Manual Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Functions

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In most cases, the miRregulated SPLs are master regulators that play divergent and redundant roles in plant morphology and development Schwab, However, whether the miRregulated ZmSPLs have similar regulatory roles remains to be further confirmed experimentally. According to the microarray expression profile analysis, we found that some duplicated gene pairs have similar expression patterns, suggesting that the duplicated genes might have redundant functions in plant growth and development.

Exceptions to this were also observed. These results suggested that most of the duplicated gene pairs were still conserved in their evolution, but that functional diversification has also accompanied the evolutionary process, as a major feature of retained duplicated genes in long-term evolution Blanc and Wolfe, The expression patterns of the 12 miRtargeted genes were further investigated at different developmental stages by RT-qPCR.

Among the 12 ZmSPLs , high expression was detected in leaf and stem. Especially, the results confirmed that some segment duplicated genes have similar expression patterns, suggesting their conserved evolution and redundant functions. The expression of the 12 ZmSPLs under drought stress was also examined. Since most of the studies about SPL family were related to developmental and biological processes, this result provided important information that the 12 miR targeted genes are involved in drought stress, which may have important implications in revealing the function and mechanism of SPL in the stress response.

With the advances of sequencing technologies, many new miRNAs have been identified, and an increasing number of studies on miRNAs are being reported. Based on our experimental results, we have identified several drought-response genes and cloned them, and this will be further studied by transgenic technology.

We thank the members of bioinformatics group of the Key Laboratory of Crop Biology of AnHui province for their assistance in this study. Curr Biol Trends Plant Sci J Mol Biol Blanc G and Wolfe KH Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell BMC Plant Biol Plant J — Gene FEBS J — Development Nucleic Acids Res W Planta Nucleic Acids Res Gaut BS Evolutionary dynamics of grass genomes. New Phytol — PLoS One 8:e Bioinformatics Annu Rev Plant Biol Plant Mol Biol Mol Genet Genomics Nucleic Acids Res DD Genome Res Cell Nucleic Acids Res D Science Nature Genetics Mehan MR A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

Hum Genomics Genes Dev Annu Rev Genet PLoS One 7:e Plant J R Foundation for Statistical Computing. Computing Schwab R The roles of miR and miR in phase change regulation.

Dinámica del genoma, complejidad genética y macroevolución

Springer, Berlin, pp Dev Cell Plant Cell Physiol Am J Bot Mol Biol Evol. Nature Int J Mol Sci Plant Physiol Dev Biol PLoS One 6:e Table S1List of gene-specific primers used in the present study. Table S4Information about orthologous genes in maize, rice, and sorghum. Send correspondence to Qing Ma. E-mail: maqingahau License information: This is an open-access article distributed under the terms of the Creative Commons Attribution License type CC-BY , which permits unrestricted use, distribution and reproduction in any medium, provided the original article is properly cited.

Services on Demand Journal. Plant Genetics Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize. Abstract SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Unfortunately, this signal is complicated by subsequent piecemeal loss and gain of gene family members. Consequently, there is heated debate over possible ancient genome duplication events in early vertebrate evolution and more recently in teleost fish, both of which must have occurred hundreds of millions of years ago McLysaght et al.

So what are the relative contributions of these different mechanisms? Not all interspersed duplicate genes are generated by retrotransposition. The initially tandem arrangement of segmental duplications can be broken up by subsequent rearrangements. In keeping with this hypothesis, duplicated genes in a tandem arrangement typically represent more recent duplication events Friedman and Hughes A duplicated gene newly arisen in a single genome must overcome substantial hurdles before it can be observed in evolutionary comparisons.

First, it must become fixed in the population, and second, it must be preserved over time. Population genetics tells us that for new alleles, fixation is a rare event, even for new mutations that confer an immediate selective advantage. Nevertheless, it has been estimated that one in a hundred genes is duplicated and fixed every million years Lynch and Conery , although it should be clear from the duplication mechanisms described above that it is highly unlikely that duplication rates are constant over time.

Genome Evolution

However, once fixed, three possible fates are typically envisaged for our gene duplication. Despite the slackened selective constraints, mutations can still destroy the incipient functionality of a duplicated gene: for example, by introducing a premature stop codon or a mutation that destroys the structure of a major protein domain.

