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A stinking, smelly plant has lost its body and much of its genetic code

For most of their lives, plants of the genus Sapria are barely anything: thin tapes of parasitic cells that curl up inside the vines in the rainforests of Southeast Asia. They become visible only when they reproduce, bursting from their host like a flower the size of a plate that smells of rotten flesh.

Now, new research on the genetic code of this rare plant reveals the lengths at which it has become a specialized parasite. The findings, published Jan. 22 in Current Biology, suggest that at least one species of Sapria lost nearly half of the genes normally found in other flowering plants and stole many others directly from their hosts.

The rewired genetics of the plant echo its strange biology. Sapria and her relatives in the Rafflesiaceae family discarded their stems, roots, and any photosynthetic tissue.

“If you’re in the woods in Borneo and these (plants) don’t produce flowers, you won’t even know they’re there,” says Charles Davis, an evolutionary biologist at Harvard University.

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For years, Davis has been studying the evolution of this group of parasites from another world, which includes the world’s largest flower, Rafflesia arnoldii (SN: 1/10/07). When some genetic data showed a close relationship between these parasites and their vine hosts, Davis suspected that there was a horizontal gene transfer. This is where genes move directly from one species to another, in this case, from host to parasite. But no one had yet deciphered the genome – the complete book of genetic instructions – for these plants.

Therefore, Davis and his team sequenced many millions of pieces of the Himalayan Sapria genetic code, bringing them together in a cohesive image of the genome of that species. When the team analyzed the genome, they found an abundance of rarities.

About 44 percent of the genes found in most flowering plants were missing in S. himalayana. However, at the same time, the genome is about 55,000 genes longer than that of some other non-parasitic plants. The team found that the count is inflated by many repeating DNA segments.

Loss of chlorophyll pigments responsible for photosynthesis is common in parasitic plants that depend on their hosts for sustenance. But S. himalayana seems to discard all the genetic remains of its chloroplasts, the cellular structures where photosynthesis takes place.

Chloroplasts have their own genome, distinct from the nuclear genome that directs the cells of a plant and the mitochondria that produce energy for the cells. S. himalayana appears to have lost this genome completely, suggesting that the plant purged the last remnants of its ancestral life that allowed it to make its own food.

“There is no other case” of an abandoned chloroplast genome among plants, Davis says. Previous work by other researchers has suggested that the genome may be missing. “Our work clearly verifies that, in fact, it is already completely extinct,” he says, noting that even the genes in the S. himalayana nuclear genome that would regulate the components of the chloroplast genome have disappeared.

It may be too early to declare that the chloroplast genome is completely missing, warns Alex Twyford, an evolutionary biologist at the University of Edinburgh who did not participate in this research. According to him, it can be difficult to definitively prove that the genome has disappeared, especially if the chloroplast is “unusual in its structure or abundance” and therefore difficult to identify.

Among the remaining parts of the nuclear genome, the team also found that more than 1 percent of the S. himalayana genome comes from genes stolen from other plants, probably its current and ancestral hosts.

The potential scale of the missing genome and the volume of repeating DNA fragments are "insane," says Arjan Banerjee, a biologist at the University of Toronto Mississauga who also did not participate in this study. The “industrial scale” of plant gene theft is also impressive, he says.

There are still many strange elements in the genome of S. himalayan to explore, says study co-author Tim Sackton, an evolutionary biologist also at Harvard. For example, the plant inflates its genome with foreign DNA, while most parasites rationalize its genome. “There’s something strange and different about this species,” he says, adding that many of the DNA fragments the parasitic plant is stealing from its host don’t seem to encode any genes and probably don’t do anything important.

The new finding illustrates the level of commitment that S. himalayana and its relatives have given in the evolution of a parasitic lifestyle and offers a comparison with other extreme plant parasites (SN: 31/07/20). And for Davis, plants like S. himalayana can help researchers determine some of the limits of biology. These plants have lost half of their genes, but still survive, he notes. "Perhaps these organisms that extend the boundaries of existence tell us something about how far the rules can be bent before they can be broken."

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