bib gene duplication (1997)

Bibliography on gene and genome duplication (1997)

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S Aparicio, K Hawker, A Cottage, Y Mikawa, L Zuo, B Venkatesh, E Chen, R Krumlauf, S Brenner (1997), "Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes", Nature Genetics, 16:79-83.
WJ Bailey, J Kim, GP Wagner and FH Ruddle (1997), "Phylogenetic reconstruction of vertebrate Hox cluster duplications", Molecular Biology and Evolution, 14:843-853.
[abstract]
David Briggs, Stuart Max Walters (1997), Plant Variation and Evolution (Cambridge University Press). ISBN 0521459184
Alexander D Cameron, Birgit Olin, Marianne Ridderström, Bengt Mannervik, TAlwyn Jones (1997), "Crystal structure of human glyoxalase I?evidence for gene duplication and 3D domain swapping", The EMBO Journal, 16:3386-3395.
[ abstract]
E Coissac, E Maillier, P Netter (1997), "A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres", Molecular Biology and Evolution, 14:1062-1074.
[ PDF]
T Endo, T Imanishi, T Gojobori, H Inoko (1997), "Evolutionary significance of intra-genome duplications on human chromosomes", Gene, 205: 19-27
abstract: Phylogenetic analyses indicated that a series of paralogous gene pairs, found in two extensive regions on human chromosomal bands 6p21.3 and 9q33-34, were created by at least two independent duplications. The duplicated genes on chromosomal band 6p21.3 include the genes for type 11 collagen 2 subunit (COL11A2), NOTCH4 (mouse int-3 homologue), 70 kDa heat shock protein (HSPA1A, HSPA1B, and HSPA1L), valyl-tRNA synthetase 2 (VARS2), complement components (C2 and C4), pre-B cell leukemia transcription factor 2 (PBX2), retinoid X receptor (RXRB), NAT/RING3, and four other proteins. Their paralogous genes on chromosomal band 9q33-34 are genes for type 5 collagen 1 subunit (COL5A1), NOTCH1, 78 kDa glucose-regulated protein (HSPA5), valyl-tRNA synthetase 1 (VARS1), complement component V (C5), PBX3, retinoid X receptor (RXRA), ORFX/RING3L, and others. Among these, the genes for collagen, complement components, NAT/RING3, PBX, and RXR appear to have been duplicated around the time of vertebrate emergence, supporting the idea that they were duplicated simultaneously at that time. Another group of genes that includes NOTCH and HSP appear to have diverged long before that time. A comparison of the physical maps of these two regions revealed that the genes which duplicated in the same period were arranged in almost the same order in the two regions, with the assumption of a few chromosomal rearrangements. We propose a possible model for the evolution of these regions, taking into account the molecular mechanisms of regional duplication, gene duplication, translocation, and inversion. We also propose that a comparative mapping of paralogous genes within the human genome would be useful for identifying new genes.
Hector Escriva, Rachid Safi, Catherine Hänni, Marie-Claire Langlois, Pierre Saumitou-Laprade, Dominique Stehelin, André Capron, Raymond Pierce, Vincent Laudet (1997), "Ligand binding was acquired during evolution of nuclear receptors", Proceedings of National Academy of Sciences, 94:6803-6808.
[abstract]
BS Gaut, JF Doebley (1997), "DNA sequence evidence for the segmental allotetraploid origin of maize", Proceedings of National Academy of Sciences, 94:6809-6814.
Comments by Skrabanek and Wolfe (1998) : The authors propose that the duplicated regions of the maize genome arose from segmental allotetraploidy and they provide a very clear and reasoned explanation of their model. Molecular clock analysis of 14 maize gene pairs yielded two non-overlapping groups of date estimates centred on 11.4 and 20.5 Mya. An allotetraploid ancestor is proposed to have gone through a phase of tetrasomic inheritance - each locus has four alleles - before becoming 'diploidised' (disomic). At each locus, genetic drift during the tetrasomic phase might result in the loss of alleles inherited from one of the progenitor species, or alleles from both progenitors might be retained. Consequently, after diploidisation, the divergence time between the two sequences at a duplicated locus could correspond either to the speciation time between the two progenitors (20.5 Mya), or to the time of establishment of disomy (11.4 Mya). It would be impossible to predict the outcome for any particular locus.
