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At least 253 records · Page 14Linked to original sources
PubMed2002

Molecular phylogenetics and mitochondrial genomic evolution in the chamaeleonidae (Reptilia, Squamata).

A phylogenetic hypothesis for the lizard family Chamaeleonidae is generated from 1503 aligned base positions (883 parsimony-informative) of mitochondrial DNA for specimens representing 59 species (57 ingroup and two outgroup). Sequences are reported for a genomic segment encoding eight transfer RNAs, NADH dehydrogenase component 2 (ND2), and portions of NADH dehydrogenase component 1 (ND1) and cytochrome c oxidase subunit 1 (COI). Newly reported genomic rearrangements and duplications support the hypothesis that mitochondrial gene order and content are destabilized by phylogenetic loss of a functional origin for light-strand replication between the genes encoding tRNA(Asn) and tRNA(Cys). A novel gene order characterizes all sampled Brookesia except B. nasus. Brookesia nasus, the apparent sister taxon of a clade formed by all other Brookesia, has the ancestral gene order but contains a large tandem duplication. An apparently noncoding 220 base pair insertion between the genes encoding ND2 and tRNA(Trp) is reported for Bradypodion tavetanum. Phylogenetic analysis identifies nine clades whose ancestral lineages diverged early in chamaeleonid evolutionary history: (1) Brookesia (possibly excluding B. nasus), (2) Chamaeleo subgenus Chamaeleo (excluding C. namaquensis), (3) Chamaeleo subgenus Trioceros, (4) viviparous Bradypodion, (5) oviparous Bradypodion, (6) genus Furcifer (except F. balteatus), and (7-9) three distinct clades of Calumma. Chamaeleo namaquensis, Brookesia nasus, Furcifer balteatus, Rhampholeon brevicaudatus, and R. spectrum represent ancient lineages dating to approximately the same time. Multiple independent losses and a possible secondary gain of horns are inferred for Trioceros. Viviparity has at least two separate origins in chameleons, one in Bradypodion and

Animals↗
PubMed2005

Mitochondrial voltage-dependent anion channel gene family in Drosophila melanogaster: complex patterns of evolution, genomic organization, and developmental expression.

Voltage-dependent anion channels (VDACs), also known as mitochondrial porins, are a family of small pore-forming proteins of the mitochondrial outer membrane found in all eukaryotes. VDACs play important roles in the regulated flux of metabolites between the cytosolic and mitochondrial compartments, energy metabolism, and apoptosis. Annotation of the genome sequence of Drosophila melanogaster revealed three genes (CG17137, CG31722-A, and CG31722-B) with homology to porin, the previously described Drosophila VDAC. Molecular analysis reveals a complex pattern of organization and expression. The genomic organization of these four genes and sequence comparisons with other insect VDAC homologs indicate that this gene family evolved through a mechanism of duplication and divergence from an ancestral VDAC gene during the radiation of the genus Drosophila. CG17137, CG31722-A, and CG31722-B are expressed in a male-specific pattern on both transcriptional and translational levels, while porin is equally expressed in both male and female flies. Additionally, CG31722-A and CG31722-B are expressed as a dicistronic transcript. Western blot analysis and immunofluorescence microscopy confirm that these proteins localize to the mitochondrion. Further expression analysis showed that CG17137 and CG31722-B are abundant in testes, while porin is ubiquitously expressed. While porin, CG17137, and CG31722-B are expressed to different degrees during embryogenesis, all of these proteins are dramatically reduced relative to cytochrome c content during larvogenesis. These studies illustrate a complex genomic organization and spatiotemporal pattern of expression for Drosophila VDACs as well as an evolutionary history consistent with either a partitioning of VDAC functions or an acquisition of novel functions among isoforms.

Amino Acid Sequence↗
PubMed1997

Rapid genomic evolution of a non-virulent coxsackievirus B3 in selenium-deficient mice.

Keshan disease, an endemic cardiomyopathy in China, can be prevented with selenium (Se) supplementation. However, the seasonal and annual nature of the disease suggests that an infectious co-factor is required along with a deficiency in Se. Using a murine model of coxsackievirus B3 (CVB3)-induced myocarditis, Se-deficient mice were shown to be more susceptible to the cardiopathologic effects of the virus. In addition, a normal benign strain of CVB3 becomes virulent in Se-deficient mice. This change in virulence was shown to be due to point mutations in the viral genome. Although the mechanism of the viral mutation is not known, the oxidative stress status of the Se-deficient host may play a role, either by directly affecting the virus and/or affecting host immune defenses.

Animals↗
PubMed2004

Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: genome evolution, interactions and adaptation.

