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Genome Duplication (genome + duplication)

Distribution by Scientific Domains

Life Sciences	61%

Selected Abstracts

Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish

DEVELOPMENTAL DYNAMICS, Issue 3 2003
William A. Cresko
Abstract Teleosts are the most species-rich group of vertebrates, and a genome duplication (tetraploidization) event in ray-fin fish appears to have preceded this remarkable explosion of biodiversity. What is the relationship of the ray-fin genome duplication to the teleost radiation? Genome duplication may have facilitated lineage divergence by partitioning different ancestral gene subfunctions among co-orthologs of tetrapod genes in different teleost lineages. To test this hypothesis, we investigated gene expression patterns for Sox9 gene duplicates in stickleback and zebrafish, teleosts whose lineages diverged early in Euteleost evolution. Most expression domains appear to have been partitioned between Sox9a and Sox9b before the divergence of stickleback and zebrafish lineages, but some ancestral expression domains were distributed differentially in each lineage. We conclude that some gene subfunctions, as represented by lineage-specific expression domains, may have assorted differently in separate lineages and that these may have contributed to lineage diversification during teleost evolution. Developmental Dynamics, 2003. © 2003 Wiley-Liss, Inc. [source]

Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution

DEVELOPMENTAL DYNAMICS, Issue 3 2006
Yuich Okuda
Abstract Group B1 Sox genes encode HMG domain transcription factors that play major roles in neural development. We have identified six zebrafish B1 sox genes, which include pan-vertebrate sox1a/b, sox2, and sox3, and also fish-specific sox19a/b. SOX19A/B proteins show a transcriptional activation potential that is similar to other B1 SOX proteins. The expression of sox19a and sox3 begins at approximately the 1,000-cell stage during embryogenesis and becomes confined to the future ectoderm by the shield stage. This is reminiscent of the epiblastic expression of Sox2 and/or Sox3 in amniotes. As development progresses, these six B1 sox genes display unique expression patterns that overlap distinctly from one region to another. sox19a expression is widespread in the early neuroectoderm, resembling pan-neural Sox2 expression in amniotes, whereas zebrafish sox2 shows anterior-restricted expression. Comparative genomics suggests that sox19a/b and mammalian Sox15 (group G) have an orthologous relationship and that the B1/G Sox genes arose from a common ancestral gene through two rounds of genome duplication. It seems likely, therefore, that each B1/G Sox gene has gained a distinct expression profile and function during vertebrate evolution. Developmental Dynamics 235:811,825, 2006. © 2006 Wiley-Liss, Inc. [source]

Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish

From genomes to morphology: a view from amphioxus

ACTA ZOOLOGICA, Issue 1 2010
Peter W. H. Holland
Abstract Holland, P.W.H. 2010. From genomes to morphology: a view from amphioxus. ,Acta Zoologica (Stockholm) 91: 81,86 As complete genome sequences are determined from an ever-increasing number of animal species, new opportunities are arising for comparative biology. For zoologists interested in the evolution of shape and form, however, there is a problem. The link between genome sequence and morphology is not direct and is obfuscated by complex and evolving genetic pathways, even when conserved regulatory genes are considered. Nonetheless, a large-scale comparison of genome sequences between extant chordates reveals an intriguing parallel between genotypic and phenotypic evolution. Tunicates have highly altered genomes, with loss of ancestral genes and shuffled genetic arrangements, while vertebrate genomes are also derived through gene loss and genome duplication. The recently sequenced amphioxus genome, in contrast, reveals much greater stasis on the cephalochordate lineage, in parallel to a less derived body plan. The opportunities and challenges for relating genome evolution to morphological evolution are discussed. [source]

Experimental and steady-state analysis of the GAL regulatory system in Kluyveromyces lactis

