bib gene duplication (1999)

Bibliography on gene and genome duplication (1999)

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L Abi-Rached, MF McDermott, P Pontarotti (1999), "The MHC big bang", Immunological Review, 167:33-44.
[ abstract: The human Major Histocompatibility Complex (MHC) shares similarities with three other chromosome regions in human. This could be the vestige of ancestral large scale duplications. We discuss here the possibility i) that these duplications occurred during two rounds of tetraploidization supposed to have taken place during chordate evolution before the jawed vertebrate radiation, and ii) that one of the quadruplicate regions, relaxed of functional constraints, gave rise to the vertebrate MHC by a quick round of gene cis-duplication and cis-exon shuffling. These different rounds of cis-duplications and exon shufflings allowed the emergence of new genes participating in novel biological functions i.e. adaptive immune responses. Cis-duplications and cis-exon shufflings are ongoing processes in the evolution of some of these genes in this region as they have occurred and were fixed at different times and in different lineages during vertebrate evolution. In contrast, other genes within the MHC have remained stable since the emergence of jawed vertebrates. ]
RC Cronn, RL Small, JF Wendel (1999), "Duplicated genes evolve independently after polyploid formation in cotton", Proceedings of National Academy of Sciences, 96(25):14406-14411.
[abstract]
R Dawkins, C Leelayuwat, S Gaudieri, G Tay, J Hui, S Cattley, P Martinez, J Kulski (1999), "Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease", Immunological Review, 167:275-304.
N El-Mabrouk, D Bryant, D Sankoff (1999), "Reconstructing the pre-doubling genome", in S Istrail, et al. eds Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB99) pp. 154-163 (ACM Press).
N. El-Mabrouk, D. Sankoff (1999), "On the reconstruction of ancient doubled circular genomes using minimum reversal", Genome Informatics, 10:83-93.
[PDF]
A Force, M Lynch, FB Pickett, A Amores, YL Yan, J Postlethwait (1999), "Preservation of duplicate genes by complementary, degenerative mutations", Genetics, 151:1531-1545.
[abstract]
PWH Holland (1999), "Gene duplication: past, present, and future", Seminars in Cell & Developmental Biology, 10(5):541-547.
AL Hughes (1999), "Phylogenics of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history", Journal of Molecular Evolution, 48:565-576.
abstract: It has been proposed that two rounds of duplication of the entire genome (polyploidization) occurred early in vertebrate history (the 2R hypothesis); and the observation that certain gene families important in regulating development have four members in vertebrates, as opposed to one in Drosophila, has been adduced as evidence in support of this hypothesis. However, such a pattern of relationship can be taken as support of the 2R hypothesis only if (1) the four vertebrate genes can be shown to have diverged after the origin of vertebrates, and (2) the phylogeny of the four vertebrate genes (A-D) exhibits a topology of the form (AB) (CD), rather than (A) (BCD). In order to test the 2R hypothesis, I constructed phylogenies for nine protein families important in development. Only one showed a topology of the form (AB) (CD), and that received weak statistical support. In contrast, four phylogenies showed topologies of the form (A) (BCD) with statistically significant support. Furthermore, in two cases there was significant support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes: in one case there was significant support for duplication of the vertebrate genes at least prior to the divergence of vertebrates and urochordates, and in one case there was weak support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes. Taken together with other recently published phylogenies of developmentally important genes, these results provide strong evidence against the 2R hypothesis.
M Kasahara (1999), "Genome dynamics of the major histocompatibility complex: insights from genome paralogy", Immunogenetics, 50:134-145.
M Kasahara (1999), "The chromosomal duplication model of the major histocompatibility complex", Immunological Review, 167:17-32.
R Martienssen, V Irish (1999), "Copying out our ABCs: the role of gene redundancy in interpreting genetic hierarchies", Trends in Genetics, 15(11):435-437.
AP Martin (1999), "Increasing genomic complexity by gene duplication and the origin of vertebrates", The American Naturalist, 154:111-128.
[PDF]
A Meyer, M Schartl (1999), "Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions", Current Opinion in Cell Biology, 11:699-704.
abstract: One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the 'one-to-two-to-four' rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest that later in the Devonian, the fish genome was duplicated for a third time to produce up to eight copies of the original deuterostome genome. This last duplication took place after the two major radiations of jawed vertebrate life, the ray-finned fish (Actinopterygia) and the sarcopterygian lineage, diverged. Therefore the sarcopterygian fish, which includes the coelacanth, lungfish and all land vertebrates such as amphibians, reptiles, birds and mammals, tend to have only half the number of genes compared with actinopterygian fish. Although many duplicated genes turned into pseudogenes, or even 'junk' DNA, many others evolved new functions particularly during development. The increased genetic complexity of fish might reflect their evolutionary success and diversity.