The Gram-negative bacteria Pseudomonas aeruginosa and Burkholderia cepacia are opportunistic human pathogens that are responsible for severe nosocomial infections in immunocompromised patients and are the major pathogens in cystic fibrosis (CF). The two bacteria not only inhabit the same environmental niches but can also form mixed biofilms in the lungs of CF patients. Hence, it appears very likely that the two organisms are capable of interacting with each other. Work of the past few years has shown that both bacteria utilize quorum-sensing systems, which rely on N-acyl-homoserine lactone signal molecules, to control the expression of virulence factors and biofilm development. Most importantly, evidence has been presented that these signal molecules also serve as a universal language for communication between the two organisms. Moreover, analyses of the diversity in P. aeruginosa revealed the presence of genome islands that contain genes that are highly homologous to genes identified in strains of Burkholderia sp. This finding suggests that there is a frequent exchange of genetic material between the two organisms.

4-Butyrolactone↗
PubMed1987

Origin of noncoding DNA sequences: molecular fossils of genome evolution.

The total amount of noncoding sequences on chromosomes of contemporary organisms varies significantly from species to species. We propose a hypothesis for the origin of these noncoding sequences that assumes that (i) an approximately equal to 0.55-kilobase (kb)-long reading frame composed the primordial gene and (ii) a 20-kb-long single-stranded polynucleotide is the longest molecule (as a genome) that was polymerized at random and without a specific template in the primordial soup/cell. The statistical distribution of stop codons allows examination of the probability of generating reading frames of approximately equal to 0.55 kb in this primordial polynucleotide. This analysis reveals that with three stop codons, a run of at least 0.55-kb equivalent length of nonstop codons would occur in 4.6% of 20-kb-long polynucleotide molecules. We attempt to estimate the total amount of noncoding sequences that would be present on the chromosomes of contemporary species assuming that present-day chromosomes retain the prototype primordial genome structure. Theoretical estimates thus obtained for most eukaryotes do not differ significantly from those reported for these specific organisms, with only a few exceptions. Furthermore, analysis of possible stop-codon distributions suggests that life on earth would not exist, at least in its present form, had two or four stop codons been selected early in evolution.

Animals↗
PubMed1993

Recombination and mammalian genome evolution.

Several lines of evidence are presented which suggest that sequence G + C content and recombination frequency are related in mammals: (i) chromosome G + C content is positively correlated to chiasmata density; (ii) the non-pairing region of the Y chromosome has one of the lowest G + C contents of any chromosomal segment; (iii) a reduction in the rate of recombination at several loci is mirrored by a decrease in G + C content; and (iv) when compared with humans, mice have a lower variance in chiasmata density which is reflected in a lower variance in G + C content. The observed relation between recombination frequency and sequence G + C content provides an elegant explanation of why gene density is higher in G + C rich isochores than in other parts of the genome, and why long interspersed elements (LINES) are exclusive to G + C poor isochores. However, the cause of the relation is as yet unknown. Several possibilities are considered, including gene conversion.

Animals↗
PubMed2000

Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution.

Comparative sequencing of Pseudomonas aeruginosa genes oriC, citS, ampC, oprI, fliC, and pilA in 19 environmental and clinical isolates revealed the sequence diversity to be about 1 order of magnitude lower than in comparable housekeeping genes of Salmonella. In contrast to the low nucleotide substitution rate, the frequency of recombination among different P. aeruginosa genotypes was high, leading to the random association of alleles. The P. aeruginosa population consists of equivalent genotypes that form a net-like population structure. However, each genotype represents a cluster of closely related strains which retain their sequence signature in the conserved gene pool and carry a set of genotype-specific DNA blocks. The codon adaptation index, a quantitative measure of synonymous codon bias of genes, was found to be consistently high in the P. aeruginosa genome irrespective of the metabolic category and the abundance of the encoded gene product. Such uniformly high codon adaptation indices of 0.55 to 0.85 fit the ubiquitous lifestyle of P. aeruginosa.

Biological Evolution↗
PubMed2006

Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis).

The karyotype of Indian muntjacs (Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bacterial artificial clones (BAC) clones selected by chromosome painting for this special muntjac species. Sequence comparison on these BAC clones uncovered sequence syntenic relationships between the muntjac genome and those of other mammals. We found that the muntjac genome has peculiar features with respect to intron size and evolutionary rates of genes. Inspection of more than 80 pairs of orthologous introns from 15 genes reveals a significant reduction in intron size in the Indian muntjac compared to that of human, mouse, and dog. Evolutionary analysis using 19 genes indicates that the muntjac genes have evolved rapidly compared to other mammals. In addition, we identified and characterized sequence composition of the first BAC clone containing a chromosomal fusion site. Our results shed new light on the genome architecture of the Indian muntjac and suggest that chromosomal rearrangements have been accompanied by other salient genomic changes.

Animals↗
PubMed1995

Rapid genomic evolution of a non-virulent coxsackievirus B3 in selenium-deficient mice results in selection of identical virulent isolates.

