But Cai and colleagues were able to take advantage of current sequencing technologies, which can handle much longer (and therefore more distinctive) stretches of DNA. Even so, they were only able to reconstruct what they estimate is 40% of the Sapria genome — the rest was still too repetitive.
This abundance of transposable elements is striking, says Saima Shahid, a plant biologist with the Donald Danforth Plant Science Center in St. Louis, who studies the functions of transposable elements in plants. It’s about twice what is seen in dodders. And in the other plant parasites sequenced to date, the dominant elements are “retrotransposons,” which move within the genome by first being transcribed into RNA. Sapria, however, is mostly filled with DNA transposons that repeatedly copy and paste themselves into the genome directly. “That’s something very interesting and unusual,” Shahid said.
But why does Sapria have so many of these jumping genes in the first place? No one is yet sure, but the answer may transform our understanding of parasite genomics.
Transposable elements are considered “selfish” genes; they replicate even at the expense of the genome they occupy. For that reason, host genomes usually rein in their expression. “Most of the time, they’re targeted for silencing,” said Shahid. It seems that either regulation has somehow gone awry in the Rafflesiaceae, or the parasites find some benefit in letting these elements jump around.
Cai, Davis and Sackton have a hunch that the superabundance of transposons is a consequence of the isolated lives these parasites lead. Because the Rafflesiaceae only invade Tetrastigma vines, each patch of vines is practically a desert island isolating its parasite inhabitants. In small populations with restricted growth and little gene flow from the outside, even less helpful genetic features can become more commonplace through sheer chance. That may mean that even deleterious copies of transposable elements “accumulate through time,” said Cai, until “you end up with these highly atypical gene structures.”
Another possibility is that the parasites can’t stop their jumping genes from jumping. Some of these elements came from their hosts, and they might be different enough that the parasite’s genetic machinery fails to recognize and silence them immediately. “It’s like an invasive species, basically,” Sackton said.
It could also be that, given how much genetic material the parasites acquire, they evolved adaptations that raised their tolerance for the extra burden of useless DNA, so there simply isn’t enough selection pressure to rid them of these jumping genes.
But to Shahid, it doesn’t make sense that a genome showing so many signs of streamlining — with the loss of genes, noncoding sequences within genes and an entire plastid genome — would be blasé about genomic dead weight. Worse, transposable elements are dangerous: “You must spend a lot of energy in order to silence them,” she said, lest they lay waste to everything. She finds it more likely that these transposons are doing something for the parasite; the question is what.
Their presence might be tied to all those stolen genes. When transposons jump, Shahid explained, they often bring bits of nearby DNA with them. “These transposable elements might be helping them to carry gene fragments, and then insert them into their own genome,” she said.
The transposons might then be the engines driving horizontal gene transfers that the parasite needs to survive. For example, they might help the parasites steal some of the host’s important gene regulators.
In a 2018 paper in Nature, Shahid and her colleagues showed that the parasitic plants called field dodders export tiny microRNA molecules into surrounding host cells as “off” signals for some of the host’s genes — presumably, to shut down defenses that would interfere with the theft of the host’s resources. Those microRNA controls may have made their way into the parasite with the help of a jumping gene. (However, no one has yet investigated whether Sapria and its relatives export microRNAs during their dormant stage.)
Transposons can influence gene regulation in other ways. When inserted into introns, for instance, they can enhance a gene’s expression, or they can guide inhibitors to shut the gene down. In Sapria, not all the introns have been reduced in length: Some are expanded to nearly 100 kilobases, making them the longest known introns from any plant. And transposable elements are responsible for 74% of all the expansions.
Transposable elements can cause chunks of the genome to move around, too, which can be dangerously destabilizing — but can also lead to gene duplication and innovation, Shahid said. That might help parasites stay a step ahead of their hosts’ defenses. Transposons could also be responsible for some of the unique features of the Rafflesiaceae: Molina has started to wonder if they have “something to do with the large flowers.”
Without more information, it’s impossible to tell how much of the huge cache of transposable elements in the Rafflesiaceae is functional and how much is just genomic clutter. Shahid said that one way to get to the bottom of all this might be to take a closer look at where different kinds of transposable elements sit in relation to other genomic features. That could help reveal whether the elements are playing pivotal roles in gene expression. She would also like to see if (or more likely when) these transposable elements are being expressed, as that could also give clues to their potential functions in the genome.
Cultivating Curiosity
Further research on these floral oddities could teach us a lot about everything from plastids to jumping genes, but the scarcity of the plants makes probing these questions much harder. Finding them involves hours of trekking deep into often dangerous jungles, Molina explained. In the Philippines, they’re found in forests where armed rebels often hide out — “We have to coordinate with a mayor to make sure it’s safe,” she said. And grueling fieldwork aside, the countries where these flowers grow often restrict their export, in part because the plants are critically endangered.
Because of their rarity, Molina is working with the United States Botanic Garden in Washington, D.C., to cultivate these parasites and their host vines domestically. Coaxing them to grow and bloom in Washington would bring them into the public eye, and she thinks allowing people to see them in person would aid in conservation efforts and enable much more detailed research. For now, though, these parasites that stretch the definition of what plants can be are keeping their secrets.
The Link LonkApril 21, 2021 at 09:39PM
https://www.quantamagazine.org/dna-of-giant-corpse-flower-parasite-surprises-biologists-20210421/
DNA of Giant 'Corpse Flower' Parasite Surprises Biologists - Quanta Magazine
https://news.google.com/search?q=Flower&hl=en-US&gl=US&ceid=US:en
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