FEBS JOURNAL, Issue 14 2010
Venkat R. Pannala
The galactose uptake mechanism in yeast is a well-studied regulatory network. The regulatory players in the galactose regulatory mechanism (GAL system) are conserved in Saccharomyces cerevisiae and Kluyveromyces lactis, but the molecular mechanisms that occur as a result of the molecular interactions between them are different. The key differences in the GAL system of K. lactis relative to that of S. cerevisiae are: (a) the autoregulation of KlGAL4; (b) the dual role of KlGal1p as a metabolizing enzyme as well as a galactose-sensing protein; (c) the shuttling of KlGal1p between nucleus and cytoplasm; and (d) the nuclear confinement of KlGal80p. A steady-state model was used to elucidate the roles of these molecular mechanisms in the transcriptional response of the GAL system. The steady-state results were validated experimentally using measurements of ,-galactosidase to represent the expression for genes having two binding sites. The results showed that the autoregulation of the synthesis of activator KlGal4p is responsible for the leaky expression of GAL genes, even at high glucose concentrations. Furthermore, GAL gene expression in K. lactis shows low expression levels because of the limiting function of the bifunctional protein KlGal1p towards the induction process in order to cope with the need for the metabolism of lactose/galactose. The steady-state model of the GAL system of K. lactis provides an opportunity to compare with the design prevailing in S. cerevisiae. The comparison indicates that the existence of a protein, Gal3p, dedicated to the sensing of galactose in S. cerevisiae as a result of genome duplication has resulted in a system which metabolizes galactose efficiently. [source]

Retention of the duplicated cellular retinoic acid-binding protein 1 genes (crabp1a and crabp1b) in the zebrafish genome by subfunctionalization of tissue-specific expression

FEBS JOURNAL, Issue 14 2005
Rong-Zong Liu
The cellular retinoic acid-binding protein type I (CRABPI) is encoded by a single gene in mammals. We have characterized two crabp1 genes in zebrafish, designated crabp1a and crabp1b. These two crabp1 genes share the same gene structure as the mammalian CRABP1 genes and encode proteins that show the highest amino acid sequence identity to mammalian CRABPIs. The zebrafish crabp1a and crabp1b were assigned to linkage groups 25 and 7, respectively. Both linkage groups show conserved syntenies to a segment of the human chromosome 15 harboring the CRABP1 locus. Phylogenetic analysis suggests that the zebrafish crabp1a and crabp1b are orthologs of the mammalian CRABP1 genes that likely arose from a teleost fish lineage-specific genome duplication. Embryonic whole mount in situ hybridization detected zebrafish crabp1b transcripts in the posterior hindbrain and spinal cord from early stages of embryogenesis. crabp1a mRNA was detected in the forebrain and midbrain at later developmental stages. In adult zebrafish, crabp1a mRNA was localized to the optic tectum, whereas crabp1b mRNA was detected in several tissues by RT-PCR but not by tissue section in situ hybridization. The differential and complementary expression patterns of the zebrafish crabp1a and crabp1b genes imply that subfunctionalization may be the mechanism for the retention of both crabp1 duplicated genes in the zebrafish genome. [source]

The evolution of teleost pigmentation and the fish-specific genome duplication

JOURNAL OF FISH BIOLOGY, Issue 8 2008
I. Braasch
Teleost fishes have evolved a unique complexity and diversity of pigmentation and colour patterning that is unmatched among vertebrates. Teleost colouration is mediated by five different major types of neural-crest derived pigment cells, while tetrapods have a smaller repertoire of such chromatophores. The genetic basis of teleost colouration has been mainly uncovered by the cloning of pigmentation genes in mutants of zebrafish Danio rerio and medaka Oryzias latipes. Many of these teleost pigmentation genes were already known as key players in mammalian pigmentation, suggesting partial conservation of the corresponding developmental programme among vertebrates. Strikingly, teleost fishes have additional copies of many pigmentation genes compared with tetrapods, mainly as a result of a whole-genome duplication that occurred 320,350 million years ago at the base of the teleost lineage, the so-called fish-specific genome duplication. Furthermore, teleosts have retained several duplicated pigmentation genes from earlier rounds of genome duplication in the vertebrate lineage, which were lost in other vertebrate groups. It was hypothesized that divergent evolution of such duplicated genes may have played an important role in pigmentation diversity and complexity in teleost fishes, which therefore not only provide important insights into the evolution of the vertebrate pigmentary system but also allow us to study the significance of genome duplications for vertebrate biodiversity. [source]

