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Journal ArticleDOI

Divergence in the spatial pattern of gene expression between human duplicate genes.

01 Jul 2003-Genome Research (Cold Spring Harbor Laboratory Press)-Vol. 13, Iss: 7, pp 1638-1645

TL;DR: The present study analyzes the spatial expression pattern of human duplicate gene pairs by using oligonucleotide microarray data, and study the relationship between coding sequence divergence and expression divergence, finding a strong positive correlation.

AbstractMicroarray gene expression data provide a wealth of information for elucidating the mode and tempo of molecular evolution. In the present study,we analyze the spatial expression pattern of human duplicate gene pairs by using oligonucleotide microarray data,and study the relationship between coding sequence divergence and expression divergence. First,we find a strong positive correlation between the proportion of duplicate gene pairs with divergent expression (as presence or absence of expression in a tissue) and both synonymous (K(S)) and nonsynonymous divergence (K(A)). The divergence of gene expression between human duplicate genes is rapid, probably faster than that between yeast duplicates in terms of generations. Second,we compute the correlation coefficient (R) between the expression levels of duplicate genes in different tissues and find a significant negative correlation between R and K(S). There is also a negative correlation between R and K(A), when K(A) <or= 0.2. These results indicate that protein sequence divergence and divergence of spatial expression pattern are initially coupled. Finally,we compare the functions of those duplicate genes that show rapid divergence in spatial expression pattern with the functions of those duplicate genes that show no or little divergence in spatial expression.

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Citations
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Journal ArticleDOI
TL;DR: Functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploidy, and the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs.
Abstract: To study the evolutionary effects of polyploidy on plant gene functions, we analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences functional categories, which indicates a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, and those involved in DNA repair have been preferentially lost. Although the two members of each gene pair must originally have had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. We identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. We also find that the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs. Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids.

978 citations


Cites background or result from "Divergence in the spatial pattern o..."

  • ...cerevisiae and human, which showed a rapid divergence in expression between duplicated genes (Gu et al., 2002b; Makova and Li, 2003)....

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  • ...This observation is in agreement with previous analyses in S. cerevisiae and human, which showed a rapid divergence in expression between duplicated genes (Gu et al., 2002b; Makova and Li, 2003)....

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Journal ArticleDOI
TL;DR: Concept and technological advances in gene duplication research from this early research in comparative cytology up to recent research on whole genomes, "transcriptomes," and "interactomes" are document.
Abstract: ▪ Abstract Over 35 years ago, Susumu Ohno stated that gene duplication was the single most important factor in evolution (97). He reiterated this point a few years later in proposing that without duplicated genes the creation of metazoans, vertebrates, and mammals from unicellular organisms would have been impossible. Such big leaps in evolution, he argued, required the creation of new gene loci with previously nonexistent functions (98). Bold statements such as these, combined with his proposal that at least one whole-genome duplication event facilitated the evolution of vertebrates, have made Ohno an icon in the literature on genome evolution. However, discussion on the occurrence and consequences of gene and genome duplication events has a much longer, and often neglected, history. Here we review literature dealing with the occurence and consequences of gene duplication, begining in 1911. We document conceptual and technological advances in gene duplication research from this early research in comparat...

761 citations


Cites background from "Divergence in the spatial pattern o..."

  • ...A recent study investigating microarray-based expression data of human duplicated genes confirmed these observations, and showed that when the generation time of both species was taken into account, expression divergence was more rapid in humans than in yeast (83)....

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Journal ArticleDOI
06 Sep 2007-Nature
TL;DR: This work develops a procedure that resolves the evolutionary history of all genes in a large group of species and applies it to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species.
Abstract: Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.

