Genetics can get weird. Especially so in plants, which are more conducive to hybridization and duplications of their entire genome. Polyploidy, as such a duplication is called, is often rampant across ancestral lineages of plants and makes species classification taxing, to say the least.
The Flowers and the Carnivores
The flowering plants, also known as angiosperms, are an even more difficult group to pin down a label for. Known as the most diverse group of land plants, angiosperms make up a super phylum that includes several hundred thousand species. This incredible spread of diversity includes a large amount of gene duplication, as you might expect, that still baffles taxonomists today on how to group the families under this heading. But, slowly and surely, phylogenetics and cladistics are fitting together the pieces of the puzzle.
Not all of the flowering plants live on the land however, some of the species have retained their aquatic roots even while being flowering species. The bladderworts are one of the most peculiar genuses in this category, as they not only have flower characteristics, but they also are carnivorous. This alone adds a whole new layer of genetic complexity to them and the unique grouping of genes they contain.
It is this variety of special traits, being a carnivorous, flowering plant organism, that makes their genome so strange in comparison. For a phylum made up of gene duplication and multiplicity, the particular species called the humped bladderwort, Utricularia gibba, has an incredibly small and compact genome. This is even though the species is known to have had at least two whole genome duplication events even after the genus diverged from its ancestral lineage connected to grapevines and tomatoes.
Evolutionary Gene Resilience
Researchers from the University at Buffalo took an interest in this bizarre confluence of genes in the species. In addition, a past study had found that the species gains new genes and loses others far more rapidly than other species on record, essentially forcing the population as a whole to keep to a compact genome.
This is especially striking when considering that the current U. gibba genome only measures in at 82 megabases (82 million bases) in nucleotide length, while its ancestral version has been estimated to be 1.5 gigabases (1.5 billion bases) in nucleotide length.
It can be supposed from this that the genes that have survived that process did so while under extreme selection pressures, streamlining them into compact forms for precisely the environmental niche the species requires. This has resulted in an organism that has less than 5% of its genome being non-coding information, compared to 98% of the human genome being as such. Almost every single gene sequence in the U. gibba genome has a direct protein to be translated and used.
The Important Duplications
The researchers hypothesized that a combination of two kinds of gene duplication was involved in creating such a specialized genome. The first are known as tandem repeats, when a sequence of nucleotides is duplicated and inserted directly after the original sequence. It is suspected that these sequences were then modified to create genes related to the carnivorous activities of bladderworts.
The second kind are called syntenic duplicates, which are duplicates of linked genes on the same chromosome. These are highly conserved sequences that appear frequently the same even within different species. In bladderworts they are heavily involved in controlling transcription of the genome. Duplication of them allows more direct modification and control over transcription.
While the genome of the bladderwort has already been sequenced in the past, the scientists were able to use new technology and techniques that gave a much higher resolution and detailed version. This allowed them to identify the tandem repeats in the first place. Since such tandem duplications are often lost over time, the fact that they were conserved in the compact bladderwort genome means they must have involvement in the evolutionary fitness of the species.
Increasing Carnivorous Strength
Indeed, from their deeper dive into the genes, the researchers found that genes related to oligopeptide transport were highly expressed from the repeats. These genes are strongly expressed in the bladderwort’s carnivorous trap system, likely involved in transporting the trap fluid that allows them to suck in prey.
Several other families of transport genes were also found to be heavily expressed, including energy transportation of ATPase to catalyze energy release. In order to create the high amount of suction required to activate their trap, a large amount of energy needs to also be available.
A comparison was made to the model organism Arabidopsis and its whole genome duplication events. The researchers found that, similarly to the bladderwort, genes that survived the culling and deletion after such a large-scale duplication were heavily leaning toward transcription control.
Unique Tandem Enhancement
However, they did not find any highly expressed genes related to biological activities. The bladderwort seems to be unique, for now, in how it uses tandem repeat duplications in order to enhance its biological ability to trap and digest prey like water fleas and other microscopic crustaceans.
Their ultimate conclusion was that tandem repeats are far more important, at least in some species, for specialized gene creation than previously known. Instead of being largely removed from the genome, they can play an important and crucial role in transcription and even certain biological functions.
The repeats do appear to have unique biological influences depending on the species, so they open up an entirely new avenue of investigation in every genome sequenced thus far. They also have the potential for modification that can be used for any number of as yet unknown benefits.
A Whole New Game
With one simple study, the researchers at the University at Buffalo have given a lot more work to all the other biologists out there in almost every field. It is doubtful though that anyone will be complaining about having new discoveries awaiting them.
Photo CCs: Utricularia gibba3 from Wikimedia Commons