gene order

..Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind...

..Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and ..

..The mitochondrial gene arrangements of the 20 genomes=are also consistent with our results...

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..This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective...

..This is discussed in relation to the identification of the loci contributing to color pattern evolution in butterflies...

Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence, but comparisons of the Arabidopsis thaliana sequence to partial gene orders of other angiosperms (flowering plants) sharing common ..

..Together, our data indicate that TPS systems may contribute to the virulence of N. meningitidis...

..the complete mitogenome of the cyclopoid copepod Paracyclopina nana with emphasis on the highly rearranged gene order and high divergence against published copepod mitogenomes. The P. nana mtDNA is 15,981 bp in length (70...

..Our results further emphasize the importance of secondary reduction at both the cellular and genome levels during chlorophyte evolution...

..The distribution of placentally expressed genes, in contrast, does have an effect...

Chloroplast genome organization, gene order, and content are highly conserved among land plants. We sequenced the chloroplast genome of Trachelium caeruleum L...

..We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison with other SGC sequences available...

..It remains unclear whether the virtually identical gene repertoires are the result of convergence or descent...

..Both gene order conservation and breakpoint reuse can result from the existence of functional constraints on where chromosomal ..

..The functional significance, if any, of this repeat structure remains unknown...

..striatellus mitogenome is identical to other completely sequenced insect mitogenomes, while the gene order is different from the common arrangement found in most insects: five tRNA genes and three PCGs in the L...

..It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information...

..g., Orussus and Schlettererius). It is likely that only a small proportion of the total number of mitochondrial gene rearrangements that have occurred during the evolution of the Hymenoptera have been sampled in the present study...

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..Unlike the relatively conserved gene arrangement found for most chromadorean taxa, E. vermicularis mtDNA gene order is very unique, not sharing similarity to any other nematode species reported to date...

..This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data...

..It also presents a survey of cell and animal models under development to mimic the pathophysiology of human mitochondrial disorders...

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..The genome stability in Corynebacterium species will give us hints of the speciation mechanism with the non-shuffled genome, particularly the importance of horizontal gene transfer and nucleotide substitution in the genome...

Two main gene orders exist in birds: the ancestral gene order and the remnant control region (CR) 2 gene order. These gene orders differ by the presence of 1 or 2 copies of the CR, respectively...

..We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales)...

..g. Mollusca, Brachiozoa or Platyhelminthes. Mitochondrial genomes contributed well with sequence data and gene order characters to the deep metazoan phylogeny debate.

The phylogenetic placement of Thermodesulfovibrio yellowstonii was investigated on the basis of gene order data from completely sequenced bacterial genomes. T...

..birds has highly conserved features, with protein genes similar to mammals and amphibians, several variations in gene order around the hypervariable control region have been found...

..In this study, we describe the mitochondrial genome of the European house dust mite Dermatophagoides pteronyssinus, the most important member of this largely neglected group...

..ICEVchB33 revealed a new genetic organization, different from other ICEs of the SXT/R391 family, demonstrating the genomic plasticity of these elements...

The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during ..

..We conclude that gene orientation and transcription of ncRNAs are candidate modulators of noise...

Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear...

..iredalei and Saccostrea mordax) for a comprehensive analysis...

..We propose a simple, unified model in which a single mechanism--passive gene loss-enabled whole--genome duplication and led to the rapid emergence of new yeast species...

..Smith, M.J., 2001. Mol. Biol. Evol. 18, 61-73). The mitochondrial gene order of the stalked crinoid G. richeri differs from that of F. serratissima and P...

..As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution,..

..The evolution of these overlapping gene structures is probably related to the evolutionary time scale, which suggests that the evolution of overlapping genes occurs at a universal mutation rate across species...

..In addition, the analyses of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group...

..Sequence comparison of the BAC end sequences with the human genome sequence showed that the centromeric part of SSC13 is homologous with HSA3p24...

..Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide ..

