bib gene duplication (2002)

Bibliography on gene and genome duplication (2002)

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L Abi-Rached, A Gilles, T Shiina, P Pontarotti, H Inoko (2002), "Evidence of en bloc duplication in vertebrate genomes", Nature Genetics, 31:100-105.
Jeffrey A Bailey, Zhiping Gu, Royden A Clark, Knut Reinert, Rhea V Samonte, Stuart Schwartz, Mark D Adams, Eugene W Myers, Peter W Li, Evan E. Eichler (2002),
"Recent segmental duplications in the human genome", Science, 297:1003-1007.
Jeffrey A Bailey, Amy M Yavor, Luigi Viggiano, Doriana Misceo, Juliann E. Horvath, Nicoletta Archidiacono, Stuart Schwartz, Mariano Rocchi, Evan E. Eichler (2002), "Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22 ", American Journal of Human Genetics, 70:83-100.
Esther Betran, Manyuan Long (2002), "Expansion of genome coding regions by acquisition of new genes", Genetica, 115(1):65-80.
[ abstract]
Ashish Bhan , David J Galas, T Gregory Dewey (2002), "A duplication growth model of gene expression networks", Bioinformatics, 18(11):1486-1493.
[abstract]
Guillaume Bourque, Pavel A Pevzner (2002),
"Genome-scale evolution: reconstructing gene orders in the ancestral species",
Genome Research, 112:26-36.
Sean B Carroll (2002) "Homeotic genes and the evolution of arthropods and chordates", Nature, 376:479-485.
[abstract]
Gavin C Conant, Andreas Wagner (2002), "GenomeHistory: a software tool and its application to fully sequenced genomes", Nucleic Acids Research, 30(15):3378-3386.
[abstract]
Rick Durrett (2002), Probability Models for DNA Sequence Evolution (Springer). ISBN 038795435X
N El-Mabrouk (2002), "Reconstructing an ancestral genome using minimum segments duplications and reversals", Journal of Computer and System Sciences, 65:442-464.
RF Furlong, PWH Holland (2002), "Were vertebrates octoploid?", Philosophical Transactions of Royal Society B: Biological Sciences, 357:531-544.
abstract: It has long been suggested that gene and genome duplication play important roles in the evolution of organismal complexity. For example, work by Ohno proposed that two rounds of whole genome doubling (tetraploidy) occurred during the evolution of vertebrates: the extra genes permitting an increase in physiological and anatomical complexity. Several modifications of this 'two tetraploidies' hypothesis have been proposed, taking into account accumulating data, and there is wide acceptance of the basic scheme. In the past few years, however, several authors have raised doubts, citing lack of direct support or even evidence to the contrary. Here, we review the evidence for and against the occurrence of tetraploidies in early vertebrate evolution, and present a new compilation of molecular phylogenetic data for amphioxus. We argue that evidence in favour of tetraploidy, based primarily on genome and gene family analyses, is strong. Furthermore, we show that two observations used as evidence against genome duplication are in fact compatible with the hypothesis: but only if the genome doubling occurred by two closely spaced sequential rounds of autotetraploidy. We propose that early vertebrates passed through an autoautooctoploid phase in the evolution of their genomes.
Xun Gu, Wei Huang (2002), "Testing the parsimony test of genome duplications: a counterexample",
Genome Research, 12:1-2.
[ PDF]
X Gu, Y Wang, J Gu (2002), "Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution", Nature Genetics, 31:205-209.
Zhenglong Gu, Andre Cavalcanti, Feng-Chi Chen, Peter Bouman, Wen-Hsiung Li (2002), "Extent of gene duplication in the genomes of Drosophila, Nematode, and Yeast", Molecular Biology and Evolution, 19:256-262.
[PDF]
Z Gu, D Nicolae, HS Lu, WH Li (2002), "Rapid divergence in expression between duplicate genes inferred from microarray gene expression data", Trends in Genetics, 18:609-613.
[ abstract]
Ken Inoue, James R Lupski (2002), "Molecular mechanisms for genomic disorders", Annual Review of Genomics and Human Genetics, 3:199-242.
