NEW YORK (GenomeWeb) – The Antarctic midge genome appears to have jettisoned a slew of sequences from its genome during adaptation to its extreme environment, but has managed to avoid dramatic reductions in its protein-coding gene set, according to a new Nature Communications study.
Researchers from Ohio State University, Washington State University, Stanford University, and elsewhere used Illumina and Pacific Biosciences instruments to tackle the tiny genome of the Antarctic midge, Belgica antarctica, a wingless creature that constitutes that continent's only endemic insect species.
The resulting genome assembly represents the smallest insect genome so far, the study's authors explained, pointing to genome streamlining as the Antarctic midge became suited to the extreme cold, ultraviolet light, and other stresses that characterize life in the Antarctic.
For the most part, the sequence losses identified in the genome seem to have affected its architecture rather than leading to gene losses, the team noted. For instance, the midge genome contained very few repeats or transposable elements. It was also home to shorter-than-usual intron sequences compared to other organisms in the same insect order.
On the other hand, the genome was rife with protein-coding genes involved in development, metabolism, and responses to environmental cues, suggesting these processes are important to the Antarctic midge's survival and environmental adaptation.
"As the first polar insect and first freeze-tolerant insect to be sequenced, B. antarctica offers a unique opportunity to probe the genome architecture of an extremophile," the study's senior author David Denlinger, an entomology researcher at Ohio State University, and his colleagues wrote.
"Our interpretation is … that the small midge genome is the result of genome adaptation via fixation of strongly selected mutations that overcame the opposing action of genetic drift inherent in small populations," they concluded.
Previous studies have started to unravel some of the unusual tactics that B. antarctica uses to survive the extreme changes in temperature, salinity, sunlight, and water availability it's exposed to in the Antarctic. The wingless fly has the wherewithal to survive freezing and desiccation as well as heat and exposure to ultraviolet radiation, for example, with larvae growing over years and adults living just over a week or so.
For their new genomic analysis, Denlinger and his colleagues used Illumina's HiSeq 2000 to sequence genomic DNA from an Antarctic midge larva collected on Cormorant Island in Antarctica. To that, they added DNA sequences generated from one PacBio RSII library, along with transcript sequences produced using the Illumina instrument.
All told, the assembly spanned 89.6 million bases — more than 90 percent — of the B. antarctica genome. The group's analysis of this sequence unearthed more than 13,517 predicted protein-coding genes, which comprised almost one-fifth of the genome.
On the other hand, the genome contained just a smattering of repeat sequences. Less than 0.5 percent of assembled genome sequences stemmed from repeat elements, which made up an estimated 10 percent of the overall Antarctic midge genome.
When they considered the types of transposable elements present in the genome, the researchers saw a lack of species-species transposons. And when transposable element insertions did turn up, they often represented ancient retroelements that are no longer active in the midge genome.
The team's comparison between the new midge genome and sequences for other diptheran insects — including Drosophila melanogaster and a few mosquito species — revealed 4,910 B. antarctica-specific genes, along with thousands more genes shared across multiple species in the insect order.
Amongst the most well represented genes in the Antarctic midge genome were those involved in development, regulation, and response to stimuli from the environment, researchers reported. On the other hand, the insect had fewer-than-usual sensory perception genes such as genes coding for proteins related to odor detection.
In the Antarctic midge genes that were orthologous to those in related species, meanwhile, the team noted that introns tended to be abbreviated, contributing to a compact but robust protein-coding repertoire.
The researchers speculated that the intron size reduction in the Antarctic midge might be a consequence of its limited transposable element collection, since intron sizes seem to coincide with transposable element content in related creatures such as the fruit fly.
They noted that the lack of transposable elements, in turn, might relate to enhanced expression of heat shock proteins in the Antarctic midge, though more research is needed to explore such interactions in B. antarctica and creatures living in comparable environments.
"Having heat-shock proteins turned on all the time could offer some clues about how you might be able to preserve other tissues for a long time," Denlinger said in a statement. "Midges have figured out how to do that, so that means it is possible for some animal tissues to survive freezing temperatures."