Patrick J O'Brien, Daniel Herschlag (1999), "Catalytic promiscuity and the evolution of new enzymatic activities", Chemistry & Biology, 6(4):R91-R105.
[abstract] abstract: Several contemporary enzymes catalyze alternative reactions distinct from their normal biological reactions. In some cases the alternative reaction is similar to a reaction that is efficiently catalyzed by an evolutionary related enzyme. Alternative activities could have played an important role in the diversification of enzymes by providing a duplicated gene a head start towards being captured by adaptive evolution.
Susumu Ohno (1999), "Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999", Seminars in Cell and Developmental Biology, 10(5):517-522.
[abstract]
C Semple, KH Wolfe (1999), "Gene duplication and gene conversion in the Caenorhabditis elegans genome", Journal of Molecular Evolution, 48:555-564.
[ PDF ]
abstract: A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only 2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative rates of duplication and deletion may contribute to the compactness of the C. elegans genome.
C Seoighe, KH Wolfe (1999), "Updated map of duplicated regions in the yeast genome", Gene, 238: 253-261.
[PDF]
abstract: We have updated the map of duplicated chromosomal segments in the Saccharomyces cerevisiae genome originally published by Wolfe and Shields in 1997 (Nature 387, 708-713). The new analysis is based on the more sensitive Smith-Waterman search method instead of BLAST. The parameters used to identify duplicated chromosomal regions were optimized such as to maximize the amount of the genome placed into paired regions, under the assumption that the hypothesis that the entire genome was duplicated in a single event is correct. The core of the new map, with 52 pairs of regions containing three or more duplicated genes, is largely unchanged from our original map. 39 tRNA gene pairs and one snRNA pair have been added. To find additional pairs of genes that may have been formed by whole genome duplication, we searched through the parts of the genome that are not covered by this core map, looking for putative duplicated chromosomal regions containing only two duplicate genes instead of three, or having lower-scoring gene pairs. This approach identified a further 32 candidate paired regions, bringing the total number of protein-coding genes on the duplication map to 905 (16% of the proteome). The updated map suggests that a second copy of the ribosomal DNA array has been deleted from chromosome IV.
Nick GC Smith, Robert Knight, Laurence D Hurst (1999), "Vertebrate genome evolution: a slow shuffle or a big bang?", BioEssays, 21(8):697-703.
Abstract: In vertebrates it is often found that if one considers a group of genes clustered on a certain chromosome, then the homologues of those genes often form another cluster on a different chromosome. There are four explanations, not necessarily mutually exclusive, to explain how such homologous clusters appeared. Homologous clusters are expected at a low probability even if genes are distributed at random. The duplication of a subset of the genome might create homologous clusters, as would a duplication of the entire genome. Alternatively, it may be adaptive for certain combinations of genes to cluster, although clearly the genes must have duplicated prior to rearrangement into clusters. Molecular phylogenetics provides a means to examine the origins of homologous clusters, although it is difficult to discriminate between the different explanations using current data. However, with more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters.
Douglas E Soltis, Pamela S Soltis (1999), "Polyploidy: recurrent formation and genome evolution", Trends in Ecology and Evolution, 14(9):348-352.
[abstract]
EJ Stellwag (1999), "Hox gene duplication in fish", Seminars in Cell and Developmental Biology, 10(5):531-540.
[abstract]
A Stoltzfus (1999), "On the possibility of constructive neutral evolution", Journal of Molecular Evolution, 49:169-181.
Hiroshi Suga, Mitsumasa Koyanagi, Daisuke Hoshiyama, Kanako Ono, Naoyuki Iwabe, Kei-ichi Kuma, Takashi Miyata (1999), "Extensive gene duplication in the early evolution of animals before the Parazoan-Eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra", Journal of Molecular Evolution, 48(6):1432-1432.
[abstract]
F Tekaia, B Dujon (1999), "Pervasiveness of gene conservation and persistence of duplicates in cellular genomes", Journal of Molecular Evolution, 49:591-600.
