Complex Plant Thrives with a Genome Purged of Noncoding DNA

Functional genes—those encoding specific proteins—comprise only about 2% of the human genome while the rest of the genome consists of noncoding DNA. A recent series of papers suggested that the majority of noncoding DNA (about 80%) appeared to play a role in biochemical functions such as regulation and promotion of DNA conversion into RNA and ultimately into proteins.

A paper published in the May 12, 2013, online edition of the journal Nature questioned this role for noncoding DNA by observing that U. gibba thrives with practically no noncoding DNA.

An international team of genomic researchers based at Laboratorio Nacional de Genómica para la Biodiversidad (Irapuato, Mexico) and the University of Buffalo (NY, USA) reported that the U. gibba genome contains about 80 million DNA base pairs comprising about 28,500 genes. This genome is much smaller than those found in relatives like grape and tomato, which have much larger genomes that comprise 490 and 780 million base pairs, respectively. The difference in size results from a drastic reduction in noncoding DNA in the U. gibba genome.

“The big story is that only 3% of the bladderwort’s genetic material is so-called “junk” DNA,” said contributing author Dr. Victor Albert, professor of biological sciences at the University of Buffalo. “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 extremely limited content of noncoding DNA in the U. gibba genome is particularly remarkable considering that the species has undergone three complete genome doublings since its evolutionary lineage split from that of the tomato. Thus, at three distinct times in the course of its evolution, the bladderwort’s genome doubled in size. “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 senior author Dr. Herrera-Estrella, professor of physiology and metabolic engineering of plants at Laboratorio Nacional de Genómica para la Biodiversidad.

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Laboratorio Nacional de Genómica para la Biodiversidad
University of Buffalo