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Genome Digest

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

By | October 15, 2012

 

Wikimedia, I. G. Safonov
Budding buttons
 
Species: Button mushrooms, Agaricus bisporus
Genome size: ~30 million base pairs
 
Interesting fact: Button mushrooms are one of the most common commercially grown mushroom in the world—comprising a multibillion dollar industry—and the release of the first genome sequencing for the species reveals their secrets to living in leafy litter and forest floors. These ecologically valuable decomposers have an arsenal of polysaccharide-degrading enzymes that deconstruct wood and other plant material, which they switch on depending on their surroundings. Researchers also identified key genes involved in starting mushroom reproduction, known as budding, which is the biggest challenge for mushroom growers around the world.
 
E. Morin, et al., “Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche,” Proceedings of the National Academies of Science, doi: 10.1073/pnas.1206847109, 2012.
 

A quarter of cotton

Wikimedia, USDA
Species: South American cotton, Gossypium raimondii
Genome size: 880 million base pairs
 
Interesting fact: Researchers suspect that the ancestral diploid genome of Gossypium raimondii, a wild cotton from Peru and Ecuador, may have been incorporated as one of the four “sub-genomes” into the genetic code of two other cotton species, G. hirsutum and G. barbadense, plants used for commercial fiber production that both carry tetraploid genomes. The researchers reasoned that sequencing the less complex diploid genome of G. raimondii will serve as a useful step to decoding the tangled tetraploid genomes of the two commercially relevant species.
 
K. Wang, et al. “The draft genome of a diploid cotton Gossypium raimondii,” Nature Genetics, 44:1098-1103, 2012.
 

How to grow a limb

Wikimedia, US Fish and Wildlife Service
Species: American paddlefish, Polyodon spathula
Genome size: 1.9 billion base pairs
 
Interesting fact: The American paddlefish, known for its long, paddle-like snout, may have duplicated its genome about 42 million years ago, which would throw a wrench into the study of limb development. Paddlefish sit at the base of the evolutionary branch where boney fish climbed into tetrapods, and thus have been the focus of research into the evolution of limbs. Duplications in the genome would provide extra genetic blueprints from which new features can evolve, scientists speculate.
 
K.D. Crow, et al., “An independent genome duplication inferred from Hox paralogs in the American paddlefish-a representative basal ray-finned fish and important comparative reference,” Genome Biology, doi: 10.1093/gbe/evs067, 2012.
 

Cracking stress tolerance

Wikimedia, Urville86
Species: Pacific oyster, Crassostrea gigas
Genome size: ~823 million base pairs
 
Interesting fact: The Pacific oyster genome is the first mollusk genome to be sequenced, and it reveals pearls of information about how the hard-shelled creatures tolerate marine stresses, like fluctuations in salinity, exposure to heavy metals, and temperature swings. For example, the newly sequenced genome contains an expanded array of anti-cell death proteins that could be key to dodging apoptosis under stressful conditions. Transcriptional analysis also found that immune-related genes were highly expressed in the oyster’s gut, suggesting that the filter-feeder best wards off invading pathogens by protecting its digestive system.
 
G. Zhang, et al., “The oyster genome reveals stress adaptation and complexity of shell formation,” Nature, doi: 10.1038/nature11413, 2012.
 

Reading rice genomes

Wikimedia, echiner1
Species: Wild Asian rice, Oryza rufipogon
Genome size: 370 million base pairs
Species: Long-grain rice, Oryza sativa L. ssp. indica
Genome size: 466 million base pairs
Species: Short-grain rice, Oryza sativa L. ssp. japonica 
Genome size: 488 million base pairs
 
Interesting fact: A comparative study of the newly sequenced wild Asian rice and the sequences of nearly 1,500 variants of two domesticated varieties—long-grain and short-grain rice—finds that long-grain rice actually evolved from an ancestor of short-grain rice, contradicting a long-held belief that the two domestic rice types were both domesticated from wild rice. The comparison also found 55 genetic signatures of the two domesticated varieties, helping rice breeders and evolutionary scientists better understand the genetics of domestication.
 
X. Huang, et al., “A map of rice genome variation reveals the origin of cultivated rice.” Nature, doi: 10.1038/nature11532, 2012.
 
 
 

 

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