Genome complexity: polyploidy (Introduction)

by David Turell , Monday, September 11, 2023, 00:18 (230 days ago) @ David Turell

Duplicated genomes newly recognized as good for organisms:

https://www.science.org/content/article/cells-extra-genomes-may-help-tissues-respond-in...

"As polyploid cells emerge as common and seemingly crucial, this once obscure topic is now bringing together cancer researchers, developmental biologists, evolutionary biologists, cell biologists, and agricultural scientists. About 150 researchers gathered in Florida in May for a meeting Losick helped organize, Polyploidy Across the Tree of Life, trading information from their normally siloed fields.

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"Polyploidy may be a coping method not just for individual organisms, but for entire species. About 30% of plants are fully polyploid, meaning all their cells have double or more the number of chromosomes found in their ancestors. The same is true for a small number of animals—several salamanders, for example. Evolutionary biologists have found that polyploid organisms are often at a competitive disadvantage compared with diploid counterparts, raising questions about why the trait persists. By pinpointing when genome duplications occurred millions of years ago, researchers are glimpsing a potential answer: Polyploidy may help species weather catastrophic environmental changes. At all sorts of spatial and temporal scales, polyploidy is a “damage response,” suggests Douglas Soltis, a plant evolutionary biologist at the University of Florida. “It’s the single most important evolutionary thing that nobody talks about.”

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"Fox, Losick, and others also documented how the cells contribute to healing. In fruit flies, some of the mammoth cells quickly plug the space left by puncture wounds, and because they have multiple copies of various genes, they can make extra proteins that speed healing. For example, where the needle poke destroys muscle, these cells make a lot of myosin protein, which helps muscles contract. The extra DNA of polyploid cells, Losick suggests, may also make them resistant to injury-induced DNA damage from inflammation that would cause a normal diploid cell to die, bogging down recovery.

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"Losick has identified a protein that helps control polyploidy in fruit flies: the fly equivalent of a mammalian molecule called YAP1, for yes1 associated transcriptional regulator. YAP1 was known to help regulate genes that control organ size. It also turns out to stimulate polyploidy in insect wound healing, and to curb the process when its activity falls. The Florence team found YAP1 has the same role in mouse kidneys. “It was amazing that we were seeing very similar things, in the Drosophila [abdomen] and in the mammalian kidney,” Romagnani says.

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"Sometimes these joined genomes duplicated yet again—wheat has six sets of chromosomes; strawberries have eight. The multiple copies of key genes for growth and nutrients can result in denser heads of grain, bigger fruit, and taller, sweeter stalks.

"Those traits may delight human consumers, but for plants, “many, if not most, whole genome duplications are actually maladaptive,” says Yves Van de Peer, an evolutionary biologist at Ghent University. Polyploid plants need more nutrients, for example, and seem to grow slower than their diploid counterparts. Yet the trait persists, and Van de Peer believes the answer, again, comes down to coping with stress.

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"Tia-Lynn Ashman and Martin Turcotte, evolutionary ecologists at the University of Pittsburgh, have also studied polyploidy in duckweed populations. The polyploid plants tended to grow more slowly and reached smaller population sizes than their diploid counterparts. But they supported a more diverse ecosystem of microbes, Ashman reported at the meeting.

"That could be another beneficial consequence of polyploidy. Increasingly, researchers are recognizing that an organism’s microbiome helps it survive, so a more diverse roster of microbial guests may enable the host to digest more kinds of food or enhance resilience in other ways. The increased diversity “could provide a mechanism for the broader ecological range of polyploids seen at the global scale,” Ashman suggests.

"What is certain is the polyploid cells, far from being abnormal, are one of life’s major mechanisms for coping with the stresses of injury, disease, and a hostile environment. At the meeting, “There was the increasing realization that whole-genome doubling does not simply double everything in the cell—rather we are seeing unique biology,” says Pamela Soltis, a plant evolutionary biologist at the Florida Museum of Natural History."

Comment: a whole new research field is opening up. Genetics in just becoming even more complex. Excess sets of chromosomes are helpful.