The species divergence times and demographic histories of Drosophila melanogaster and its three sibling species, D. mauritiana, D. simulans, and D. yakuba, were investigated using a maximum likelihood (ML) method. Thirty-nine orthologous loci for these four species were retrieved from DDBJ/EMBL/GenBank database. Both autosomal and X-linked loci were used in this study. A significant degree of rate heterogeneity across loci was observed for each pair of species. Most loci have the GC content greater than 50% at the third codon position. The codon usage bias in Drosophila loci is considered to result in the high GC content and the heterogenous rates across loci. The chi-square, G, and Fisher's exact tests indicated that data sets with 11, 23, and 9 pairs of DNA sequences for the comparison of D. melanogaster with D. mauritiana, D. simulans, and D. yakuba, respectively, retain homogeneous rates across loci. We applied the ML method to these data sets to estimate the DNA sequence divergences before and after speciation of each species pair along with their standard deviations. Using 1.6 × 10-8 as the rate of nucleotide substitutions per silent site per year, our results indicate that the D. melanogaster lineage split from D. yakuba approximately 5.1 ± 0.8 million years ago (mya), D. mauritiana 2.7 ± 0.4 mya, and D. simulans 2.3 ± 0.3 mya. It implies that D. melanogaster became distinct from D. mauritiana and D. simulans at approximately the same time and from D. yakuba no earlier than 10 mya. The effective ancestral population size of D. melanogaster appears to be stable over evolutionary time. Assuming 10 generations per year for Drosophila, the effective population size in the ancestral lineage immediately prior to the time of species divergence is approximately 3 × 106, which is close to that estimated for the extant D. melanogaster population. The D. melanogaster did not encounter any obvious bottleneck during the past 10 million years.
HERV-H, a family of endogenous retroviral elements that has undergone successive expansions in the human genome, includes sequences that are expressed in placenta and T cells. With a PCR approach to the HERV-H using human monochromosomal somatic cell hybrid DNA, we identified 8 new HERV-H sequences on the X chromosome, and one novel HERV-H element, HY-1, the first reported such element on the Y chromosome, and compared these with sequences in the nucleotide sequence database. Phylogenetic analysis indicated that clone HX-1 and BAC clone 523A23 on the X chromosome were found to be in close relationship to the sequences of DJ088A21 on the human chromosome 7q31. This finding allows us to speculate that HERV-H elements may have evolved by intra-chromosomal spread. Our data may relevant to an understanding of human genomic plasticity.
Portions of two mitochondrial genes (12S and 16S ribosomal RNAs) were sequenced to analyze the phylogenetic relationships of the Mabuya group from the Australian region (Corucia, Egernia and Tiliqua). Results indicated the monophyly of these genera and their divergence from Asian and African members of this group. This suggests that the diversity of the Mabuya group in the Australian region has increased through an endemic radiation, not through multiple colonizations from outside. Among the genera from this region, Corucia and Tiliqua were closest to each other. This result contradicts with those of the previous hypotheses on the basis of morphological and immunological data that, respectively, suggested closest affinities between Corucia and Egernia, and Egernia and Tiliqua. We suppose that the morphological characters exclusively joining Corucia and Egernia are actually in plesiomorphic state.
The CHS genes encoding chalcone synthase for flavonoid biosynthesis in the common and Japanese morning glories comprise a multigene family. Among these Ipomoea CHS genes, the CHS-D gene is the most abundantly expressed in the pigmented young flower buds and is primarily responsible for flower pigmentation. Majority of the remaining CHS transcripts in the flower buds are produced from the CHS-E gene. We characterized the genomic DNA segments of these CHS-D and CHS-E genes. Both genes have two exons with identical intron positions and carry several copies of two mobile element-like sequences with short terminal inverted repeats, MELS3 and MELS6 of around 200-300 bp. Small tandem repeats were also found in these CHS gene regions. The CHS-D and CHS-E genes are expressed predominantly in flower limbs and tubes, respectively. These structural and functional features and their evolutionary implications are discussed.