..9-Mb sequence of P. ramorum. In these regions with conserved synteny, the gene order is largely similar; however, genome rearrangements also have occurred...

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b>Gene order is not random with regard to gene expression in mammals: coexpressed genes, and in particular housekeeping genes, are clustered along chromosomes more often than expected by chance...

..Relative to most vertebrates, the Rhineuridae has the block nad6, trnE switched in order with the block cob, trnT, trnP, as they are in birds...

..The mtDNA of E. floccosum has the same gene order as Trichophyton rubrum mtDNA, with the exception of some tRNA genes...

..An extensive bioinformatic analysis and comparison of SAGE transcriptomes of the total testis, testicular somatic cells and other mouse tissues was performed and the theory of male-biased gene accumulation on the X chromosome was tested...

..Binding at genuine regulatory sites on DNA would thus be optimized by co-transcriptionally translating regulators in their vicinity...

..biologically inspired computational approach for inferring genome-scale rearrangement phylogeny and ancestral gene order has been developed. This has been applied to eight Drosophila genomes...

..This also represents the first time that microsynteny with Arabidopsis has been exploited for positional cloning purposes in a different plant family...

..The genome organization, i.e., the size, presence of intergenic sequences, and gene order, as well as polymorphism within the coding regions, indicate that Saccharomyces mtDNA molecules are dynamic ..

..Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes...

..In particular, our analysis suggests a new improved rearrangement scenario for a very difficult Campanulaceae cpDNA dataset and a putative rearrangement scenario for human, mouse and cat genomes...

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..Our phylogenetic analysis confirms with overwhelming support that H. curvatum is a member of the chytridiomycete fungi, specifically related to the Monoblepharidales...

..b>Gene order is not conserved between B...

..melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius...

..Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2)...

..Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes...

..a species of the suborder Mesothelae and a representative of the most basal clade of Araneae, possesses a gene order identical to that of Limulus polyphemus of Xiphosura. On the other hand, O...

..Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway...

..Assays of 3-galactosidase activity of P. massiliensis T7PB carrying a nifB-lacZ fusion under different concentrations of NH4+ and O2 showed that the expression of nifB-lacZ was strongly inhibited by O2...

..Moreover, the scaC gene, being short and variable, appears to be a promising functional phylotyping target for metagenomic population studies of R. flavefaciens in the rumen as a function of the individual host animal...

..The nitrile hydratase/amidase enzymes of strain AJ270 are inducible with acetonitrile or acetamide. Interestingly although a number of Fe-type nitrile hydratases have been shown to be photosensitive, the enzyme from strain AJ270 is not...

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..We conclude that sequences from these two cps regions are very useful in detecting K57 and the new cps genotype...

..Comparison with HP15, HP23, and PAP-3 sequences suggested an evolutionary pathway of the dual clip-domain serine proteinases in M. sexta...

..However, questions about the biological significance of gene order conservation, or synteny, remain open...

..Four gene regions remained that were conserved and specific for microcystin-producing Planktothrix strains, and thus qualified to detect the respective chemotypes in environmental samples...

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..This is the first example of a regulator gene involved in aerobactin-enhanced production of IutA...

..The data implies that the pandemic O4:K68 V. parahaemolyticus strain emerged from the pandemic O3:K6 strain by replacement of the putative O and K antigen gene clusters...

..The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp...

..reuteri's success in colonizing the gastrointestinal tract. This information on gene organization, gene transcription and gene acquisition is relevant for the development of (fermented) foods and probiotics enriched in B(12)...

..Thus, we describe for the first time a mechanism that may explain the observed horizontal transfer of chromosomal DNA in Legionella...

..A pyrrolo-quinoline quinone binding domain in TetH was predicted by bioinformatic analysis, and the presence of an o-quinone moiety was experimentally verified, suggesting a mechanism for tetrathionate oxidation...

..We showed that OPS and OC confer resistance to human complement and polymyxin B; the OPS effect on polymyxin B resistance could be observed only in the absence of OC...

..This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography...

