GSTDTAP  > 气候变化
DOI10.1126/science.abc1796
Evolution after genome duplication
Ian M. Ehrenreich
2020-06-26
发表期刊Science
出版年2020
英文摘要Genome duplication generates an extra copy of nearly all genes carried by an organism, providing a potential substrate for evolution. Although many duplicate genes will be eliminated after a genome duplication, those that are retained may evolve distinct functions over time. This process can be studied by characterizing the shared and divergent functions of duplicate genes in present-day organisms whose ancestors experienced genome duplication in the past. However, such work requires examining the functional relationships between each copy of a duplicated gene and the other genes in the genome. This is inherently difficult for duplicate genes because of their redundancy. However, on page 1445 of this issue, Kuzmin et al. ([ 1 ][1]) show that systematic analysis of di- and trigenic genetic interactions in budding yeast can overcome this challenge. With this approach, they discover general constraints that influence the retention and divergence of duplicate genes. In 1970, it was proposed that gene duplication provides the critical fuel for evolution ([ 2 ][2]). Owing to their functional redundancy, it was hypothesized that duplicate genes are able to evolve in ways that single-copy genes cannot. Over time, different copies of a duplicate gene might diverge to have distinct or even new functions. These ideas preceded genome sequencing by decades and were difficult to study empirically when first proposed. However, duplicate genes were subsequently found to be prevalent in the genomes of many organisms, supporting their potential importance to evolution ([ 3 ][3], [ 4 ][4]). Gene duplication arises through a variety of mechanisms and can occur on scales ranging from individual genes to entire genomes ([ 2 ][2]). Evidence of genome duplication exists in a number of eukaryotic lineages ([ 5 ][5]). These genome duplications likely enhanced organisms' robustness to genetic and environmental perturbations, although they might have also facilitated evolutionary innovations ([ 5 ][5]). The budding yeast Saccharomyces cerevisiae —the same organism used to make beer, bread, and wine—is an excellent model system for studying how duplicate genes evolve after genome duplication. The ancestor of this organism experienced a genome duplication, and hundreds of duplicate genes produced by this event have been retained ([ 6 ][6]). These duplicate genes provide a foundation for research on duplicate gene retention and divergence. Numerous approaches have been used to study these duplicate genes in budding yeast, including comparative genomics ([ 7 ][7]), transcriptomics ([ 8 ][8]), and single gene deletions ([ 9 ][9]). This work suggests that retained duplicate genes are enriched for essential cellular components ([ 7 ][7]). They also show much greater transcriptional divergence than protein sequence divergence ([ 8 ][8]). Potentially consistent with this last point, individual deletion of many duplicate genes has little phenotypic effect, which implies that both copies maintain overlapping function ([ 9 ][9]). This past work was unable to directly probe the functional relationships between duplicate genes and the other genes in the genome. Such information is the most useful for understanding how duplicate genes have functionally diverged, but is also more difficult to obtain ([ 10 ][10]). Analysis of genetic interactions is one potential high-throughput strategy for mapping these functional relationships ([ 11 ][11]). A genetic interaction occurs when a combination of mutations, such as deletions, exhibits unexpected phenotypic consequences ([ 12 ][12]). Although most studies focus on digenic interactions, analysis of genetic interactions among three or more genes can also provide important biological insights ([ 13 ][13], [ 14 ][14]). ![Figure][15] Duplicate gene evolution After genome duplication, how duplicate genes evolve depends on functional entanglements. When entanglement is high, one copy is likely to be lost. By contrast, when entanglement is low, the chance that both copies will be retained and able to diverge is higher. Duplicate genes with intermediate levels of entanglement may be retained but are less able to diverge. GRAPHIC: KELLIE HOLOSKI/ SCIENCE Kuzmin et al. used trigenic genetic interaction analysis to measure the shared and distinct functional relationships of duplicate genes. They examined 240 pairs of nonessential duplicate genes in budding yeast. To do this, they combined single and double gene deletions for each duplicate gene pair with a library of ∼1200 single gene deletions spanning all major cellular processes. This produced 537,911 double-mutant and 256,861 triple-mutant yeast strains, resulting in the detection (through phenotypic changes) of 7197 digenic and 4557 trigenic genetic interactions. On the basis of these genetic interactions, Kuzmin et al. distinguished two main classes of duplicate genes: those that are more functionally divergent, and those that have retained a high degree of functional overlap. In silico modeling informed by the genetic interaction data revealed that duplicate gene retention and divergence heavily depended on whether the different functions of these genes were entangled (i.e., unable to evolve independently). Such functional entanglements influenced how the copies of a duplicate gene accumulated degenerative mutations over time. High entanglement tended to result in one duplicate gene copy amassing degenerative mutations and being lost (see the figure). When entanglement was lower, duplicate genes were more likely to be retained, with their functional divergence inversely related to their entanglement. This suggests that the two classes of duplicate genes that were found in budding yeast possess different levels of entanglement. Increasingly, evidence shows that evolution after genome duplication is not entirely random ([ 1 ][1], [ 10 ][10], [ 15 ][16]). For many duplicate genes, the potential for retention and divergence is constrained by functional entanglements ([ 1 ][1]). This finding provides further insight about how genome duplication contributes to evolution. For example, it bolsters the idea that many duplicate genes, as a result of their limited ability to evolve, may contribute more to robustness than to innovation ([ 3 ][3]–[ 5 ][5]). Yet it also indicates that particular duplicate genes have greater potential to facilitate innovation because they may be less affected by entanglements. These points illustrate how determining the shared and divergent functions of duplicate genes in organisms such as budding yeast can improve the understanding of the evolutionary process. 1. [↵][17]1. E. Kuzmin et al ., Science 368, aaz5667 (2020). [OpenUrl][18] 2. [↵][19]1. S. Ohno , Evolution by Gene Duplication (Springer, 1970). 3. [↵][20]1. A. Force et al ., Genetics 151, 1531 (1999). [OpenUrl][21][Abstract/FREE Full Text][22] 4. [↵][23]1. M. Lynch, 2. J. S. Conery , Science 290, 1151 (2000). [OpenUrl][24][Abstract/FREE Full Text][25] 5. [↵][26]1. K. D. Crow, 2. G. P. Wagner , SMBE Tri-National Young Investigators, Mol. Biol. Evol. 23, 887 (2006). [OpenUrl][27][CrossRef][28][PubMed][29][Web of Science][30] 6. [↵][31]1. K. H. Wolfe, 2. D. C. Shields , Nature 387, 708 (1997). 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领域气候变化 ; 资源环境
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文献类型期刊论文
条目标识符http://119.78.100.173/C666/handle/2XK7JSWQ/278200
专题气候变化
资源环境科学
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Ian M. Ehrenreich. Evolution after genome duplication[J]. Science,2020.
APA Ian M. Ehrenreich.(2020).Evolution after genome duplication.Science.
MLA Ian M. Ehrenreich."Evolution after genome duplication".Science (2020).
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