Since clear identification of individual chromosomes in Capsicum species was not possible due to the gradient in sizes and similar morphology, in situ hybridization using 5S rDNA and 18S-26S rDNA probes was utilized to karyotype the chromosomes of the five species, Capsicum annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens. The 5S rDNA located on only one pair of chromosomes in all five species. The 5S rDNA carrying chromosome was designated as chromosome 1 by the synteny relationship with tomato. In two species, C. baccatum and C. pubescens, the 5S rDNA was physically linked with a 18S-26S rDNA locus. The number and chromosomal location of 18S-26S rDNA loci were highly variable among the species. The number of loci was as few as two in C. annuum and as many as 14 in C. baccatum. The chromosomal positions of the 18S-26S loci were in the telomere regions in the corresponding chromosomes and some chromosomes showed hybridization signals in this region of both long and short arms. A pair of acrocentric chromosomes carrying the 18S-26S rDNA locus in the satellite region was found in all five species. The in situ and Southern hybridization patterns of the rDNAs were similar between C. annuum and C. chinense. C. frutescens was similar to C. chinense. C. baccatum and C. pubescens were speculated to be less related to the former three Capsicum species. The variable nature of the 18S-26S rDNA loci in the Capsicum species might provide a good model for rDNA evolution.
Several human neurodegenerative disorders are caused by expansion of CAG repeats that occurs during meiosis or gametogenesis. We anticipated that the CAG repeats cloned in a plasmid of Saccharomyces cerevisiae might undergo a change in the number of repeats during meiosis and sporulation. To test this possibility, we devised a new method to change in vitro the number of CAG repeats and constructed plasmids carrying (CAG)39, (CAG) 65 or (CAG)123 from a plasmid carrying (CAG)18. We monitored the number of colonies showing an altered length of the repeat tracts during mitosis and meiotic growth. Contraction of long CAG repeat was found to occur frequently, whereas a few cases of expansion were observed. The contraction was equally enhanced in both orientations when the host cells grew through meiosis. Thus, our results suggest that long CAG repeats are destabilized during meiosis or gametogenesis in S. cerevisiae.
Genetic diversity and differentiation among the wild soybeans, Glycine soja, collected from riversides of five major rivers in Korea have been analyzed with simple sequence repeat variations. When the genetic diversity in this study was compared to those of cultivated soybeans reported by others, the wild soybeans showed significantly higher genetic diversity and differentiation than those of cultivated soybeans. The number of alleles observed in this study varied from a low of 9 to high of 14 and 82 different alleles were observed among the 57 wild soybeans at seven SSR loci. The genetic diversity measured by the number of effective alleles also varied from 4.8 to 9.1 with an average of 6.8. When the genetic diversity was converted to population differentiation, the SSR alleles showed 0.8 to 0.89 depending on the SSR locus with an average of 0.86. There was no predominantly present allele (or alleles) to specific sub population. Although the highest genetic diversity was observed in the subpopulation from Nakdong river, the subpopulation from Sumjin river showed the highest genetic differentiation value. In the phenetic relationship analysis, the 57 wild soybeans were differentiated at the genetic similarity of 0.83. Since the clustering pattern did not correspond with the geographical origins where they collected, the genetic diversity and differentiation of the wild soybeans could predate the dispersal of the wild soybeans along the rivers.
The Salmonella flagellar operons are divided into three classes with reference to their relative positions in the transcriptional hierarchy. Expression of the class 2 operons requires the class 1 gene products, FlhD and FlhC, and is enhanced by an unknown mechanism in the presence of the class 3-specific sigma factor, FliA, and in the absence of its cognate anti-sigma factor, FlgM. In this study, the transcriptional start site mapping was performed by primer extension analysis for five class 2 operons, flgA, flgB, flhB, fliE and fliL. In all cases, one or a few major transcriptional start sites were identified. These start signals disappeared in the flhDC-mutant background, and their intensity decreased and increased in the fliA-mutant and flgM-mutant backgrounds, respectively. Therefore, we conclude that the FlhD/FlhC-dependent transcription is responsible for the FliA-dependent enhancement. Sequence comparison revealed that an imperfect inverted repetitious sequence is conserved upstream of the class 2 operons. Truncation of this sequence from the flgB promoter reduced its transcriptional activity to the background level, indicating that this is an essential cis-acting element for transcription of the class 2 operons.