Towards natural polyploid model organisms

MOLECULAR ECOLOGY, Issue 8 2008
RICHARD J. A. BUGGS
Abstract Populations of natural allopolyploids with available and well-developed genomic resources are currently hard to come by. These are needed because whole genome duplication and hybridization , both combined in allopolyploids , are significant processes in evolution, especially the evolution of plants. The new characterization of a naturally occurring allopolyploid in the genus Mimulus by Sweigart et al. in this issue of Molecular Ecology is therefore to be welcomed. Mimulus is rapidly emerging as a model system for evolutionary functional genomics. Sequences of the whole genome and 200 000 expressed sequence tags of diploid M. guttatus, a putative parent of the polyploid described in this issue, will soon be available. These will facilitate investigation of the fates of genes duplicated by whole genome duplication, and their effects on morphology, mating system and ecology in natural populations. [source]

The X philes: structure-specific endonucleases that resolve Holliday junctions

MOLECULAR MICROBIOLOGY, Issue 4 2001
Gary J. Sharples
Genetic recombination is a critical cellular process that promotes evolutionary diversity, facilitates DNA repair and underpins genome duplication. It entails the reciprocal exchange of single strands between homologous DNA duplexes to form a four-way branched intermediate commonly referred to as the Holliday junction. DNA molecules interlinked in this way have to be separated in order to allow normal chromosome transmission at cell division. This resolution reaction is mediated by structure-specific endonucleases that catalyse dual-strand incision across the point of strand cross-over. Holliday junctions can also arise at stalled replication forks by reversing the direction of fork progression and annealing of nascent strands. Resolution of junctions in this instance generates a DNA break and thus serves to initiate rather than terminate recombination. Junction resolvases are generally small, homodimeric endonucleases with a high specificity for branched DNA. They use a metal-binding pocket to co-ordinate an activated water molecule for phosphodiester bond hydrolysis. In addition, most junction endonucleases modulate the structure of the junction upon binding, and some display a preference for cleavage at specific nucleotide target sequences. Holliday junction resolvases with distinct properties have been characterized from bacteriophages (T4 endo VII, T7 endo I, RusA and Rap), Bacteria (RuvC), Archaea (Hjc and Hje), yeast (CCE1) and poxviruses (A22R). Recent studies have brought about a reappraisal of the origins of junction-specific endonucleases with the discovery that RuvC, CCE1 and A22R share a common catalytic core. [source]

Polyploidy in atypical grade II choroid plexus papilloma of the posterior fossa

NEUROPATHOLOGY, Issue 3 2009
María Sol Brassesco
Cytogenetic studies of choroid plexus tumors, particularly for atypical choroid plexus papillomas, have been rarely described. In the present report, the cytogenetic investigation of an atypical choroid plexus papilloma occurring at the posterior fossa of a 16-year-old male is described. Comparative genome hybridization analysis demonstrated gains of genetic material from almost all chromosomes. Chromosome losses involved 19p, regional losses at chromosome X and loss of chromosome Y. The presence of polyploid cells was confirmed by fluorescence in situ hybridization analysis with probes directed to centromeric regions. Furthermore, the microscopic analysis of cultures showed nuclear buds, nucleoplasmic bridges, and micronuclei in 23% of tumor cells suggesting the presence of complex chromosomal abnormalities. Previous cytogenetic studies on choroid plexus papillomas showed either normal, hypodiploid or hyperdiploid karyotypes. To the best of our knowledge, this is the first report of polyploidy in choroid plexus papilloma of intermediate malignancy grade. Although the mechanisms beneath such genome duplication remain to be elucidated, the observed abnormal nuclear shapes indicate constant restructuring of the tumor's genome and deserves further investigation. [source]

Selenium metabolism in zebrafish: multiplicity of selenoprotein genes and expression of a protein containing 17 selenocysteine residues

