Bibliography on gene and genome duplication (2000)

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  1. L Abi-Rached, P Pontarotti (2000), "The MHC 'big-bang': duplication and exon shuffling during chordate evolution: a hypothetico-deductive approach", in Major Histocompatibility Complex: Evolution, Structure, and Function , ed. M Kasahara (Springer-Verlag), pp.45-52.

  2. Arabidopsos Genome Initiative (2000), "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature, 408(6814):796-815.

  3. Guillaume Achaz, Eric Coissac, Alain Viari, Pierre Netter (2000), "Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: a possible model for their origin", Molecular Biology and Evolution, 17:1268-1275.
    abstract: The complete genome of the yeast Saccharomyces cerevisiae was investigated for intrachromosomal duplications at the level of nucleotide sequences. The analysis was performed by looking for long approximate repeats (from 30 to 3,885 bp) present on each of the chromosomes. We show that direct and inverted repeats exhibit very different characteristics: the two copies of direct repeats are more similar and longer than those of inverted repeats. Furthermore, contrary to the inverted repeats, a large majority of direct repeats appear to be closely spaced. The distance (delta) between the two copies is generally smaller than 1 kb. Further analysis of these "close direct repeats" shows a negative correlation between delta and the percentage of identity between the two copies, and a positive correlation between delta and repeat length. Moreover, contrary to the other categories of repeats, close direct repeats are mostly located within coding sequences (CDSs). We propose two hypotheses in order to interpret these observations: first, the deletion/conversion rate is negatively correlated with delta; second, there exists an active duplication mechanism which continuously creates close direct repeats, the other intrachromosomal repeats being the result, by chromosomal rearrangements of these "primary repeats."

  4. K Chen, D Durand, M Farach-Colton (2000), "Notung: a program for dating gene duplications and optimizing gene family trees", Journal of Computational Biology, 7(3/4):429-447.

  5. Luca Comai (2000), "Genetic and epigenetic interactions in allopolyploid plants", Plant Molecular Biology, 43:387-399.
    [ abstract]

  6. N El-Mabrouk (2000), "Genome rearrangement by reversals and insertions/deletions of contiguous segments", in Combinatorial Pattern Matching, 11th annual symposium, Lecture Notes in Computer Science, Vol 1848, pp. 222-234.

  7. N El-Mabrouk (2000), "Recovery of ancestral tetraploids", in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map alignment and the Evolution of Gene Families pp.465-477 (Kluwer Academic Publishers).

  8. N El-Mabrouk (2000), "Duplication, rearrangement and reconciliation", in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map alignment and the Evolution of Gene Families pp. 537-550 (Kluwer Academic Publishers).

  9. TJ Gibson, J Spring (2000), "Evidence in favor of ancient octaploidy in the vertebrate genome", Biochemical Society Transactions, 2:259-264.

  10. D Grant, P Cregan, RC Shoemaker (2000), "Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis", Proceedings of National Academy of Sciences, 97:4168-4173.
    abstract: Synteny between soybean and Arabidopsis was studied by using conceptual translations of DNA sequences from loci that map to soybean linkage groups A2, J, and L. Synteny was found between these linkage groups and all four of the Arabidopsis chromosomes, where GenBank contained enough sequence for synteny to be identified confidently. Soybean linkage group A2 (soyA2) and Arabidopsis chromosome I showed significant synteny over almost their entire lengths, with only 2-3 chromosomal rearrangements required to bring the maps into substantial agreement. Smaller blocks of synteny were identified between soyA2 and Arabidopsis chromosomes IV and V (near the RPP5 and RPP8 genes) and between soyA2 and Arabidopsis chromosomes I and V (near the PhyA and PhyC genes). These subchromosomal syntenic regions were themselves homeologous, suggesting that Arabidopsis has undergone a number of segmental duplications or possibly a complete genome duplication during its evolution. Homologies between the homeologous soybean linkage groups J and L and Arabidopsis chromosomes II and IV also revealed evidence of segmental duplication in Arabidopsis. Further support for this hypothesis was provided by the observation of very close linkage in Arabidopsis of homologs of soybean Vsp27 and Bng181 (three locations) and purple acid phosphatase-like sequences and homologs of soybean A256 (five locations). Simulations show that the synteny and duplications we report are unlikely to have arisen by chance during our analysis of the homology reports.

  11. HM Ku, T Vision, J Liu, SD Tanksley (2000), "Comparing sequence segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny", Proceedings of National Academy of Sciences, 97:9121-9126.

