureus (9), Vibrio cholerae (4), Haemophilus influenzae (6) and Escherichia coli (7). It was found that some spacer sequence blocks were highly conserved between operons of a genome, whereas the presence of others was variable. When these variations were analysed using the program PLATO and partial likelihood phylogenies determined by DNAml for each operon set, three regions showed significant (Z>3.3) spatial variation [Region I was 78-184 nt long (2.1<Z<49.4), Region II was 10-60 nt long (3.7<Z<23)] and Region III was 6 nt long (3.4<Z>4.4) possibly due to recombination or selection. Within Region I, there was sequence block variation in all operon sets [some operons contained tRNA genes (tRNAala, tRNAile or tRNAglu), whereas others had sequence blocks such as VS2 (S. aureus) or rsl (E. coli)]. Q Analysis of the ISR sequence from E. faecalis and E. faecium showed that there was more interspecies than intraspecies variation (both in DNA sequence and in the presence or absence of blocks). Dot matrix analysis of the sequence blocks in the nine rrn ISRs from S. aureus showed that there was significant homology between VS2 and VS5/VS6. Furthermore, repeat motifs with only A or T were present in higher copy numbers in VS5/VS6 than in VS2. Since these sequence blocks (VS2 and VS5-VS6) are related, intragenic evolution resulting in AT expansion may have occurred between these two regions. A model is proposed that postulates a role for recombination and AT-expansion in intra-genomic ISR variations. This process may represent a general mechanism of concerted evolution for bacterial ISR rearrangements.

Identifying mutations in Drosophila genes by direct sequencing of PCR products.

BioTechniquesVol. 27, No. 2 BenchmarksOpen AccessIdentifying Mutations in Drosophila Genes by Direct Sequencing of PCR ProductsErin M. Schlag & David A. WassarmanErin M. Schlag*Address correspondence to Erin M. Schlag, Cell Biology and Metabolism Br., National Institute of Child Health and Human Dev., Bldg. 18T, Rm. 101, National Institutes of Health, Bethesda, MD 20892, USA. Internet: E-mail Address: eschlag@helix.nih.govNational Institute of Child Health and Human Development, NIH, Bethesda, MD, USASearch for more papers by this author & David A. WassarmanNational Institute of Child Health and Human Development, NIH, Bethesda, MD, USASearch for more papers by this authorPublished Online:22 Aug 2018https://doi.org/10.2144/99272bm09AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail "Identifying Mutations in Drosophila Genes by Direct Sequencing of PCR Products." , 27(2), pp. 262–264FiguresReferencesRelatedDetailsCited ByInter-individual and intragenomic variations in the ITS region of Clonorchis sinensis (Trematoda: Opisthorchiidae) from Russia and VietnamInfection, Genetics and Evolution, Vol. 55Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach21 September 2008 | Genetica, Vol. 138, No. 4echinoid mutants exhibit neurogenic phenotypes and show synergistic interactions with the Notch signaling pathwayDevelopment, Vol. 130, No. 25MASK, a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signalingDevelopment, Vol. 129, No. 1The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis1 November 2001 | Genes & Development, Vol. 15, No. 21Developmental and Transcriptional Consequences of Mutations in Drosophila TAFII60Molecular and Cellular Biology, Vol. 21, No. 20Clinical Use of Capillary PCR To Diagnose Mycoplasma PneumoniaJournal of Clinical Microbiology, Vol. 38, No. 4TAF250 is required for multiple developmental events in Drosophila1 February 2000 | Proceedings of the National Academy of Sciences, Vol. 97, No. 3 Vol. 27, No. 2 Follow us on social media for the latest updates Metrics Downloaded 114 times History Published online 22 August 2018 Published in print August 1999 Information© 2018 Author(s)PDF download

Nucleotide substitution rate of mammalian mitochondrial genomes.

We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some important "genomic laws." The main conclusions can be summarized as follows. (1) High intragenomic variability in the evolutionary dynamic of mtDNA was found. The substitution rate is strongly dependent on the region considered, and slow- and fast-evolving regions can be identified. Nonsynonymous sites, the D-loop central domain, and tRNA and rRNA genes evolve much more slowly than synonymous sites and the two peripheral D-loop region domains. The synonymous rate is fairly uniform over the genome, whereas the rate of nonsynonymous sites depends on functional constraints and therefore differs considerably between genes. (2) The commonly accepted statement that mtDNA evolves more rapidly than nuclear DNA is valid only for some regions, thus it should be referred to specific mitochondrial components. In particular, nonsynonymous sites show comparable rates in mitochondrial and nuclear genes; synonymous sites and small rRNA evolve about 20 times more rapidly and tRNAs about 100 times more rapidly in mitochondria than in their nuclear counterpart. (3) A species-specific evolution is particularly evident in the D-loop region. As the divergence times of the organism pairs under consideration are known with sufficient accuracy, absolute nucleotide substitution rates are also provided.

