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Understanding how microsatellites are distributed in eukaryotic genomes is important to clarify the differential abundance of these repeats under an evolutionary scenario. We have concatenated data from 3165 DNA sequences of 326 Bivalvia species to search for taxonomic patterns of microsatellite distribution in genomic regions of markedly different functionality. Some microsatellite motifs in bivalves...
A comparison is made between orthologous proteins from a nonbarophile (Pyrococcus furiosus) and a barophile (Pyrococcus abyssi) organism. The pattern of asymmetries in the amino acid substitution process identifies the amino acids arginine, serine, glycine, valine and aspartic acid as those having the most barophilic behaviour, and tyrosine and glutamine as the least barophilic. The construction of...
In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences...
Mutations in the human parkin gene (huParkin) are the predominant genetic cause of familial parkinsonism. The huParkin locus, spanning about 1.4 Mb, is one of the largest in the human genome. Despite its huge size, huParkin codes for a rather short transcript of about 4.5 kb. To gain an insight into the structure, function and evolutionary history of huParkin, we have characterized the pufferfish...
We have characterized the apolipoprotein multigene family of the pufferfish Takifugu rubripes. The pufferfish mainly contains 28-kDa, 27-kDa, and 14-kDa apolipoproteins in its plasma and was designated apo-28 kDa, apo-27 kDa, and apo-14 kDa, respectively. N-terminal amino acid sequencing revealed that pufferfish apo-28 kDa and apo-27 kDa have an identical amino acid sequence except an additional propeptide...
The involvement of cytochrome P450 (CYP) enzymes in olfaction has been demonstrated in vertebrates over the past decade. In insects, these enzymes are well known for their role in biosynthesis of endogenous compounds as well as xenobiotic metabolism, but the presence of olfactory cytochrome P450s was poorly investigated. Using a PCR-based strategy, we have isolated cDNAs of two new microsomal P450s...
The chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small. The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1–2%. Recently, direct nucleotide sequencing confirmed...
The complete mitochondrial DNA sequence for an Australian agamid Pogona vitticepes was determined. Twenty-two tRNA genes, two rRNA genes, thirteen protein-coding genes, and two control regions were identified in this mitochondrial genome. The second control region was inserted between NADH dehydrogenase subunits 5 and 6 genes. The duplication of the control region was found in all Australasian agamids...
The comparison of proteins from a non-barophilous and a barophilous organism makes it possible to define the barophily ranks of amino acids. The correlation of these ranks with the number of codons attributed to amino acids in the genetic code, together with another straightforward argument based on an optimisation percentage of a barophily index (BI) (easily defined by barophily ranks) which can...
F116 is a temperate, pilus-specific, generalized transducing phage belonging to the Podoviridae virus family. Its genome is linear, ds, TR, and CP DNA with a GC content of 63.2%. The 65 195-bp genome contains 70 putative ORFs, only 16 of which showed sequence similarity to Pseudomonas genomic or phage genes.While the current literature suggests that F116 is a non-integrating phage that maintains itself...
During the course of evolution, the genome should have toned down various types of genomic noise, such as those that cause the unstable expression or gene silencing observed in transgenic organisms. We found a rice genomic segment where two genes, encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) and ribosomal protein small subunit 20 (rps20), are located in a tail-to-tail orientation and...
The enhancer complex regulatory region at the 3′ of the immunoglobulin heavy cluster (IgH3′EC) is duplicated in apes along with four constant genes and the region is highly conserved throughout humans. Both human IgH3′ECs consist of three loci high sensitive (HS) to DNAse I with enhancer activity. It is thus possible that the presence of structural divergences between the two IgH3′ECs and of relative...
Olfactory receptor (OR) genes form the largest multigene family in mammalian genomes. Humans have ∼800 OR genes, but >50% of them are pseudogenes. By contrast, mice have ∼1400 OR genes and pseudogenes are ∼25%. To understand the evolutionary processes that shaped the difference of OR gene families between humans and mice, we studied the genomic locations of all human and mouse OR genes and conducted...
Here, we sequenced two large telomeric regions obtained from the pathogen protozoan Trypanosoma cruzi. These sequences, together with in silico assembled contigs, allowed us to establish the general features of telomeres and subtelomeres of this parasite. Our findings can be summarized as follows: We confirmed the presence of two types of telomeric ends; subtelomeric regions appeared to be enriched...
Hox genes encode DNA binding proteins that specify cell fate in the anterior–posterior axis of metazoan animal embryos. While each Hox cluster contains the same genes among the different mammalian species, this does not happen in ray-finned fish, in which both the number and organization of Hox genes and even Hox clusters are variables. Ray-finned fish are believed to have undergone an additional...
About 20 ethnic groups reside in Mongolia. On the basis of genetic and anthropological studies, it is believed that Mongolians have played a pivotal role in the peopling of Central and East Asia. However, the genetic relationships among these ethnic groups have remained obscure, as have their detailed relationships with adjacent populations. We analyzed 16 binary and 17 STR polymorphisms of human...
Through differential analysis of transcripts (SDDM), 85 cDNA sequences specifically or preferentially expressed in wheat spikelets at heading time were identified and cloned; 54 of them had significant homology with genomic, cDNA and protein and 16 with EST sequences. Among these 54 clones, 44 matched genes with known functions, whereas 10 detected homology with putative genes encoding proteins whose...
Linkage disequilibrium (LD) mapping is often used in searches for genes governing economically significant traits and diseases. The D′ coefficient is a commonly used measure of the extent of LD between all possible pairs of alleles at two markers. This study aimed to test the utility of the D′ coefficient for LD mapping of a trait in a thoroughbred population. Microsatellite genotype data and grey...
The involvement of clay surfaces in the origin of the first genetic molecules on Earth has long been suggested. However, the formation of these polymers was not sufficient by itself to initiate the evolutionary process leading to the appearance of life. These macromolecules had to persist in primeval habitats so that their biological potentiality could be expressed.In this study, we assess the possibility...
In this study, we have determined the complete sequence of the mitochondrial genome of an Old World tree frog Polypedates megacephalus (Anura: Rhacophoridae) by using a long polymerase chain reaction (PCR) technique and shotgun strategy of sequencing. The entire mtDNA sequence is 16,473 nt long with a novel mitogenomic gene organization in amphibians. Unlike other neobatrachian frogs, the transfer...
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