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Genome Digest

What researchers are learning as they sequence, map, and decode species’ genomes

By | August 27, 2014

FLICKR, KEVIN DOOLEY

Kitty can has genome?

Species: Domestic cat (Felis catus)
Genome size: 3.1 billion base pairs

Domestic cats can develop diseases like leukemia and feline immunodeficiency virus . To better understand these diseases, an international team of researchers sequenced and annotated the genomes of three domestic cats. The results, published this month (August 5) in GigaScience, include a new feline genome browser, Genome Annotation Resource Fields (GARfield), which encompasses methylation patterns in cat blood cells and more than 21,000 annotated genomic features.

A team led by investigators at Nova Southeastern University in Florida sequenced and analyzed the genomes of three cats using three different methods. While the feline genome was previously published, Nova Southeastern researcher Stephen O’Brien and his colleagues noted that their work helps to close gaps in the low-coverage shotgun sequencing methods previously used in earlier work. O’Brien’s team also uncovered several new features in the cat genome, including new retrovirus-like elements and single nucleotide variants. Approximately 55.7 percent of the genome is comprised of repetitive elements.

The analysis suggests a “highly conserved ancestral mammal genome organization,” and offers data to “connect the rich veterinary and natural history of cats to genome discovery,” the authors wrote in their paper.

Insect extremophile

NATURE COMMUNICATIONS, RICHARD LEE JR.Species: Antarctic midge (Belgica antarctica)
Genome size: 99 million base pairs

The sequence of Antarctica’s only native entirely terrestrial animal reveals how living in extreme environments can constrain genomic architecture, according to a study published this month (August 12) in Nature Communications.  

The flightless midge’s genome—the smallest insect genome sequenced to date—comprises a mere 99 million base pairs. Small as it is, the Antarctic midge genome includes approximately 13,500 functional genes; its reduced size appears to be a result of shorter introns, sparser repeat sequences, and very few transposable elements.

“It will be interesting to know if other extremophiles—ticks, mites, and other organisms that live in Antarctica—also have really small genomes, or if this is unique to the midge,” study coauthor David Denlinger of Ohio State University said in a press release.

Previous studies have revealed unusual expression patterns in heat shock proteins, antioxidant enzymes, an aquaporin, and genes responsive to changes in hydration. These genomic adaptations have likely helped the midge survive its harsh home environment, where extreme temperatures, desiccation, and intense UV exposure are common.

“This is the first insect extremophile to be sequenced, which means it is a fantastic foundation for future comparative studies,” coauthor Joanna Kelley of Washington State University in Pullman told BBC Nature. “Previous work has suggested that small effective population sizes should lead to larger genomes, which is the opposite of what we see in the midge.”

Corn killer

FLICKR, RUBEN HOLTHUIJSENSpecies: Maize leaf spot fungus (Curvularia lunata)
Genome size: 35.5 million base pairs

A team from Shanghai Jiao Tong University in China has sequenced the genome of a fungus that has been responsible for significant losses of maize crops in China in an effort to better understand its virulence. The work was published in BMC Genomics last month (July 24).

Five pathogenic C. lunata strains of varying virulence affect different agricultural areas in China, infecting maize, barley, wheat, sorghum, and other grasses. Sequencing the C. lunata strain CX-3 and comparing it to two other pathogens, Jie Chen and her colleagues discovered that CX-3 and another strain, C. lunata m118, diverged from another maize pathogen, Bipolaris maydis, approximately 24 million to 50 million years ago. The three strains remain closely related.

The C. lunata CX-3 sequence encodes more than 11,000 protein-coding genes, and contains several unique genomic islands which may play key roles in virulence, according to the authors. The genome also includes more transposase elements than either B. maydis or the m118 strain.

Comparing the transcriptomes of the three species, the researchers found differences in expression of secondary metabolic pathways and detoxification-linked genes; CX-3 expressed several genes crucial for fungal survival in stressful environments. Overall, this comparative analysis “will contribute to better understanding of what is required to develop flexible strategies to control the pathogen infection,” the authors wrote in their paper.

Honeybee history

NATURE GENETICS, MATTHEW WEBSTERSpecies: Honeybee (Apis mellifera)
Genome size: 236 million base pairs

Researchers have sequenced 140 honeybees spanning 14 global populations in an attempt to understand the insect’s evolutionary history. An analysis of 8.3 million single nucleotide polymorphisms (SNPs) revealed the bees’ genetic adaptations to pathogens and climate change. The results were published this week (August 24) in Nature Genetics.

Contrary to previous studies that suggested an African origin for honeybees, this latest study hinted at an Asian origin for Apis mellifera. The authors, led by Matthew Webster of Uppsala University in Sweden, found that bee population sizes have fluctuated significantly in the past, perhaps as a result of climatic changes.  

Human beekeeping, the researchers found, appears to have increased genetic diversity among domestic honeybees compared to ancestral populations in the wild. “The findings may also indicate that high levels of inbreeding are not a major cause of global colony losses,” Webster said in a press release.

The work also found that African and European honeybees differed in genes involved in disease resistance as well as sperm motility and development; the latter led the team to suggest that sperm competition may have been a major factor driving bee evolution. The results “establish a framework for investigating the biological mechanisms behind disease resistance and adaptation to climate, knowledge that could be vital for protecting honeybees in a rapidly changing world,” said Webster.

Important oil

FLICKR, HARRY ROSESpecies: Canola oilseed plant (Brassica napus)
Genome size: 525.8 million base pairs

Agricultural selection has shaped the genome of the canola oilseed plant, increasing the expression of genes linked to oil production and causing the loss of those behind the production of glucosinolates—compounds that are toxic in animal feed—according to a study published last month (July 29) in Science.

Like many domesticated plants, Brassica napus is an allopolyploid, formed when chromosomes from Asian cabbage (B. rapa) and Mediterranean cabbage (B. oleracea) merged. People began cultivating the plant more than 7,000 years ago, primarily as a source of oil and food. With time, other species emerged from cabbage—including rutabaga and kale.

Boulos Chalhoub of the National Institute of Agronomic Research in France and his colleagues produced a draft genome of B. napus, finding within it several regions where a gene from one of its two cabbage ancestors had been converted to the form found in the other ancestral variety. Humans may have sped selection for some of these characteristics in attempts to improve crops, the authors suggested.

“Understanding the genomes of B. rapa and B. oleracea was key to piecing together the canola genome,” study coauthor Andrew Paterson of the University of Georgia said in a press release. “It's like a genetic love triangle between the three species, with canola sometimes favoring genes from B. rapa or B. oleracea or sometimes both.”

Understanding these events and how the species has evolved could “contribute to sustainable increases in oilseed crop production to meet growing demands for both edible and biofuel oils,” the authors wrote in their paper.

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