[ abstract] [ Abstract: Genomic rearrangements play a major role in the pathogenesis of human genetic diseases. Nonallelic homologous recombination (NAHR) between low-copy repeats (LCRs) that flank unique genomic segments results in changes of genome organization and can cause a loss or gain of genomic segments. These LCRs appear to have arisen recently during primate speciation via paralogous segmental duplication, thus making the human species particularly susceptible to genomic rearrangements. Genomic disorders are defined as a group of diseases that result from genomic rearrangements, mostly mediated by NAHR. Molecular investigations of genomic disorders have revealed genome architectural features associated with susceptibility to rearrangements and the recombination mechanisms responsible for such rearrangements. The human genome sequence project reveals that LCRs may account for 5% of the genome, suggesting that many novel genomic disorders might still remain to be recognized. ]
Fyodor A Kondrashov, Igor B Rogozin, Yuri I Wolf, Eugene V Koonin1 (2002),
"Selection in the evolution of gene duplications",
Genome Biology, 3(2):research0008.1-0008.9.
Jerzy K. Kulski Takashi Shiina, Tatsuya Anzai, Sakae Kohara, Hidetoshi Inoko (2002) "Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man", Immunological Reviews, 190(1):95-122.
[ abstract]
I Letunic, RR Copley, P Bork (2002), "Common exon duplication in animals and its role in alternative splicing", Human Molecular Genetics, 11(13):1561-1567.
[abstract]
AA Levy, M Feldman (2002), "The impact of polyploidy on grass genome evolution", Plant Physiology, 130:1587-1593.
Dan Larhammar, Lars-Gustav Lundin, and Finn Hallböök (2002), "The human Hox-bearing chromosome regions did srise by block or chromosome (or even genome) duplications", Genome Research, 12:1910-1920.
[abstract]
A Locascio, M. Manzanares, MJ Blancom MA Neito (200), "Modularity and reshuffling of Snail and Slug expression during vertebrate evolution", Proceedings of National Academy of Sciences, 99:16841-16846.
M Lynch (2002),
"Gene duplication and evolution" (in perspectives),
Science, 297: 945-947.
J McClintock, M Kheirbek, VE Prince (2002), "Knock-down of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention", Development, 129:2339-2354.
A McLysaght, K Hokamp, KH Wolfe (2002), "Extensive genomic duplication during early chordate evolution", Nature Genetics, 31:200-204.
V Nembaware, K Crum, J Kelso, C Seoighe (2002), "Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs", Genome Research, 12(9):1370-1376.
[abstract]
SP Otto, P Yong (2002), "The evolution of gene duplicates", Adv. Genetics, 46:451-483.
Victoria E Prince (2002), "The Hox paradox: more complex(es) than imagined", Developmental Biology, 249(1):1-15.
[ abstract]
VE Prince, FB Pickett (2002), "Splitting pairs: diverging fates of duplicated genes", Nature Reviews Genetics, 3:827-837.
C Simillion, K Vandepoele, M Van Montagu, M Zabeau, Y van de Peer (2002), "The hidden duplication past of Arabidopsis thaliana", Proceedings of National Academy of Sciences, 99:13627-13632.
M Skaer, D Pistillo, JM Gibert, P Lio, C Wulbeck, P Simpson (2002), "Gene duplication at the achaete-scute complex and morphological complexity of the peripheral nervous system in Diptera", Trends in Genetics, 18(8): 399-405.
abstract: The number of achaete-scute genes increased during insect evolution, particularly in the Diptera lineage. Sequence comparison indicates that the four achaete-scute genes of Drosophila result from three independent duplication events. After duplication, the new genes acquired individual expression patterns but, in Drosophila, their products can compensate for one another, which raises the question: why retain all four genes? The complexity of the spatial expression of these genes on the notum increased in the lineage leading to the higher Diptera, allowing the development of stereotyped bristle patterns. This probably coincided in time with gene duplication events, raising the possibility that an increase in gene copy number might have provided the flexibility necessary for more complex transcriptional regulation.
Y van de Peer, T Frickey, JS Taylor, A Meyer (2002), "Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes", Gene, 295:205-211.
Y van de Peer, JS Taylor, A Meyer (2002), "Wanda: A database of duplicated fish genes", Nucleic Acids Research, 30:109-112.
[abstract]
K Vandepoele, C Simillion, Y van de Peer (2002), "Detecting the undetectable: Uncovering duplicated segments in Arabidopsis by comparison with rice", Trends in Genetics, 18:606-608.
Andreas Wagner (2002), "Selection and gene duplication: a view from the genome", Genome Biology, 3(5):reviews1012.
Andreas Wagner (2002), "Asymmetric functional divergence of duplicate genes", Molecular Biology and Evolution, 19:1760-1768.
Jonathan F Wendel, RC Cronn (2002), "Polyploidy and the evolutionary history of cotton", Advances in Agronomy, 87:139-186.