S Henikoff, EA Greene, S Pietrokovski, P Bork, TK Attwood, L Hood (1997), "Gene families: the taxonomy of protein paralogs and chimeras", Science, 278:609-614.
PW Holland (1997), "Vertebrate evolution: something fishy about Hox genes", Current Biology, 7:R570-R572.
M Kasahara (1997), "New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system", Hereditas, 127:59-65.
M Kasahara, J Nakaya, Y Satta, N Takahata (1997), "Chromosomal duplication and the emergence of the adaptive immune system", Trends in Genetics, 13(3):90-92.
V Laudet (1997), "Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor", Journal of Molecular Endocrinology, 19(3):207-226.
[abstract]
IJ Leitch, MD Bennett (1997), "Polyploidy in angiosperms", Trends in Plant Science, 2:470-476.
B Mirkin, I Muchnik, TF Smith (1997), "A biologically consistent model for comparing molecular phylogenies", Journal of Computational Biology, 4:177-187.
abstract: In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model is employed for embedding a phylogeny tree into another one via the so-called duplication/speciation principle requiring that the gene duplicated evolves in such a way that any of the contemporary species involved bears only one of the gene copies diverged. The number of biologically meaningful elements in the embedding result (duplications, losses, information gaps) is considered a (asymmetric) dissimilarity measure between the trees. The model duplication concept is compared with that one defined previously in terms of a mapping procedure for the trees. A graph-theoretic reformulation of the measure is derived.
JH Nadeau, D Sankoff (1997), "Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution", Genetics, 147:1259-1266.
[abstract]
JA Scheffler, AG Sharpe, H Schmidt, P Sperling, IAP Parkin, W Lühs, DJ Lydiate, E Heinz (1997), "Desaturase multigene families of Brassica napus arose through genome duplication", TAG Theoretical and Applied Genetics, 94(5):583-591.
[ abstract]
J Spring (1997), "Vertebrate evolution by interspecific hybridization - are we polyploid?", FEBS Letters, 400:2-8.
Javier Tamames, Georg Casari, Christos Ouzounis, Alfonso Valencia (1997), "Conserved clusters of functionally related genes in two bacterial genomes", Journal of Molecular Evolution, 44(1):66-73.
abstract: An approach for genome comparison, combining function classification of gene products and sequence comparison, is presented. The genomes of Haemophilus influenzae and Escherichia coli are analyzed, and all genes are classified into nine major functional classes, corresponding to important cellular processes. To study gene order relationships and genome organization in the two bacteria, we performed statistics on neighboring pairs of genes. To estimate the significance of the observations, a statistical model based on binomial distributions has been developed. Significant patterns of gene order are observed within, as well as between, the two bacterial genomes: Functionally related genes tend to be neighbors more often than do unrelated genes. Some of these groups represent well-known operons, but additional gene clusters are identified. These clusters correspond to genomic elements that have been conserved during bacterial evolution. In addition to nearest-neighbor relationships, the method is also useful to study the relative direction of transcription in genomes, which is also highly conserved between homologous gene pairs. This new approach combines the high-level description of molecular function with pair statistics that express genome organization. It is expected to complement traditional methods of sequence analysis in the study of genomic structure, function, and evolution. ]
Hidemi Watanabe, Hirotada Mori, Takeshi Itoh, Takashi Gojobori (1997), "Genome plasticity as a paradigm of eubacteria evolution", Journal of Molecular Evolution, 44(suppl 1):S057-S064.