  12. RB Langkjaer, ML Nielsen, PR Daugaard, W Liu, J Piskur (2000), "Yeast chromosomes have been significantly reshaped during their evolutionary history", Journal of Molecular Biology, 304(3):271-288.

  13. M Lynch, JS Conery (2000), "The evolutionary fate and consequences of duplicate genes", Science, 290:1151-1155.
    [ PDF ]
    abstract: Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.

  14. M Lynch, A Force (2000), "The probability of duplicate gene preservation by subfunctionalization", Genetics, 154:459-473.
    [ PDF]
    abstract: It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 105 or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.

  15. M Lynch, AG Force (2000), "The origin of interspecific genomic incompatibility via gene duplication", The American Naturalist, 156:590-605.

  16. AP Martin (2000), "Choosing among alternative trees of multigene families", Molecular Phylogenetics and Evolution, 16:430-439.

  17. A McLysaght, AJ Enright, L Skrabanek, KH Wolfe (2000), "Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human", Yeast, 17:22-36.

  18. K Naruse, S Fukamachi, H Mitani, M Kondo, T Matsuoka, S Kondo, N Hanamura, Y Morita, K Hasegawa, R Nishigaki, A Shimada, H Wada, T Kusakabe, N Suzuki, M Kinoshita, A Kanamori, T Terado, H Kimura, M Nonaka, A Shima (2000), "A detailed linkage map of Medaka, Oryzias latipes: comparative genomics and genome evolution", Genetics, 154:1773-1784.

  19. Tomoko Ohta (2000), "Evolution of gene families", Gene, 259(1-2):45-52.
    [ abstract]

  20. SP Otto, J Whitton (2000), "Polyploid incidence and evolution", Annual Review of Genetics, 34:401-437.
    abstract: Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates that this phenomenon is a common and successful evolutionary transition, whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question. Here we review evidence for the creative role of polyploidy in evolution. We present new estimates for the incidence of polyploidy in ferns and flowering plants based on a simple model describing transitions between odd and even base chromosome numbers. These new estimates indicate that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in ferns. Speciation via polyploidy is likely to be one of the more predominant modes of sympatric speciation in plants, owing to its potentially broad-scale effects on gene regulation and developmental processes, effects that can produce immediate shifts in morphology, breeding system, and ecological tolerances. Theoretical models support the potential for increased adaptability in polyploid lineages. The evidence suggests that polyploidization can produce shifts in genetic systems and phenotypes that have the potential to result in increased evolutionary diversification, yet conclusive evidence that polyploidy has changed rates and patterns of diversification remains elusive.

  21. Eran Pichersky, David R Gang (2000), "Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective", Trends in Plant Science, 5(10):439-445.
    [ abstract]

  22. John H Postlethwait, Ian G Woods, Phuong Ngo-Hazelett, Yi-Lin Yan, Peter D Kelly, Felicia Chu, Hui Huang, Alicia Hill-Force, William S Talbot (2000), "Zebrafish comparative genomics and the origins of vertebrate chromosomes", Genome Research, 10(12):1890-1902.
    [abstract]

  23. Lorraine Potocki, Ken-Shiung Chen, Sung-Sup Park, Doreen E Osterholm, Marjorie A Withers, Virginia Kimonis, Anne M Summers, Wendy S Meschino, Kwame Anyane-Yeboa, Catherine D Kashork, Lisa G Shaffer, James R Lupski, (2000), "Molecular mechanism for duplication 17p11.2? the homologous recombination reciprocal of the Smith-Magenis microdeletion", Nature Genetics, 24:84-87.
    [ abstract]

  24. Leonore Reiser, Patricia Sánchez-Baracaldo, Sarah Hake (2000), "Knots in the family tree: evolutionary relationships and functions of knox homeobox genes", Plant Molecular Biology, 42(1):151-166.
    [ abstract]

  25. Todd E Richter, Pamela C Ronald (2000), " The evolution of disease resistance genes", Plant Molecular Biology, 42(1):195-204.
    [ abstract]

  26. Antonis Rokas, Peter W. H. Holland (2000), "Rare genomic changes as a tool for phylogenetics", Trends in Ecology & Evolution, 15(11):454-459.
    [ abstract]

  27. edited, David Sankoff, Joseph H Nadeau (2000), Comparative Genomics: Empirical and Analytical (Springer). ISBN: 0792365844

