Flesh-eating plant discards DNA ‘junk’

Scientists have spent decades puzzling over why noncoding DNA makes up the majority (98%) of the human genome, but studying the genome of carnivorous bladderwort plant, Utricularia gibba has offered an unexpected insight.

Sequencing the flesh-eating water plant’s genome, which has 80 million DNA base pairs, has revealed that 97% of it consists of genes and small pieces of DNA that control these genes. The researchers suggest the plant has been deleting noncoding “junk” DNA from its genome over many generations.

“The big story is that only 3% of the bladderwort’s genetic material is so-called junk DNA,” said Victor Albert, Professor of Biological Sciences from the University of Buffalo who co-directed the study detailed in Nature. “Somehow this plant has purged most of what makes up plant genomes. What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed.”

The bladderwort’s genome suggests that having a myriad of noncoding DNA isn’t crucial for complex life. U. gibba lives in aquatic habitats and has developed highly specialised hunting methods. To capture its prey, the plant pumps water from tiny chambers, turning each into a vacuum that can suck in and trap unsuspecting creatures. A recent series of papers from ENCODE have begun to offer an explanation to the mystery of noncoding DNA’s existence, suggesting it plays a role in biochemical functions such as regulation and promotion of DNA conversion into RNA in order to make proteins.

However, the researchers behind the bladderwort study argue that organisms may not possess genetic junk for reasons of benefit. They suggest that some species may simply have an inherent, mechanistic bias toward deleting a lot of noncoding DNA, while others have a built-in bias to do the opposite.

U. gibba has a miniscule number of base pairs compared to other complex plants, such as its tomato relative (780 million) which the researchers say the deleting of noncoding DNA accounts for. The small size of the bladderwort genome is even more surprising considering the species has undergone three complete genome doublings since its evolutionary lineage split from that of tomato.

“This surprisingly rich history of duplication, paired with the current small size of the bladderwort genome, is further evidence that the plant has been prolific at deleting nonessential DNA, but at the same time maintaining a functional set of genes similar to those of other plant species,” said study leader Professor Herrera-Estrella, director of the LANGEBIO in Mexico.

Reference: (Ibarra-Laclette et al 2013) Architecture and evolution of a minute plant genome