GENES TO CELLS, Issue 12 2000
Gregory V. Kryukov
Fish are an important source of selenium in human nutrition and the zebrafish is a potentially useful model organism for the study of selenium metabolism and its role in biology and medicine. Selenium is present in vertebrate proteins in the form of selenocysteine (Sec), the 21st natural amino acid in protein which is encoded by UGA. We report here the detection of 18 zebrafish genes for Sec-containing proteins. We found two zebrafish orthologs of human SelT, glutathione peroxidase 1 and glutathione peroxidase 4, and single orthologs of several other selenoproteins. In addition, new zebrafish selenoproteins were identified that were distant homologues of SelP, SelT and SelW, but their direct orthologs in other species are not known. This multiplicity of selenoprotein genes appeared to result from gene and genome duplications, followed by the retention of new selenoprotein genes. We found a zebrafish selenoprotein P gene (designated zSelPa) that contained two Sec insertion sequence (SECIS) elements and encoded a protein containing 17 Sec residues, the largest number of Sec residues found in any known protein. In contrast, a second SelP gene (designated zSelPb) was also identified that contained one SECIS element and encoded a protein with a single Sec. We found that zSelPa could be expressed and secreted by mammalian cells. The occurrence of zSelPa and zSelPb suggested that the function of the N-terminal domain of mammalian SelP proteins may be separated from that of the C-terminal Sec-rich sequence: the N-terminal domain containing the UxxC motif is likely involved in oxidoreduction, whereas the C-terminal portion of the protein may function in selenium transport or storage. Our data also suggest that the utilization of Sec is more common in zebrafish than in previously characterized species, including mammals. [source]

The evolution of teleost pigmentation and the fish-specific genome duplication

Perspectives on polyploidy in plants , ancient and neo

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2004
MICHAEL D. BENNETT
It is timely to re-examine the phenomenon of polyploidy in plants. Indeed, the power of modern molecular technology to provide new insights, and the impetus of genomics, make polyploidy a fit, fashionable and futuristic topic for review. Some historical perspective is essential to understand the meaning of the terms, to recognize what is already known and what is dogma, and to frame incisive questions for future research. Polyploidy is important because life on earth is predominantly a polyploid phenomenon. Moreover, civilization is mainly powered by polyploid food , notably cereal endosperm. Ongoing uncertainty about the origin of triploid endosperm epitomizes our ignorance about somatic polyploidy. New molecular information makes it timely to reconsider how to identity polyploids and what is a polyploid state. A functional definition in terms of a minimal genome may be helpful. Genes are known that can raise or lower ploidy level. Molecular studies can test if, contrary to dogma, the relationship between diploids and polyploids is a dynamic two-way system. We still need to understand the mechanisms and roles of key genes controlling ploidy level and disomic inheritance. New evidence for genome duplications should be compared with old ideas about cryptopolyploidy, and new views of meiosis should not ignore premeiotic genome separation. In practice, new knowledge about polyploidy will be most useful only when it reliably predicts which crops can be usefully improved as stable autopolyploids and which genomes combined to create successful new allopolyloids. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 411,423. [source]

Polyploidy and new chromosome counts in Helichrysum (Asteraceae, Gnaphalieae)

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2008
MERCÈ GALBANY-CASALS
Mitotic chromosome numbers are reported for 31 populations representing 28 taxa of Helichrysum. Twelve are new and eight others provide confirmation of a unique previous reference. A new chromosome number, 2n = 42, is reported for H. odoratissimum. Polyploidy is confirmed as the most significant evolutionary trend in chromosome number within the genus. Chromosome data agree with trends observed in phylogenetic studies: a South African and diploid origin of the genus, followed by a radiation and diversification in southern Africa and several migrations towards the north of the African continent, the Mediterranean basin and Asia. Expansion and diversification of the genus have been accompanied by several genome duplications which have led to the acquisition of the tetraploid, hexaploid and octoploid levels, all in several independent events. Both autopolyploidy and allopolyploidy are suggested as probable speciation agents within the genus. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 511,521. [source]