  28. Erik A Schultes, David P Bartel (2000), "One sequence, two ribozymes: implications for the emergence of new ribozyme folds", Science, 289:448-452.
    [abstract]

  29. C Seoighe, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, Oliver K, Taylor K, Rajandream MA, Barrell BG, Wolfe KH (2000), "Prevalence of small inversions in yeast gene order evolution", Proceedings of National Academy of Sciences, 97:14433-14437.
    abstract: Gene order evolution in two eukaryotes was studied by comparing the Saccharomyces cerevisiae genome sequence to extensive new data from whole-genome shotgun and cosmid sequencing of Candida albicans. Gene order is substantially different between these two yeasts, with only 9% of gene pairs that are adjacent in one species being conserved as adjacent in the other. Inversion of small segments of DNA, less than 10 genes long, has been a major cause of rearrangement, which means that even where a pair of genes has been conserved as adjacent, the transcriptional orientations of the two genes relative to one another are often different. We estimate that about 1,100 single-gene inversions have occurred since the divergence between these species. Other genes that are adjacent in one species are in the same neighborhood in the other, but their precise arrangement has been disrupted, probably by multiple successive multigene inversions. We estimate that gene adjacencies have been broken as frequently by local rearrangements as by chromosomal translocations or long-distance transpositions. A bias toward small inversions has been suggested by other studies on animals and plants and may be general among eukaryotes.

  30. Sebastian M Shimeld, Peter W. H. Holland (2000), "Vertebrate innovations", Proceedings of National Academy of Sciences, 97(9):4449-4452.
    [abstract]

  31. Pamela S Soltis, Douglas E Soltis (2000), "The role of genetic and genomic attributes in the success of polyploids", Proceedings of National Academy of Sciences, 97:7051-7057.

  32. James W Valentine (2000), "Two genomic paths to the evolution of complexity in bodyplans", Paleobiology, 26(3):513-519.
    [abstract]

  33. TJ Vision, DG Brown, SD Tanksley (2000), "The origins of genomic duplications in Arabidopsis", Science, 290(5499):2114-2117.

  34. A Wagner (2000), "The role of pleiotropy, population size fluctuations, and fitness effects of mutations in the evolution of redundant gene functions", Genetics, 154:1389-1401.

  35. A Wagner (2000), "Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate", Proceedings of National Academy of Sciences, 97:6579-6584.

  36. Yufeng Wang, Xun Gu (2000), "Evolutionary patterns of gene families generated in the early stage of vertebrates", Journal of Molecular Evolution, 51(1):88-96.
    abstract: In this paper we have analyzed 49 vertebrate gene families that were generated in the early stage of vertebrates and/or shortly before the origin of vertebrates, each of which consists of three or four member genes. We have dated the first (T(1)) and second (T(2)) gene duplications of 26 gene families with 3 member genes. The means of T(1) (594 mya) and T(2) (488 mya) are largely consistent to a well-cited version of two-round (2R) genome duplication theory. Moreover, in most cases, the time interval between two successive gene duplications is large enough that the fate of duplicate genes generated by the first gene duplication was likely to be determined before the second one took place. However, the phylogenetic pattern of 23 gene families with 4 members is complicated; only 5 of them are predicted by 2R model, but 11 families require an additional gene (or genome) duplication. For the rest (7 families), at least one gene duplication event had occurred before the divergence between vertebrate and Drosophila, indicating a possible misleading of the 4:1 rule (member gene ratio between vertebrates and invertebrates). Our results show that Ohno's 2R conjecture is valid as a working hypothesis for providing a most parsimonious explanation. Although for some gene families, additional gene duplication is needed, the credibility of the

  37. JF Wendel (2000), "Genome evolution in polyploids", Plant Molecular Biology, 42(1):225-249.

  38. Amanda Wraith, Anna Törnsten, Patrick Chardon, Ingrid Harbitz, Bhanu P Chowdhary, Leif Andersson, Lars-Gustav Lundin, Dan Larhammar (2000), "Evolution of the neuropeptide Y receptor family: gene and chromosome duplications deduced from the cloning and mapping of the five receptor subtype genes in pig", Genome Research, 10(3):302-310.
    [abstract]

  39. I Yanai, CJ Camacho, C DeLisi (2000), "Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification", Physical Review Letters, 85:2641-2644.
    [ PDF ]
    abstract: A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications.

  40. J Zimmet, K Ravid (2000), "Polyploidy: occurrence in nature, mechanisms, and significance for the megakaryocyte-platelet system", Exp. Hematol. 28(1):3-16.