..This implies that Planctomycetes and Chlamydiae may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with Verrucomicrobia...

..Compared with its closest match, the streptococcin A-FF22 gene cluster, the macedocin one contains an additional structural gene and an insertion sequence between the regulatory and the biosynthetic operons...

..davawensis ribG gene coding for the missing pyrimidine deaminase/reductase (EC 3.5.4.26 and EC 1.1.1.193) of the riboflavin biosynthetic pathway and ribY coding for a second (monofunctional) GTP cyclohydrolase II were identified...

..Within the genus Microcystis, microcystin and cyanopeptolin synthetases have an evolutionary history of genomic coexistence. However, the data indicated that the two classes of peptide synthetase gene clusters have evolved independently...

..This operon structure has not been reported in any other bacterial species so far. Transcriptional analysis revealed three major transcripts, the mono-cistronic gap and eno and the tetra-cistronic gap-pgk-tpi-eno...

..innocua strains altered by horizontal transfer. It is more likely that they are distinct relics of the evolution of L. innocua from an ancestral L. monocytogenes, as postulated by others...

..As VirB6 is known to associate with other VirB proteins to form a membrane-spanning structure, this finding suggests that a T4SS may function in Wolbachia...

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..These findings provide the basis to further genetically manipulate and improve lipodepsipeptide antibiotics via combinatorial and chemical methods...

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..The possible role of the putative efflux pump coded by the ame genes is discussed...

..boydii O11, which share the identical O-antigen, also have the same genes and organization for their respective O-antigen gene clusters. Three genes specific for the S. boydii O11 and E. coli O105 gene clusters were identified...

..The structural components of the S motility apparatus were unaffected in the che4 mutants, suggesting that the Che4 system affects reversal frequency of cells by modulating the function of the type IV pilus...

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..Yet, expression per aerial hypha was similar to that in the wild-type strain, indicating that expression of the rdl genes is initiated after the hypha has sensed that it has grown into the air...

..Results of this study indicated that globally distributed naphthalene catabolic genes are highly conserved among different bacterial species...

..epidermidis and S. aureus it does not contain an open reading frame that codes for a protein with homologies to the delta-toxin. Using PCR, the agr was found to be present in clinical isolates of S. saprophyticus...

..Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to resuscitate such meaningful data...

..Only a slight sensitivity in response to oxidative conditions could be assigned to either single or double mutants, revealing the probable redundancy of the sigma factors implied in stress response in Streptomyces...

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..We also demonstrate that although MesDEs from strains Y105 and FR52 have significant sequence differences, both transporters were capable of assuring secretion of either bacteriocin...

..Specific Aim 3. To dissect the role of gene order, domains, and flanking cis-acting regulatory sequences in determining the fetal thymic V-gamma gene ..

..These will provide candidate genes for mutations and will delineate chromosome segments in which gene order has been conserved in vertebrate evolution...

..Moreover, we and others have shown that coronaviruses tolerate gene order rearrangements, but as a consequence are attenuated in replication efficiency and pathogenesis...

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..The evolutionary proximity of baboon and human, and the high degree of conservation of gene order between these species, imply that genetic factors identified in the baboon genome will be directly relevant to ..

..In addition, we will assess the gene order relationship between egl-4 and pde-4 is regulating sensory gating...

..we will use reverse genetics and the full length TGE construct to systematically address the role of gene order, cis and trans acting regulatory sequences, and N gene function in coronavirus transcription and replication...

..In addition, we will assess the gene order relationship between egl-4 and pde-4 is regulating sensory gating...

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..model using experimental data from a panel of recombinant VSV strains, and (3) employ the model to predict how gene order affects VSV growth...

..between zebrafish and human genomes by identifying the boundaries of conserved chromosomal segments and defining gene order within these segments...

..Humans and dogs have similar physiology, share extensive genome homology with a high degree of preserved gene order, and are exposed to the same environment...

..Genetic linkage maps provide information on gene order and crossover frequency but not on the influence of chromosome structure on recombination, while chiasmata ..