These degenerative mutations result in the creation of a pseudogene nonfunctionalization. Over time, the likelihood of such a mutation being introduced increases. Recent studies suggest that there is a relatively narrow time window for evolutionary exploration before degradation becomes the most likely outcome, typically of the order of 4 million years Lynch and Conery During the relatively brief period of relaxed selection following gene duplication, a new, advantageous allele may arise as a result of one of the gene copies gaining a new function neofunctionalization.

This can be revealed by an accelerated rate of amino-acid change after duplication in one of the gene copies. This burst of selection is necessarily episodic—once a new function is attained by one of the duplicates, selective constraints on this gene are reasserted. These patterns of selection can be observed in real data: most recently duplicated gene pairs in the human genome have diverged at different rates from their ancestral amino-acid sequence Zhang et al.

A convincing instance of neofunctionalization is the evolution of antibacterial activity in the ECP gene in Old World Monkeys and hominoids after a burst of amino-acid changes following the tandem duplication of the progenitor gene EDN a ribonuclease some 30 MYA Zhang et al. The divergence of duplicated genes over time can be also monitored in genome-wide functional studies. In both yeast and nematodes, the ability of a gene to buffer the loss of its duplicate declines over time as their functional overlap decreases.

Rather than one gene duplicate retaining the original function, while the other either degrades or evolves a new function, the original functions of the single-copy gene may be partitioned between the duplicates subfunctionalization. Many genes perform a multiplicity of subtly distinct functions, and selective pressures have resulted in a compromise between optimal sequences for each role.

Duplication of genomes

Partitioning these functions between the duplicates may increase the fitness of the organism by removing the conflict between two or more functions. This outcome has become associated with a population genetic model known as the Duplication—Degeneration—Complementation DDC model, which focuses attention on the regulatory changes after duplication Force et al.

In this model, degenerative changes occur in regulatory sequences of both duplicates, such that these changes complement each other, and the union of the expression patterns of the two duplicates reconstitutes the expression pattern of the original Figure 2. A new duplication in a gene blue with two tissue-specific promoters arrows arises in a population of single copy genes.

Fixation within the population results in a minority of cases. After fixation, one gene is inactivated degradation or assumes a new function neofunctionalization , or the expression pattern of the original gene is partitioned between the two duplicates as one promoter is silenced in each duplicate in a complementary manner subfunctionalization. A recent study by Dorus and colleagues Dorus et al. In the mouse, both Cdyl genes produce two distinct transcripts, one of which is expressed ubiquitously while the other is testis-specific. By contrast, in humans both CDYL genes produce a single ubiquitously expressed transcript, and CDY exhibits testis-specific expression.

As CDY is a retrogene see above that has not been duplicated together with its ancestral regulatory sequences, it is clear that the DDC model is not the only route by which to achieve spatial partitioning of ancestral expression patterns.

Subfunctionalization can also lead to the partitioning of temporal as well as spatial expression patterns. One gene is expressed in embryos, another in foetuses, and the third from neonates onwards. In addition, coding sequence changes have co-evolved with the regulatory changes so that the O 2 binding affinity of haemoglobin is optimised for each developmental stage. This coupling between coding and regulatory change is similarly noted at a genomic level when expression differences between many duplicated genes pairs are correlated with their coding sequence divergence Makova and Li If duplication results in the formation of a novel function as a result of interaction between the two diverged duplicates, which of the above categories of evolutionary outcome does this innovation fall into?

Not all new biological functions resulting from gene duplications can be ascribed to individual genes. Protein—protein interactions often occur between diverged gene duplicates.


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This is especially true for ligand—receptor pairs, which are often supposed to coevolve after a gene duplication event, and thus progress from homophilic to heterophilic interactions. The proposition that large scale evolution has occurred via gene duplication is contradicted by numerous lines of evidence. It also is clear that the evidence for gene duplication at present is totally inferential, and not empirical or experimental.

Chromosome duplication can produce useable variety—but only within what are most likely created kinds—in plants and invertebrates, and single gene duplication appears to do likewise in rare cases in vertebrates, but otherwise gene duplication generally causes disease and deformity. The existing experimental evidence does not support gene duplication as a source of new genes for at least populations of fewer than one billion. In other words, evolution by gene-duplication is yet another example of just-so story-telling. We have supplied this link to an article on an external website in good faith.

But we cannot assume responsibility for, nor be taken as endorsing in any way, any other content or links on any such site. Even the article we are directing you to could, in principle, change without notice on sites we do not control. Also Available in:. This article is from Journal of Creation 20 1 —, April Browse our latest digital issue Subscribe.


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