		Bibliography on gene and genome duplication (2002)
	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, A Gilles, T Shiina, P Pontarotti, H Inoko (2002), "Evidence of en bloc duplication in vertebrate genomes", Nature Genetics, 31:100-105. Jeffrey A Bailey, Zhiping Gu, Royden A Clark, Knut Reinert, Rhea V Samonte, Stuart Schwartz, Mark D Adams, Eugene W Myers, Peter W Li, Evan E. Eichler (2002), "Recent segmental duplications in the human genome", Science, 297:1003-1007. Jeffrey A Bailey, Amy M Yavor, Luigi Viggiano, Doriana Misceo, Juliann E. Horvath, Nicoletta Archidiacono, Stuart Schwartz, Mariano Rocchi, Evan E. Eichler (2002), "Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22 ", American Journal of Human Genetics, 70:83-100. Esther Betran, Manyuan Long (2002), "Expansion of genome coding regions by acquisition of new genes", Genetica, 115(1):65-80. [ abstract] Ashish Bhan , David J Galas, T Gregory Dewey (2002), "A duplication growth model of gene expression networks", Bioinformatics, 18(11):1486-1493. [abstract] Guillaume Bourque, Pavel A Pevzner (2002), "Genome-scale evolution: reconstructing gene orders in the ancestral species", Genome Research, 112:26-36. Sean B Carroll (2002) "Homeotic genes and the evolution of arthropods and chordates", Nature, 376:479-485. [abstract] Gavin C Conant, Andreas Wagner (2002), "GenomeHistory: a software tool and its application to fully sequenced genomes", Nucleic Acids Research, 30(15):3378-3386. [abstract] Rick Durrett (2002), Probability Models for DNA Sequence Evolution (Springer). ISBN 038795435X N El-Mabrouk (2002), "Reconstructing an ancestral genome using minimum segments duplications and reversals", Journal of Computer and System Sciences, 65:442-464. RF Furlong, PWH Holland (2002), "Were vertebrates octoploid?", Philosophical Transactions of Royal Society B: Biological Sciences, 357:531-544. abstract: It has long been suggested that gene and genome duplication play important roles in the evolution of organismal complexity. For example, work by Ohno proposed that two rounds of whole genome doubling (tetraploidy) occurred during the evolution of vertebrates: the extra genes permitting an increase in physiological and anatomical complexity. Several modifications of this 'two tetraploidies' hypothesis have been proposed, taking into account accumulating data, and there is wide acceptance of the basic scheme. In the past few years, however, several authors have raised doubts, citing lack of direct support or even evidence to the contrary. Here, we review the evidence for and against the occurrence of tetraploidies in early vertebrate evolution, and present a new compilation of molecular phylogenetic data for amphioxus. We argue that evidence in favour of tetraploidy, based primarily on genome and gene family analyses, is strong. Furthermore, we show that two observations used as evidence against genome duplication are in fact compatible with the hypothesis: but only if the genome doubling occurred by two closely spaced sequential rounds of autotetraploidy. We propose that early vertebrates passed through an autoautooctoploid phase in the evolution of their genomes. Xun Gu, Wei Huang (2002), "Testing the parsimony test of genome duplications: a counterexample", Genome Research, 12:1-2. [ PDF] X Gu, Y Wang, J Gu (2002), "Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution", Nature Genetics, 31:205-209. Zhenglong Gu, Andre Cavalcanti, Feng-Chi Chen, Peter Bouman, Wen-Hsiung Li (2002), "Extent of gene duplication in the genomes of Drosophila, Nematode, and Yeast", Molecular Biology and Evolution, 19:256-262. [PDF] Z Gu, D Nicolae, HS Lu, WH Li (2002), "Rapid divergence in expression between duplicate genes inferred from microarray gene expression data", Trends in Genetics, 18:609-613. [ abstract] Ken Inoue, James R Lupski (2002), "Molecular mechanisms for genomic disorders", Annual Review of Genomics and Human Genetics, 3:199-242. [ abstract] [ Abstract: Genomic rearrangements play a major role in the pathogenesis of human genetic diseases. Nonallelic homologous recombination (NAHR) between low-copy repeats (LCRs) that flank unique genomic segments results in changes of genome organization and can cause a loss or gain of genomic segments. These LCRs appear to have arisen recently during primate speciation via paralogous segmental duplication, thus making the human species particularly susceptible to genomic rearrangements. Genomic disorders are defined