Previous work from our laboratory demonstrated that selenium deficiency in the mouse allows a normally benign (amyocarditic) cloned and sequenced Coxackievirus to cause significant heart damage. Furthermore, Coxsackievirus recovered from the hearts of selenium-deficient mice inoculated into selenium-adequate mice still induced significant heart damage, suggesting that the amyocarditic Coxsackievirus had mutated to a virulent phenotype. Here we report that sequence analysis revealed six nucleotide changes between the virulent virus recovered from the selenium-deficient host and the avirulent input virus. These nucleotide changes are consistent with known differences in base composition between virulent and avirulent strains of Coxsackievirus. To the best of our knowledge, this is the first report of a specific nutritional deficiency driving changes in a viral genome, permitting an avirulent virus to acquire virulence due to genetic mutation.

Animals↗
PubMed1982

Genome evolution in pocket gophers (genus Thomomys). I. Heterochromatin variation and speciation potential.

A basic dichotomy exists in the amount and chromosomal position of constitutive heterochromatin (C-bands) in species of pocket gophers, genus Thomomys. Members of the "talpoides-group" of species (e.g., T. talpoides and T. monticola) have C-bands restricted to the centromeric regions. These taxa are characterized by Robertsonian patterns of karyotypic evolution. In contrast, species within the "bottae-group" are characterized by extensive amounts of heterochromatin, placed as whole-arm and apparent whole-chromosome (T. bottae) or as large interstitial blocks (T. umbrinus). These species are characterized by extensive non-Robertsonian variation in karyotype, variation which may be expressed from local population polymorphism to between population or species polytypy. Within T. bottae, the number of whole-arm heterochromatic autosomes is inversely proportional to the number of uniarmed chromosomes in the complement, which ranges from 0 to 36 across the species populations. In all-biarmed karyotypic populations, upward to 60 percent of the linear length of the genome is composed of heterochromatin. Populations with extensive heterochromatin variation and those with similar amounts meet and hybridize freely in nature. The implications of these date for current ideas on the function of heterochromatin, particularly as related to speciation models, are discussed.

Animals↗
PubMed2000

Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human.

Domestic cats and dogs are important companion animals and model animals in biomedical research. The cat has a highly conserved karyotype, closely resembling the ancestral karyotype of mammals, while the dog has one of the most extensively rearranged mammalian karyotypes investigated so far. We have constructed the first detailed comparative chromosome map of the domestic dog and cat by reciprocal chromosome painting. Dog paints specific for the 38 autosomes and the X chromosomes delineated 68 conserved chromosomal segments in the cat, while reverse painting of cat probes onto red fox and dog chromosomes revealed 65 conserved segments. Most conserved segments on cat chromosomes also show a high degree of conservation in G-banding patterns compared with their canine counterparts. At least 47 chromosomal fissions (breaks), 25 fusions and one inversion are needed to convert the cat karyotype to that of the dog, confirming that extensive chromosome rearrangements differentiate the karyotypes of the cat and dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints on cat and human chromosomes has refined the human/cat comparative genome map and, most importantly, has revealed 15 cryptic inversions in seven large chromosomal regions of conserved synteny between humans and cats.

Animals↗
PubMed2004

Strains of Peru tomato virus infecting cocona (Solanum sessiliflorum), tomato and pepper in Peru with reference to genome evolution in genus Potyvirus.

Two isolates (SL1 and SL6) of Peru tomato virus (PTV, genus Potyvirus) were obtained from cocona plants (Solanum sessiliflorum) growing in Tingo María, the jungle of the Amazon basin in Peru. One PTV isolate (TM) was isolated from a tomato plant (Lycopersicon esculentum) growing in Huaral at the Peruvian coast. The three PTV isolates were readily transmissible by Myzus persicae. Isolate SL1, but not SL6, caused chlorotic lesions in inoculated leaves of Chenopodium amaranticolor and C. quinoa. Isolate TM differed from SL1 and SL6 in causing more severe mosaic symptoms in tomato, and vein necrosis in the leaves of cocona. Pepper cv. Avelar (Capsicum annuum) showed resistance to the PTV isolates SL1 and SL6 but not TM. The 5'- and 3'-proximal sequences of the three PTV isolates were cloned, sequenced and compared to the corresponding sequences of four PTV isolates from pepper, the only host from which PTV isolates have been previously characterised at the molecular level. Phylogenetic analyses on the P1 protein and coat protein amino acid sequences indicated, in accordance with the phenotypic data from indicator hosts, that the PTV isolates from cocona represented a distinguishable strain. In contrast, the PTV isolates from tomato and pepper were not grouped according to the host. Inclusion of the sequence data from the three PTV isolates of this study in a phylogenetic analysis with other PTV isolates and other potyviruses strengthen the membership of PTV in the so-called "PVY subgroup" of Potyvirus. This subgroup of closely related potyvirus species was also distinguishable from other potyviruses by their more uniform sizes of the protein-encoding regions within the polyprotein.