abstract: To test the hypotheses that eubacterial genomes leave evolutionarily stable structures and that the variety of genome size is brought about through genome doubling during evolution, the genome structures of Haemophilus influenzae, Mycoplasma genitalium, Escherichia coli, and Bacillus subtilis were compared using the DNA sequences of the entire genome or substantial portions of genome. In these comparisons, the locations of orthologous genes were examined among different genomes. Using orthologous genes for the comparisons guaranteed that differences revealed in physical location would reflect changes in genome structure after speciation. We found that dynamic rearrangements have so frequently occurred in eubacterial genomes as to break operon structures during evolution, even after the relatively recent divergence between E. coli and H. influenzae. Interestingly, in such eubacterial genomes of high plasticity, we could find several highly conservative regions with the longest conserved region comprising the S10, spc, and ! operons. This suggests that such exceptional conservative regions have undergone strong structural constraints during evolution. ]
KH Wolfe, DC Shields (1997), "Molecular evidence for an ancient duplication of the entire yeast genome", Nature, 387:708-713.
abstract: Gene duplication is an important source of evolutionary novelty. Most duplications are of just a single gene, but Ohno proposed that whole-genome duplication (polyploidy) is an important evolutionary mechanism. Many duplicate genes have been found in Saccharomyces cerevisiae, and these often seem to be phenotypically redundant. Here we show that the arrangement of duplicated genes in the S. cerevisiae genome is consistent with Ohno's hypothesis. We propose a model in which this species is a degenerate tetraploid resulting from a whole-genome duplication that occurred after the divergence of Saccharomyces from Kluyveromyces. Only a small fraction of the genes were subsequently retained in duplicate (most were deleted), and gene order was rearranged by many reciprocal translocations between chromosomes. Protein pairs derived from this duplication event make up 13% of all yeast proteins, and include pairs of transcription factors, protein kinases, myosins, cyclins and pheromones. Tetraploidy may have facilitated the evolution of anaerobic fermentation in Saccharomyces.

		Bibliography on gene and genome duplication (1997)
	front page glossary 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 1993 1992 1991 1990 80s 70s 60s 50s 40s 30s 20s 10s	S Aparicio, K Hawker, A Cottage, Y Mikawa, L Zuo, B Venkatesh, E Chen, R Krumlauf, S Brenner (1997), "Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes", Nature Genetics, 16:79-83. WJ Bailey, J Kim, GP Wagner and FH Ruddle (1997), "Phylogenetic reconstruction of vertebrate Hox cluster duplications", Molecular Biology and Evolution, 14:843-853. [abstract] David Briggs, Stuart Max Walters (1997), Plant Variation and Evolution (Cambridge University Press). ISBN 0521459184 Alexander D Cameron, Birgit Olin, Marianne Ridderström, Bengt Mannervik, TAlwyn Jones (1997), "Crystal structure of human glyoxalase I?evidence for gene duplication and 3D domain swapping", The EMBO Journal, 16:3386-3395. [ abstract] E Coissac, E Maillier, P Netter (1997), "A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres", Molecular Biology and Evolution, 14:1062-1074. [ PDF] T Endo, T Imanishi, T Gojobori, H Inoko (1997), "Evolutionary significance of intra-genome duplications on human chromosomes", Gene, 205: 19-27 abstract: Phylogenetic analyses indicated that a series of paralogous gene pairs, found in two extensive regions on human chromosomal bands 6p21.3 and 9q33-34, were created by at least two independent duplications. The duplicated genes on chromosomal band 6p21.3 include the genes for type 11 collagen 2 subunit (COL11A2), NOTCH4 (mouse int-3 homologue), 70 kDa heat shock protein (HSPA1A, HSPA1B, and HSPA1L), valyl-tRNA synthetase 2 (VARS2), complement components (C2 and C4), pre-B cell leukemia transcription factor 2 (PBX2), retinoid X receptor (RXRB), NAT/RING3, and four other proteins. Their paralogous genes on chromosomal band 9q33-34 are genes for type 5 collagen 1 subunit (COL5A1), NOTCH1, 78 kDa glucose-regulated protein (HSPA5), valyl-tRNA synthetase 1 (VARS1), complement component V (C5), PBX3, retinoid X receptor (RXRA), ORFX/RING3L, and others. Among these, the genes for collagen, complement components, NAT/RING3, PBX, and RXR appear to have been duplicated around the time of vertebrate emergence, supporting the idea that they were duplicated simultaneously at that time. Another group of genes that includes NOTCH and HSP appear to have diverged long before that time. A comparison of the physical maps of these two regions revealed that the genes which duplicated in the same period were arranged in almost the same order in the two regions, with the assumption of a few chromosomal rearrangements. We propose a possible model for the evolution of these regions, taking into account the molecular mechanisms of regional duplication, gene duplication, translocation, and inversion. We also propose that a comparative mapping of paralogous genes within the human genome would be useful for identifying new genes. Hector Escriva, Rachid Safi, Catherine Hänni, Marie-Claire Langlois, Pierre Saumitou-Laprade, Dominique Stehelin, André Capron, Raymond Pierce, Vincent Laudet (1997), "Ligand binding was acquired during evolution of nuclear receptors", Proceedings of National Academy of Sciences, 94:6803-6808. [abstract] BS Gaut, JF Doebley (1997), "DNA sequence evidence for the segmental allotetraploid origin of maize", Proceedings of National Academy of Sciences, 94:6809-6814. Comments by Skrabanek and Wolfe (1998) : The authors propose that the duplicated regions of the maize genome arose from segmental allotetraploidy and they provide a very clear and reasoned explanation of their model. Molecular clock analysis of 14 maize gene pairs yielded two non-overlapping groups of date estimates centred on 11.4 and 20.5 Mya. An allotetraploid ancestor is proposed to have gone through a phase of tetrasomic inheritance - each locus has four alleles - before becoming 'diploidised' (disomic). At each locus, genetic drift during the tetrasomic phase might result in the loss of alleles inherited from one of the progenitor species, or alleles from both progenitors might be retained. Consequently, after diploidisation, the divergence time between the two sequences at a duplicated locus could correspond either to the speciation time between the two progenitors (20.5 Mya), or to the time of establishment of disomy (11.4 Mya). It would be impossible to predict the outcome for any particular locus. S Henikoff, EA Greene, S Pietrokovski, P Bork, TK Attwood, L Hood (1997), "Gene families: the taxonomy of protein paralogs and chimeras", Science, 278:609-614. PW Holland (1997), "Vertebrate evolution: something fishy about Hox genes", Current Biology, 7:R570-R572. M Kasahara (1997), "New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system", Hereditas, 127:59-65. M Kasahara, J Nakaya, Y Satta, N Takahata (1997), "Chromosomal duplication and the emergence of the adaptive immune system", Trends in Genetics, 13(3):90-92. V Laudet (1997), "Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor", Journal of Molecular Endocrinology, 19(3):207-226. [abstract] IJ Leitch, MD Bennett (1997), "Polyploidy in angiosperms", Trends in Plant Science, 2:470-476. B Mirkin, I Muchnik, TF Smith (1997), "A biologically consistent model for comparing molecular phylogenies", Journal of Computational Biology, 4:177-187. abstract: In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model is employed for embedding a phylogeny tree into another one via the so-called duplication/speciation principle requiring that the gene duplicated evolves in such a way that any of the contemporary species involved bears only one of the gene copies diverged. The number of biologically meaningful elements in the embedding result (duplications, losses, information gaps) is considered a (asymmetric) dissimilarity measure between the trees. The model duplication concept is compared with that one defined previously in terms of a mapping procedure for the trees. A graph-theoretic reformulation of the measure is derived. JH Nadeau, D Sankoff (1997), "Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution", Genetics, 147:1259-1266. [abstract] JA Scheffler, AG Sharpe, H Schmidt, P Sperling, IAP Parkin, W Lühs, DJ Lydiate, E Heinz (1997), "Desaturase multigene families of Brassica napus arose through genome duplication", TAG