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Paleopolyploidy - Wikipedia, the free encyclopedia

Paleopolyploidy
From Wikipedia, the free encyclopedia

Paleopolyploidy refers to ancient genome duplications which occurred at least several million years ago (mya). The genome doubling event could either be an autopolyploidy or an allopolyploidy. Due to functional redundancy, genes are rapidly silenced and/or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently referred to as "diploids" (e.g. baker's yeast, Arabidopsis, and perhaps humans). Paleopolyploidy is extensively studied in plant lineages. It Overview of Paleopolyploidy Process. Many has been found that almost all flowering plants have higher eukaryotes were paleopolyploids at some undergone at least one round of genome duplication at some point during their evolutionary history. point during their evolutionary history. Ancient genome duplications are also found in the early ancestor of vertebrates (which includes the human lineage) and another near the origin of the bony fishes. Evidence suggests that baker's yeast (Saccharomyces cerevisiae), which has a compact genome, experienced polyploidization during its evolutionary history.

Contents
1 Eukaryotes 2 Detection method 3 Evolutionary importance 4 Vertebrates as paleopolyploid 5 See also 6 References

Eukaryotes
Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. Studies suggest that the common ancestor of Poaceae, the grass family which includes important crop species such as maize, rice, wheat, and sugar cane, had a genome duplication 5070 mya[1]. Further independent whole genome duplications have occurred in the lineages leading to maize, sugar cane and wheat, but not rice. The core eudicots -- rosids and asterids -- also share a common whole genome duplication and many species within these groups have experiences additional whole genome duplications. For example, the model plant Arabidopsis thaliana, the first plant to be have its entire genome sequenced, experienced at least two additional rounds of whole genome duplication since the duplication shared by the core eudicots[2]. The most

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recent event took place before the divergence of the Arabidopsis and Brassica lineages, 2540 mya. Compared with plants, paleopolyploidy is much rarer in the animal kingdom. It has been identified mainly in amphibians and bony fishes. Although some studies suggested one or more common genome duplications are shared by all vertebrates (including humans), the evidence is not as strong as in the other cases because the duplications, if they exist, happened so long ago, and it is still under debate. The idea that vertebrates share a common whole genome duplication is known as the 2R Hypothesis. Many researchers are interested in the reason why animal lineages, particularly mammals, have had so many fewer whole genome duplications than plant lineages. A well-supported paleopolyploidy has been found in baker's yeast (Saccharomyces cerevisiae), despite its small, compact genome (~13Mbp) after the divergence from K. waltii.[3] Through genome streamlining, yeast has lost 90% of the duplicated genome over evolutionary time and is now recognized as a diploid organism.
A diagram that summarizes all well-known paleoploidization events.

Detection method
Duplicated genes can be identified through sequence homology on the DNA or protein level. Paleopolyploidy can be identified as massive gene duplication at one time using a molecular clock. To distinguish between whole-genome duplication and a collection of single gene duplication (which is a common phenomenon in the genome) events, the following rules are often applied: 1. Duplicated genes are located in large duplicated blocks. Single gene duplication is a random process and tends to make duplicated genes scattered throughout the genome. 2. Duplicated blocks are non-overlapping because they were created simultaneously. Segmental duplication within the genome can fulfill Rule #1; but multiple independent segmental duplications could overlap each other. In theory, the two duplicated genes should have the same "age"; that is, the divergence of the sequence should be Detection of Paleopolyploidy using Ks. equal between the two genes duplicated by paleopolyploidy (homeologs). Synonymous substitution rate, Ks, is often used as a molecular clock to determine the time of gene duplication. Thus, paleopolyploidy is identified as a "peak" on the duplicate number vs. Ks graph (shown on the right).

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Duplication events that occurred a long time ago in the history of various evolutionary lineages can be difficult to detect because of subsequent diploidization (such that a polyploid starts to behave cytogenetically as a diploid over time) as mutations and gene translations gradually make one copy of each chromosome unlike its counterpart. This usually results in a low confidence for identifying a very ancient paleopolyploidy.