A Wagner (1999), "Redundant Gene Functions and Natural Selection", Journal of Evolutionary Biology, 12:1-16.

		Bibliography on gene and genome duplication (1999)
	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	L Abi-Rached, MF McDermott, P Pontarotti (1999), "The MHC big bang", Immunological Review, 167:33-44. [ abstract: The human Major Histocompatibility Complex (MHC) shares similarities with three other chromosome regions in human. This could be the vestige of ancestral large scale duplications. We discuss here the possibility i) that these duplications occurred during two rounds of tetraploidization supposed to have taken place during chordate evolution before the jawed vertebrate radiation, and ii) that one of the quadruplicate regions, relaxed of functional constraints, gave rise to the vertebrate MHC by a quick round of gene cis-duplication and cis-exon shuffling. These different rounds of cis-duplications and exon shufflings allowed the emergence of new genes participating in novel biological functions i.e. adaptive immune responses. Cis-duplications and cis-exon shufflings are ongoing processes in the evolution of some of these genes in this region as they have occurred and were fixed at different times and in different lineages during vertebrate evolution. In contrast, other genes within the MHC have remained stable since the emergence of jawed vertebrates. ] RC Cronn, RL Small, JF Wendel (1999), "Duplicated genes evolve independently after polyploid formation in cotton", Proceedings of National Academy of Sciences, 96(25):14406-14411. [abstract] R Dawkins, C Leelayuwat, S Gaudieri, G Tay, J Hui, S Cattley, P Martinez, J Kulski (1999), "Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease", Immunological Review, 167:275-304. N El-Mabrouk, D Bryant, D Sankoff (1999), "Reconstructing the pre-doubling genome", in S Istrail, et al. eds Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB99) pp. 154-163 (ACM Press). N. El-Mabrouk, D. Sankoff (1999), "On the reconstruction of ancient doubled circular genomes using minimum reversal", Genome Informatics, 10:83-93. [PDF] A Force, M Lynch, FB Pickett, A Amores, YL Yan, J Postlethwait (1999), "Preservation of duplicate genes by complementary, degenerative mutations", Genetics, 151:1531-1545. [abstract] PWH Holland (1999), "Gene duplication: past, present, and future", Seminars in Cell & Developmental Biology, 10(5):541-547. AL Hughes (1999), "Phylogenics of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history", Journal of Molecular Evolution, 48:565-576. abstract: It has been proposed that two rounds of duplication of the entire genome (polyploidization) occurred early in vertebrate history (the 2R hypothesis); and the observation that certain gene families important in regulating development have four members in vertebrates, as opposed to one in Drosophila, has been adduced as evidence in support of this hypothesis. However, such a pattern of relationship can be taken as support of the 2R hypothesis only if (1) the four vertebrate genes can be shown to have diverged after the origin of vertebrates, and (2) the phylogeny of the four vertebrate genes (A-D) exhibits a topology of the form (AB) (CD), rather than (A) (BCD). In order to test the 2R hypothesis, I constructed phylogenies for nine protein families important in development. Only one showed a topology of the form (AB) (CD), and that received weak statistical support. In contrast, four phylogenies showed topologies of the form (A) (BCD) with statistically significant support. Furthermore, in two cases there was significant support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes: in one case there was significant support for duplication of the vertebrate genes at least prior to the divergence of vertebrates and urochordates, and in one case there was weak support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes. Taken together with other recently published phylogenies of developmentally important genes, these results provide strong evidence against the 2R hypothesis. M Kasahara (1999), "Genome dynamics of the major histocompatibility complex: insights from genome paralogy", Immunogenetics, 50:134-145. M Kasahara (1999), "The chromosomal duplication model of the major histocompatibility complex", Immunological Review, 167:17-32. R Martienssen, V Irish (1999), "Copying out our ABCs: the role of gene redundancy in interpreting genetic hierarchies", Trends in Genetics, 15(11):435-437. AP Martin (1999), "Increasing genomic complexity by gene duplication and the origin of vertebrates", The American Naturalist, 154:111-128. [PDF] A Meyer, M Schartl (1999), "Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions", Current Opinion in Cell Biology, 11:699-704. abstract: One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the 'one-to-two-to-four' rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest that later in the Devonian, the fish genome was duplicated for a third time to produce up to eight copies of the original deuterostome genome. This last duplication took place after the two major radiations of jawed vertebrate life, the ray-finned