623 citations


Journal ArticleDOI
01 Feb 2005-Genetics
TL;DR: It is shown that neither NF nor SF alone adequately explains the genome-wide patterns of yeast protein interaction and human gene expression for duplicate genes, suggesting a new model termed subneofunctionalization (SNF), and demonstrate that enormous numbers of new functions have originated via gene duplication.
Abstract: Gene duplication is the primary source of new genes. Duplicate genes that are stably preserved in genomes usually have divergent functions. The general rules governing the functional divergence, however, are not well understood and are controversial. The neofunctionalization (NF) hypothesis asserts that after duplication one daughter gene retains the ancestral function while the other acquires new functions. In contrast, the subfunctionalization (SF) hypothesis argues that duplicate genes experience degenerate mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We here show that neither NF nor SF alone adequately explains the genome-wide patterns of yeast protein interaction and human gene expression for duplicate genes. Instead, our analysis reveals rapid SF, accompanied by prolonged and substantial NF in a large proportion of duplicate genes, suggesting a new model termed subneofunctionalization (SNF). Our results demonstrate that enormous numbers of new functions have originated via gene duplication.

604 citations


Cites methods from "Divergence in the spatial pattern o..."

  • ...To identify singleton identified by Makova and Li (2003) and the dS values weregenes, all-against-all BLASTP searches were conducted with estimated by these authors using PAML....

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Journal ArticleDOI
16 Sep 2005-Science
TL;DR: It is found that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage, and patterns suggestive of positive selection on sequence changes as well as expression changes are seen.
Abstract: The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.

576 citations


References
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Journal ArticleDOI
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

61,038 citations


"Divergence in the spatial pattern o..." refers methods in this paper

  • ...All gene pairs were aligned using CLUSTALW (Thompson et al. 1994)....

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Book
01 Jan 1970

6,780 citations



Journal ArticleDOI
TL;DR: The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models, which include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences.
Abstract: PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate constancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of substitution rates at sites and reconstruction of ancestral nucleotide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models. These include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences. Multifurcating trees are supported, as well as trees in which some sequences are ancestral to some others. A heuristic tree search algorithm (star decomposition) is used in the package, but tree making is not a strong point of the current version, although work is under way to implement efficient search algorithms. Major programs in the package, as well as the types of analyses they perform, are listed in Table 1. More details are available in the documentation included in the package, written using Microsoft Word. PAML is distributed free of charge for academic use only. The package, including ANSI C source codes, documentation, example data sets, and control files, can be obtained by anonymous ftp at mw511.biol.berkeley.edu/pub, or from the Indiana molecular biology ftp site at ftp.bio.indiana.edu under the directory Incoming or molbio/evolve . MAC and PowerMac executables are also available, although DOS executables are not prepared yet. Further information about the package is available from the World Wide Web at

4,760 citations


"Divergence in the spatial pattern o..." refers methods in this paper

  • ...The yn00 module (Yang and Nielsen 2000) of PAML (Yang 1997) with default parameters was used to calculate the number of synonymous substitutions per synonymous site (KS) and the number of nonsynonymous substitutions per nonsynonymous site (KA)....

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Journal ArticleDOI
08 Sep 1988-Nature
TL;DR: Examination of the pattern of nucleotide substitution between polymorphic alleles in the region of the antigen recognition site (ARS) indicates that in ARS the rate of nonsynonymous substitution is significantly higher than that of synonymous substitution in both humans and mice, whereas in other regions the reverse is true.
Abstract: The major histocompatibility complex (MHC) loci are known to be highly polymorphic in humans, mice and certain other mammals, with heterozygosity as high as 80-90% (ref. 1). Four different hypotheses have been proposed to explain this high degree of polymorphism: (1) a high mutation rate, (2) gene conversion or interlocus genetic exchange, (3) over dominant selection and (4) frequency-dependent selection. In an attempt to establish which of these hypotheses is correct, we examined the pattern of nucleotide substitution between polymorphic alleles in the region of the antigen recognition site (ARS) and other regions of human and mouse class I MHC genes. The results indicate that in ARS the rate of nonsynonymous (amino acid altering) substitution is significantly higher than that of synonymous substitution in both humans and mice, whereas in other regions the reverse is true. This observation, together with a theoretical study and other considerations, supports the hypothesis of overdominant selection (heterozygote advantage).

1,848 citations


"Divergence in the spatial pattern o..." refers result in this paper

  • ...This is in agreement with a strong selective pressure for adaptation in such proteins (Hughes and Nei 1988; for review, see Wolfe and Li 2003)....

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