Evolutionary importance
Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size. Gene loss during diploidization is not completely random, but heavily selected. Genes from large gene families are duplicated. On the other hand, individual genes are not duplicated. Overall, paleopolyploidy can have both short-term and long-term evolutionary effects on an organism's fitness in the natural environment. Genome Diversity genome doubling provided the organism with redundant alleles that can evolve freely with little selection pressure. The duplicated genes can undergo neofunctionalization or subfunctionalization which could help the organism adapt to the new environment or survive different stress conditions. Heterosis polyploids often have larger cell sizes and even larger organs. Many important crops, including wheat, maize and cotton, are paleopolyploids which were selected for domestication by ancient peoples. Speciation It has been suggested that many polyploidization events created new species, via a gain of adaptive traits, or by sexual incompatibility with their diploid counterparts. An example would be the recent speciation of allopolyploid Spartina S. anglica; the polyploid plant is so successful that it is listed as invasive species in many regions.

Vertebrates as paleopolyploid
The hypothesis of vertebrate paleopolyploidy originated as early as the 1970s, proposed by the biologist Susumu Ohno. He reasoned that the vertebrate genome could not achieve its complexity without large scale whole-genome duplications. The "two rounds of genome duplication" hypothesis (2R hypothesis) came about, and gained in popularity, especially among developmental biologists. However, the 2R hypothesis has been questioned by many researchers. Based on the theory, vertebrate genomes should have a 4:1 gene ratio compared with invertebrate genomes. This is not supported by findings from the 48 vertebrate genome projects available in mid-2011, for example the human genome consists of ~21,000 protein coding genes according to June, 2011 counts at UCSC and Ensembl genome analysis centers[citation needed] while an average invertebrate genome size is about 15,000 genes. Further, the recent completion of the amphioxus genome sequence does not support any such whole genome duplication with largescale retention, as predicted by the hypothesis.[4] Additional arguments against 2R were based on the lack of the (AB)(CD) tree topology amongst four members of a gene family in vertebrates. However, if the two

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genome duplications occurred close together, we would not expect to find this topology.[5]

See also
Gene duplication Genomics Karyotype Ploidy Polyploidy Speciation

References
1. ^ Paterson, A. H.; Bowers, J. E.; Chapman, B. A. (2004). "Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics". Proceedings of the National Academy of Sciences 101 (26): 9903. doi:10.1073/pnas.0307901101 (http://dx.doi.org/10.1073%2Fpnas.0307901101) . 2. ^ Bowers, J. E.; Chapman, B. A.; Rong, J.; Paterson, A. H. (2003). "Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events". Nature 422 (6930): 433438. doi:10.1038/nature01521 (http://dx.doi.org/10.1038%2Fnature01521) . PMID 12660784 (http://www.ncbi.nlm.nih.gov/pubmed/12660784) . 3. ^ Wong, S.; Butler, G.; Wolfe, K. H. (2002). "Gene order evolution and paleopolyploidy in hemiascomycete yeasts". Proceedings of the National Academy of Sciences 99 (14): 9272. doi:10.1073/pnas.142101099 (http://dx.doi.org/10.1073%2Fpnas.142101099) . 4. ^ Putnam NH, Butts T, Ferrier DE, et al. (June 2008). "The amphioxus genome and the evolution of the chordate karyotype". Nature 453 (7198): 106471. Bibcode 2008Natur.453.1064P (http://adsabs.harvard.edu/abs/2008Natur.453.1064P) . doi:10.1038/nature06967 (http://dx.doi.org/10.1038%2Fnature06967) . PMID 18563158 (http://www.ncbi.nlm.nih.gov/pubmed/18563158) . 5. ^ Furlong RF, Holland PW (April 2002). "Were vertebrates octoploid?" (http://rstb.royalsocietypublishing.org/cgi/pmidlookup?view=long&pmid=12028790) . Philos. Trans. R. Soc. Lond., B, Biol. Sci. 357 (1420): 53144. doi:10.1098/rstb.2001.1035 (http://dx.doi.org/10.1098%2Frstb.2001.1035) . PMC 1692965 (http://www.pubmedcentral.gov/articlerender.fcgi? tool=pmcentrez&artid=1692965) . PMID 12028790 (http://www.ncbi.nlm.nih.gov/pubmed/12028790) . http://rstb.royalsocietypublishing.org/cgi/pmidlookup?view=long&pmid=12028790.

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