fish (Actinopterygia) and the sarcopterygian lineage, diverged. Therefore the sarcopterygian fish, which includes the coelacanth, lungfish and all land vertebrates such as amphibians, reptiles, birds and mammals, tend to have only half the number of genes compared with actinopterygian fish. Although many duplicated genes turned into pseudogenes, or even 'junk' DNA, many others evolved new functions particularly during development. The increased genetic complexity of fish might reflect their evolutionary success and diversity. Patrick J O'Brien, Daniel Herschlag (1999), "Catalytic promiscuity and the evolution of new enzymatic activities", Chemistry & Biology, 6(4):R91-R105. [abstract] abstract: Several contemporary enzymes catalyze alternative reactions distinct from their normal biological reactions. In some cases the alternative reaction is similar to a reaction that is efficiently catalyzed by an evolutionary related enzyme. Alternative activities could have played an important role in the diversification of enzymes by providing a duplicated gene a head start towards being captured by adaptive evolution. Susumu Ohno (1999), "Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999", Seminars in Cell and Developmental Biology, 10(5):517-522. [abstract] C Semple, KH Wolfe (1999), "Gene duplication and gene conversion in the Caenorhabditis elegans genome", Journal of Molecular Evolution, 48:555-564. [ PDF ] abstract: A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only 2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative rates of duplication and deletion may contribute to the compactness of the C. elegans genome. C Seoighe, KH Wolfe (1999), "Updated map of duplicated regions in the yeast genome", Gene, 238: 253-261. [PDF] abstract: We have updated the map of duplicated chromosomal segments in the Saccharomyces cerevisiae genome originally published by Wolfe and Shields in 1997 (Nature 387, 708-713). The new analysis is based on the more sensitive Smith-Waterman search method instead of BLAST. The parameters used to identify duplicated chromosomal regions were optimized such as to maximize the amount of the genome placed into paired regions, under the assumption that the hypothesis that the entire genome was duplicated in a single event is correct. The core of the new map, with 52 pairs of regions containing three or more duplicated genes, is largely unchanged from our original map. 39 tRNA gene pairs and one snRNA pair have been added. To find additional pairs of genes that may have been formed by whole genome duplication, we searched through the parts of the genome that are not covered by this core map, looking for putative duplicated chromosomal regions containing only two duplicate genes instead of three, or having lower-scoring gene pairs. This approach identified a further 32 candidate paired regions, bringing the total number of protein-coding genes on the duplication map to 905 (16% of the proteome). The updated map suggests that a second copy of the ribosomal DNA array has been deleted from chromosome IV. Nick GC Smith, Robert Knight, Laurence D Hurst (1999), "Vertebrate genome evolution: a slow shuffle or a big bang?", BioEssays, 21(8):697-703. Abstract: In vertebrates it is often found that if one considers a group of genes clustered on a certain chromosome, then the homologues of those genes often form another cluster on a different chromosome. There are four explanations, not necessarily mutually exclusive, to explain how such homologous clusters appeared. Homologous clusters are expected at a low probability even if genes are distributed at random. The duplication of a subset of the genome might create homologous clusters, as would a duplication of the entire genome. Alternatively, it may be adaptive for certain combinations of genes to cluster, although clearly the genes must have duplicated prior to rearrangement into clusters. Molecular phylogenetics provides a means to examine the origins of homologous clusters, although it is difficult to discriminate between the different explanations using current data. However, with more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters. Douglas E Soltis, Pamela S Soltis (1999), "Polyploidy: recurrent formation and genome evolution", Trends in Ecology and Evolution, 14(9):348-352. [abstract] EJ Stellwag (1999), "Hox gene duplication in fish", Seminars in Cell and Developmental Biology, 10(5):531-540. [abstract] A Stoltzfus (1999), "On the possibility of constructive neutral evolution", Journal of Molecular Evolution, 49:169-181. Hiroshi Suga, Mitsumasa Koyanagi, Daisuke Hoshiyama, Kanako Ono, Naoyuki Iwabe, Kei-ichi Kuma, Takashi Miyata (1999), "Extensive gene duplication in the early evolution of animals before the Parazoan-Eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra", Journal of Molecular Evolution, 48(6):1432-1432. [abstract] F Tekaia, B Dujon (1999), "Pervasiveness of gene conservation and persistence of duplicates in cellular genomes", Journal of Molecular Evolution, 49:591-600. A Wagner (1999), "Redundant Gene Functions and Natural Selection", Journal of Evolutionary Biology, 12:1-16.