Theoretical and Applied Genetics, 94(5):583-591. [ abstract] J Spring (1997), "Vertebrate evolution by interspecific hybridization - are we polyploid?", FEBS Letters, 400:2-8. Javier Tamames, Georg Casari, Christos Ouzounis, Alfonso Valencia (1997), "Conserved clusters of functionally related genes in two bacterial genomes", Journal of Molecular Evolution, 44(1):66-73. abstract: An approach for genome comparison, combining function classification of gene products and sequence comparison, is presented. The genomes of Haemophilus influenzae and Escherichia coli are analyzed, and all genes are classified into nine major functional classes, corresponding to important cellular processes. To study gene order relationships and genome organization in the two bacteria, we performed statistics on neighboring pairs of genes. To estimate the significance of the observations, a statistical model based on binomial distributions has been developed. Significant patterns of gene order are observed within, as well as between, the two bacterial genomes: Functionally related genes tend to be neighbors more often than do unrelated genes. Some of these groups represent well-known operons, but additional gene clusters are identified. These clusters correspond to genomic elements that have been conserved during bacterial evolution. In addition to nearest-neighbor relationships, the method is also useful to study the relative direction of transcription in genomes, which is also highly conserved between homologous gene pairs. This new approach combines the high-level description of molecular function with pair statistics that express genome organization. It is expected to complement traditional methods of sequence analysis in the study of genomic structure, function, and evolution. ] Hidemi Watanabe, Hirotada Mori, Takeshi Itoh, Takashi Gojobori (1997), "Genome plasticity as a paradigm of eubacteria evolution", Journal of Molecular Evolution, 44(suppl 1):S057-S064. abstract: To test the hypotheses that eubacterial genomes leave evolutionarily stable structures and that the variety of genome size is brought about through genome doubling during evolution, the genome structures of Haemophilus influenzae, Mycoplasma genitalium, Escherichia coli, and Bacillus subtilis were compared using the DNA sequences of the entire genome or substantial portions of genome. In these comparisons, the locations of orthologous genes were examined among different genomes. Using orthologous genes for the comparisons guaranteed that differences revealed in physical location would reflect changes in genome structure after speciation. We found that dynamic rearrangements have so frequently occurred in eubacterial genomes as to break operon structures during evolution, even after the relatively recent divergence between E. coli and H. influenzae. Interestingly, in such eubacterial genomes of high plasticity, we could find several highly conservative regions with the longest conserved region comprising the S10, spc, and ! operons. This suggests that such exceptional conservative regions have undergone strong structural constraints during evolution. ] KH Wolfe, DC Shields (1997), "Molecular evidence for an ancient duplication of the entire yeast genome", Nature, 387:708-713. abstract: Gene duplication is an important source of evolutionary novelty. Most duplications are of just a single gene, but Ohno proposed that whole-genome duplication (polyploidy) is an important evolutionary mechanism. Many duplicate genes have been found in Saccharomyces cerevisiae, and these often seem to be phenotypically redundant. Here we show that the arrangement of duplicated genes in the S. cerevisiae genome is consistent with Ohno's hypothesis. We propose a model in which this species is a degenerate tetraploid resulting from a whole-genome duplication that occurred after the divergence of Saccharomyces from Kluyveromyces. Only a small fraction of the genes were subsequently retained in duplicate (most were deleted), and gene order was rearranged by many reciprocal translocations between chromosomes. Protein pairs derived from this duplication event make up 13% of all yeast proteins, and include pairs of transcription factors, protein kinases, myosins, cyclins and pheromones. Tetraploidy may have facilitated the evolution of anaerobic fermentation in Saccharomyces.