as a group of diseases that result from genomic rearrangements, mostly mediated by NAHR. Molecular investigations of genomic disorders have revealed genome architectural features associated with susceptibility to rearrangements and the recombination mechanisms responsible for such rearrangements. The human genome sequence project reveals that LCRs may account for 5% of the genome, suggesting that many novel genomic disorders might still remain to be recognized. ] Fyodor A Kondrashov, Igor B Rogozin, Yuri I Wolf, Eugene V Koonin1 (2002), "Selection in the evolution of gene duplications", Genome Biology, 3(2):research0008.1-0008.9. Jerzy K. Kulski Takashi Shiina, Tatsuya Anzai, Sakae Kohara, Hidetoshi Inoko (2002) "Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man", Immunological Reviews, 190(1):95-122. [ abstract] I Letunic, RR Copley, P Bork (2002), "Common exon duplication in animals and its role in alternative splicing", Human Molecular Genetics, 11(13):1561-1567. [abstract] AA Levy, M Feldman (2002), "The impact of polyploidy on grass genome evolution", Plant Physiology, 130:1587-1593. Dan Larhammar, Lars-Gustav Lundin, and Finn Hallböök (2002), "The human Hox-bearing chromosome regions did srise by block or chromosome (or even genome) duplications", Genome Research, 12:1910-1920. [abstract] A Locascio, M. Manzanares, MJ Blancom MA Neito (200), "Modularity and reshuffling of Snail and Slug expression during vertebrate evolution", Proceedings of National Academy of Sciences, 99:16841-16846. M Lynch (2002), "Gene duplication and evolution" (in perspectives), Science, 297: 945-947. J McClintock, M Kheirbek, VE Prince (2002), "Knock-down of duplicated zebrafish hoxb1 genes reveals distinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention", Development, 129:2339-2354. A McLysaght, K Hokamp, KH Wolfe (2002), "Extensive genomic duplication during early chordate evolution", Nature Genetics, 31:200-204. V Nembaware, K Crum, J Kelso, C Seoighe (2002), "Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs", Genome Research, 12(9):1370-1376. [abstract] SP Otto, P Yong (2002), "The evolution of gene duplicates", Adv. Genetics, 46:451-483. Victoria E Prince (2002), "The Hox paradox: more complex(es) than imagined", Developmental Biology, 249(1):1-15. [ abstract] VE Prince, FB Pickett (2002), "Splitting pairs: diverging fates of duplicated genes", Nature Reviews Genetics, 3:827-837. C Simillion, K Vandepoele, M Van Montagu, M Zabeau, Y van de Peer (2002), "The hidden duplication past of Arabidopsis thaliana", Proceedings of National Academy of Sciences, 99:13627-13632. M Skaer, D Pistillo, JM Gibert, P Lio, C Wulbeck, P Simpson (2002), "Gene duplication at the achaete-scute complex and morphological complexity of the peripheral nervous system in Diptera", Trends in Genetics, 18(8): 399-405. abstract: The number of achaete-scute genes increased during insect evolution, particularly in the Diptera lineage. Sequence comparison indicates that the four achaete-scute genes of Drosophila result from three independent duplication events. After duplication, the new genes acquired individual expression patterns but, in Drosophila, their products can compensate for one another, which raises the question: why retain all four genes? The complexity of the spatial expression of these genes on the notum increased in the lineage leading to the higher Diptera, allowing the development of stereotyped bristle patterns. This probably coincided in time with gene duplication events, raising the possibility that an increase in gene copy number might have provided the flexibility necessary for more complex transcriptional regulation. Y van de Peer, T Frickey, JS Taylor, A Meyer (2002), "Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes", Gene, 295:205-211. Y van de Peer, JS Taylor, A Meyer (2002), "Wanda: A database of duplicated fish genes", Nucleic Acids Research, 30:109-112. [abstract] K Vandepoele, C Simillion, Y van de Peer (2002), "Detecting the undetectable: Uncovering duplicated segments in Arabidopsis by comparison with rice", Trends in Genetics, 18:606-608. Andreas Wagner (2002), "Selection and gene duplication: a view from the genome", Genome Biology, 3(5):reviews1012. Andreas Wagner (2002), "Asymmetric functional divergence of duplicate genes", Molecular Biology and Evolution, 19:1760-1768. Jonathan F Wendel, RC Cronn (2002), "Polyploidy and the evolutionary history of cotton", Advances in Agronomy, 87:139-186.