Animals↗
PubMed2025

Genomic evolution of EGF-CFC genes in deuterostomes.

BACKGROUND: EGF-CFC proteins are a bilaterian innovation, but they are best known for their roles in Nodal signaling during gastrulation and left-right patterning in vertebrates. Species with multiple family members show evidence of functional specialization. For example, in mouse, Cripto is required for gastrulation, whereas CFC1 is involved in left-right patterning. However, members of the EGF-CFC family across model organisms exhibit limited sequence conservation beyond the EGF-CFC domain, posing challenges for determining their evolutionary history and functional conservation. RESULTS: In this study, we describe the evolutionary history of the EGF-CFC family of proteins across several branches of deuterostomes, with a particular focus on vertebrates. We trace the EGF-CFC gene family from a single gene in the deuterostome ancestor through its expansion and functional specialization in tetrapods, and subsequent gene loss and translocation in eutherian mammals. Mouse Cripto and CFC1, zebrafish Tdgf1, and each Xenopus EGF-CFC gene (Tdgf1, Tdgf1.2 and Cripto.3) are all descendants of the ancestral deuterostome Tdgf1 gene. CONCLUSIONS: We propose that subsequent to EGF-CFC family expansion in tetrapods, Tdgf1B (Xenopus Tdgf1.2) acquired specialization in the left-right patterning cascade, and then after its translocation in eutherians to a different chromosomal location, CFC1 has maintained that specialization.

Animals↗
PubMed1986

New cytogenetic techniques in the study of primate genome evolution.

Fixed metaphase chromosomes of different species and genera of Primates (five species of Macaca genus and Callithrix jacchus) have been studied after Alu I restriction enzyme digestion and DA-DAPI counterstaining, in the attempt to determine some qualitative characteristics of their DNAs and specifically of the DNA localized in the heterochromatic components of the karyotypes. The results have been discussed in the light of those already published on humans, confirming the potentiality of this approach in the study of the phyloevolutive relationships in Primates.

Animals↗
PubMed1993

Silk moth chorion pseudogenes: hallmarks of genomic evolution by sequence duplication and gene conversion.

The part of the genetic locus of the domesticated silk moth, Bombyx mori, in which high cysteine (Hc) chorion genes of late developmental specificity reside contains regions encompassing gene-like sequences which exhibit properties distinct from those of functional Hc genes. One of these regions has been characterized and shown to contain a chorion pseudogene, psi HcB.15, which shares pronounced similarities with a transcribed chorion pseudogene, psi HcB.12/13, which was characterized previously. Both pseudogenes are homologous to HcB chorion genes but bear multiple single nucleotide substitutions and short segmental mutations (insertions and deletions) which introduce translational frame shifts and termination codons in the coding regions. Structural characteristics unique to the two pseudogenes suggest that psi HcB.15 was generated first from a functional HcB gene and gave rise subsequently to psi HcB 12/13 as a result of a sequence duplication event. The two pseudogenes can be distinguished from each other by the presence of distinct regions of similarity to the consensus sequence of functional HcB genes which appear to have arisen from gene-conversion-mediated correctional events. These findings lend support to the hypothesis that chorion pseudogene sequences represent reservoirs of genetic information that participates in the evolution of the chorion locus rather than relics of inactivated genes passively awaiting extinction.

Animals↗
PubMed1982

Analysis of plasmid genome evolution based on nucleotide-sequence comparison of two related plasmids of Escherichia coli.

Plasmid Rsc13, a small derivative of the plasmid R1, contains a region necessary for replication as well as a complete copy (4957 bp) of the ampicillin resistance transposon, Tn3. We determined the nucleotide sequence of the replication region of Rsc13 to be 2937 bp and then compared this region (designated the 2.9-kb region) to the analogous region of pSM1, a small derivative of the plasmid R100 which has common ancestry with R1. Rsc13 and pSM1 were 96% homologous in this 2.9-kb region except for a discrete region of about 250 bp which showed only 44% homology. The sequence and distribution of nucleotide substitutions between Rsc13 and pSM1 supported a map of possible genes and sites which have previously been seen in the replication region of Rsc13 and pSM1 which showed only 44% homology. Analysis of the amino acid sequence and predicted conformation of the two RepA2 polypeptides, however, suggested that they were very similar. We proposed that the repA2 region of R1 and R100 was replaced by a substitution of a short DNA segment from another plasmid which was evolutionarily related to R1 and R100 but had more divergence. This event may have been mediated by a mechanism similar to that of gene conversion as described in eukaryotic systems.

Ampicillin↗