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Genome Digest

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

By | July 11, 2012

image: Genome Digest FLICKR CREATIVE COMMONS, MARTIN PETTITT

How parrots parrot
Species: Budgerigar, Melopsittacus undulatus
Genome size: 1.12 billion base pairs

Interesting fact: Using a new method that combines old and new techniques to improve efficiency and accuracy, researchers have sequenced a parrot genome for the first time, giving a clearer view of the region that may control the bird's ability to mimic human speech. The team was able to assemble the regulatory regions of the FoxP2 and Egr1 genes, involved in speech development and the brain's ability to reorganize itself based on new experiences, respectively. FoxP2 is also known to be involved in vocal learning in birds that imitate sounds, like songbirds and parrots.

S. Koren et al., "Hybrid error correction and de novo assembly of single-molecule sequencing reads," Nature Biotechnology, 30: 693–700, 2012.

The high life
Species: Yak, Bos grunniens
Genome size: 2,657 million base pairs

FLICKR CREATIVE COMMONS, JEROME BON

Interesting fact: The yak genome has evolved a series of adaptations to living on the high Tibetan plateaus, after it split from its common ancestor with the cow nearly 5 million years ago. Three genes help the yak survive in the low-oxygen environment, and five genes optimize the energy it gets from food, a scarce resource in its rocky environment. Decoding these genes could help treat and prevent altitude sickness and complications that arise when high climbers don't get enough oxygen.

Q Qiu et al., "The yak genome and adaptation to life at high altitude," Nature Genetics, doi:10.1038/ng.2343, 2012.

The sweetest melon
Species: Melon (7 varieties), Cucumis melo
Genome size: 450 million base pairs

Interesting fact: Melons are known to be highly variable, and of the 7 varieties sequenced in this study, 411 genes were recognized as important in disease resistance, suggesting the melon has a high capability for adapting to different environments. The researchers also found 26 genes related to the color of the melon flesh, and 63 related to sugar accumulation, key aspects of the melon’s commercial properties.

J Garcia-Mas et al., "The genome of melon (Cucumis melo L.)," Proceedings of the National Academy of Science, doi: 10.1073/pnas.1205415109, 2012.

Filling in the gaps
Species: Sunflower, Helianthus annuus
Genome size: 3.5 billion base pairs

FLICKR CREATIVE COMMONS, TOMÁŠ OBŠÍVAC

Interesting fact: Sunflower oil is an important commercial vegetable oil, and has no close relatives whose genomes have been fully sequenced and published. Researchers made use of high-throughput genotyping technology to combine the genetic maps of four sunflower populations and create a high-density picture of genetic linkages. Although the individual maps, containing 3,500–5,500 loci each, were very similar to each other, there were blank regions in each one where no markers could be plotted due to localized variation in recombination rates. A consensus map of 10,080 loci, however, filled in the gaps.

J. Bowers et al., "Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses," G3: Genes Genomes Genetics, 2:721-729, 2012.

The banana's roots
Species: Pahang banana, Musa acuminata
Genome size: 523 million base pairs

Interesting fact: The banana has a complex set of genetics, and is the first non-grass monocotyledon (a major group of flowering plants) to have its genome sequenced. An important crop, and a favorite fruit among industrialized nations, the banana has experienced three rounds of whole-genome duplications since it arose in the Jurassic period. Commercial bananas have been bred to be very different from their wild counterparts, and diseases and pests have evolved quickly alongside them, devastating the banana industry in certain parts of the world. Further digging into the genome should help find ways to manipulate future banana crops to avoid these disasters.

A. D'Hont et al., "The banana (Musa acuminata) genome and the evolution of monocotyledonous plants," Nature, doi:10.1038/nature11241, 2012.

 

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