Molecular cytogenetics of the ribosomal (18S + 28S and 5S) DNA loci in primitive and advanced urodele amphibians

In the present work we performed a cytogenetic analysis of the ribosomal (18S + 28S and 5S) loci in amphibian species belonging to the advanced family Salamandridae (genera Triturus, Salamandra, and Salamandrina) and in the primitive hynobiid Salamandrella keyserlingii (family Hynobiidae). In each analyzed karyotype the 5S rDNA sites appear to be stable, and definite in number, while an intraspecific variability both in number and chromosomal location of the 18S + 28S rDNA loci has been found in some Triturus species. In particular, an evolutionary trend toward a large intraspecific variability of the 18S + 28S rDNA loci has been found in the T. vulgaris species group. A structural analysis of the ribosomal repetition units demonstrates the occurrence of a length polymorphism within the 18S + 28S rDNA repeats in the examined species of the family Salamandridae; however, this polymorphism is rather limited, even in those Triturus species characterized by high intragenomic variability of the ribosomal sites. We show that in T. vulgaris meridionalis the variant repetition units actually segregate with individual chromosomes. This implies that they are not intermingled in the ribosomal clusters.

Repetitive DNA sequences from polyploid Elymus trachycaulus and the diploid progenitor species: detection and genomic affinity of Elymus chromatin added to wheat

A set of four repetitive DNA clones, pEt1, pEt2, pCb1, and pCb3, were isolated from SH-genome polyploid Elymus trachycaulus and H-genome diploid Critesion bogdanii. The clone Et1 represents a tandemly arranged telomeric sequence. Et2 represents tandem repeats interspersed along the entire length of individual chromosomes. The Cb1 sequence was more evenly dispersed. The Et1 clone shared homology with a 350 base pair family of rye sequences. The Cb3 sequence was evenly distributed in S- and H-genome species. All the repetitive DNA sequences were excellent markers for the specific detection and genomic affinity of Elymus chromatin added to wheat. All clones showed intragenomic variation in copy number and chromosomal location. Based on the analysis of this variation, we conclude that E. trachycaulus most probably originated from putative diploid H- and S-genome species resembling Critesion californicum and Pseudoroegneria spicata, respectively.Key words: wheatgrass, wheat–Elymus hybrid, addition lines, polyploidy, restriction fragment length polymorphism.

Salt tolerance potential of wild resources of the tribe Triticeae

The salt tolerance potential of variousAegilops species of different genome combinationsviz., Aegilops squarrosa, Ae. cylindrica, Ae. ovata. Ae. triuncialis, Ae. variabilis, Ae. bicornis, Ae. longissima, Ae. umbellulata, andAe. sharonensis was tested to identify the high salt-tolerant genotype(s). Screening was done in cement tanks filled with gravel and Hoagland nutrient solution. Salinity was created by mixing Na2SO4, CaCl2, MgCl2 and NaCl in the ratio of 10∶5∶1∶4 and induced by a stepwise increase in electrical conductivity number of tillers and number of leaves. Inter-and intragenomic variations for cation uptake were also significant. Species with DD and CD genome were found to be highly tolerant. Possible factors responsible for these observations have been discussed.

Structure of rDNA in the mosquito Anopheles gambiae and rDNA sequence variation within and between species of the A. gambiae complex.

The structure of the rDNA repeating unit of Anopheles gambiae (Diptera: Culicidae) was determined by restriction endonuclease mapping and hybridization analyses on four independent clones obtained from a genomic library of a colony (G3) from the Gambia (West Africa). rDNA gene coding sequences are conserved, but much intragenomic and intraspecific (geographic) variation occurs in the intergenic spacer. Hybridization of subclones from spacer and coding sequences to genomic DNA that was isolated from single mosquitoes from laboratory colonies of four other A. gambiae complex species reveals conservation of coding sequences but concerted evolution in the intergenic spacers.

Heterogeneity of wheat endosperm proteolipids (CM proteins)

Proteins extracted with CHCl 3-MeOH from wheat endosperm have been fractionated by Sephadex G-100 and the 15 000–20 000 MW range fraction, designated CM protein, has been examined by combined electrofocusing (pH range 5–8) and electrophoresis (pH 3.2) and the heterogeneity of the electrophoretic components has been ascertained. It has been shown by joint mapping and by sequential extraction that CM proteins are extracted by 70% EtOH but not by H 2O, although they can be made water-soluble after dialysis against an acid buffer, pH 3.2, 3 M urea, without losing their solubility in CHCl 3-MeOH mixtures. It is concluded that CM proteins fit the definition of a Folch—Lees proteolipid. The Triticum aestivum (genomes ABD) map can be reconstructed by mixing T. durum (AB) and Aegilops squarrosa (D). The low intragenomic variability of CM protein is confirmed.