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Compact Carnivorous Plant Genome Points to Complexity with Little Non-coding DNA

NEW YORK (GenomeWeb News) – An international team led by investigators in Mexico and the US has sequenced the genome of the carnivorous bladderwort plant, Utricularia gibba. Their findings, published online this week in Nature, suggest that the carnivorous plant has ditched virtually all its non-coding DNA, retaining a set of sequences that's almost exclusively genic.

"Somehow, this plant has purged most of what makes up plant genomes," co-corresponding author Victor Albert, a biology researcher at the University of Buffalo, said in a statement. "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' DNA]," he added.

U. gibba is a small plant found in freshwater environments, where it preys on minute aquatic animals. The carnivorous plant relies on water-filled bladders that produce suction to slurp up and trap these creatures, researcher noted, a strategy similar to that used by other members of the same carnivorous plant genus.

For the current study, the researchers used a combination of Roche 454, Illumina, and Sanger approaches to sequence the bladderwort's 82 million base genome.

Within the resulting 77 million base pair hybrid bladderwort genome assembly, the team tracked down a whopping 28,500 or so predicted protein-coding genes — far more than anticipated from its size alone.

That coding capacity comes at the cost of non-coding repetitive sequences, jumping genes, and other mobile genetic elements, which together make up just 3 percent or so of the bladderwort genome.

But the team also saw microdeletions and sizeable recombinatorial deletions across the genome in general, corresponding to compact promoters, missing introns, and other lost stretches of sequence.

"Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA," Albert and co-authors wrote.

Nevertheless, they noted that the genome seems to house a full complement of the plant genes and microRNAS tasked with retrotransposon silencing.

In addition, despite the compressed genome found in bladderworts today, researchers reported, their analyses suggest that genome duplication events are not uncommon in the plant's history.

When they compared the bladderwort genome to those of other sequenced plants, for instance, the researchers saw signs of at least three historical genome duplications in the bladderwort lineage since a split from a shared ancestor with tomato and grape plants. Together with other patterns in the genome, those events suggest that the organism is especially apt to toss out sequences that don't directly code for proteins, study authors said.

"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 non-essential DNA," co-corresponding author Luis Herrera-Estrella, with Mexico's Laboratorio Nacional de Genómica para la Biodiversidad, said in a statement, "but at the same time maintaining a functional set of genes similar to those of other plant species."

"[I]n contrast to recent publications that highlight a crucial functional role of non-coding DNA in complex organisms such as animals," he and his colleagues argued, "the necessary genomic content required to make a flowering plant may not require substantial hidden regulators in the non-coding 'dark matter' of the genome."

On the gene family front, meanwhile, Herrera-Estrella and his colleagues found representatives from almost all of the gene families present in the genomes of tomato, grape, papaya, and Arabidopsis plants. Of nearly 19,000 such families, almost 1,300 were missing in the bladderwort, while another 1,800 or so families appear to be somewhat expanded.

Such differences likely reflect the bladderwort's distinct biology and lifestyle, study authors speculated, such as its carnivorous diet, unusual development patterns, and rootlessness.