July 5, 2012

redOrbit Staff & Wire Reports Your Universe Online

Scientists say they have put together a more complete string of genetic letters that may control how well parrots learn to imitate their owners and other noises.

Researchers unraveled the certain regions of the parrots genome using a new technology, single molecule sequencing, and fixing its flaws with data from older DNA-decoding devices. Researchers also decoded hard-to-sequence genetic material from corn and bacteria as proof of their new sequencing approach. The results of the study appeared online recently in the journal Nature Biotechnology.

Single molecule sequencing got a lot of hype last year because it generates long sequencing reads, supposedly making it easier to assemble complex parts of the genome, said Duke University neurobiologist Erich Jarvis, a co-author of the study.

Jarvis is interested in the sequences that regulate parrots imitation abilities because they could give neuroscientists information about the gene regions that control speaking development in humans.

Jarvis began his project with others by trying to piece together the genome regions with what are known as next-generation sequencers, which read chunks of 100 to 400 DNA base pairs at a time and then take a few days to put them together into a draft genome. After doing the sequencing, the scientists noticed that the read lengths were not long enough to assemble the regulatory regions of some of the genes that control brain circuits for vocal learning.

University of Maryland computational biologists Adam Phillippy and Sergey Koren experts at assembling genomes heard about Jarviss sequencing struggles at a conference and approached him with a possible solution of adjusting the algorithms that order the DNA base pairs. But the fix was still not sufficient.

Last year, 1000 base-pair reads by Roch 454 became available, as did the single molecule sequencer by Pacific Biosciences. The Pacbio technology generates strands of 2,250 to 23,000 base pairs at a time and can draft an entire genome in about a day.

Jarvis and others assumed the new technologies would solve the genome-sequencing challenges. Through a competition, called the Assemblathon, the scientists discovered that the Pacbio machine had trouble accurately decoding complex regions of the parrot, Melopsittacus undulates, genome. The machine had a high error rate, generating the wrong genetic letter at every fifth or sixth spot in a string of DNA. The errors made it nearly impossible to create a genome assembly with the very long reads, Jarvis said.

See the article here:
Genetics Could Explain Parrots Ability To Parrot

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