Navigation Links
DNA sequenced for parrot's ability to parrot
Date:7/2/2012

DURHAM, N.C. -- Scientists say they have assembled more completely the string of genetic letters that could control how well parrots learn to imitate their owners and other sounds.

The research team unraveled the specific regions of the parrots' genome using a new technology, single molecule sequencing, and fixing its flaws with data from older DNA-decoding devices. The team 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 July 1 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. He is interested in the sequences that regulate parrots' imitation abilities because they could give neuroscientists information about the gene regions that control speech development in humans.

Jarvis began his project with collaborators 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 assemble them into a draft genome. After doing the sequencing, the scientists discovered 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 Jarvis's sequencing struggles at a conference and approached him with a possible solution of modifying 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 thought 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 mistakes made it nearly impossible to create a genome assembly with the very long reads, Jarvis said.

But with a team, including scientists from the DOE Genome Science Institute and Cold Spring Harbor in New York, Phillippy, Koren and Jarvis corrected the Pacbio sequencer's errors using shorter, more accurate codes from the next-generation devices. The fix reduces the single-molecule, or third-generation, sequencing machine's error rate from 15 percent to less than one-tenth of one percent.

"Finally we have been able to assemble the regulatory regions of genes, such as FoxP2 and egr1, that are of interest to us and others in vocal learning behavior," Jarvis said.

He explained that FoxP2 is a gene required for speech development in humans and vocal learning in birds that learn to imitate sounds, like songbirds and parrots. Erg1 is a gene that controls the brain's ability to reorganize itself based on new experiences.

By being able to decode and organize the DNA that regulates these regions, neuroscientists may be able to better understand what genetic mechanism causes birds to imitate and sing well. They may also be able to collect more information about genetic factors that affect a person's ability to learn how to communicate well and to speak, Jarvis said. He and his team plan to describe the biology of the parrot's genetic code they sequenced in more detail in an upcoming paper.

Jarvis added that as more scientists use the hybrid sequencing approach, they could possibly decode complex, elusive genes linked to how cancer cells develop and to the sequences that control other brain functions.


'/>"/>

Contact: Ashley Yeager
ashley.yeager@duke.edu
919-681-8057
Duke University
Source:Eurekalert

Related biology news :

1. Asiatic pear genome sequenced
2. Ancient civilizations reveal ways to manage fisheries for sustainability
3. New genetic bar code technique establishes ability to derive DNA information from RNA
4. University of Minnesota invention helps advance reliability of alternative energy
5. Estrogen hormone reveals protective ability after traumatic brain injury
6. New form of intellectual disability discovered
7. Evidence of familial vulnerability for epilepsy and psychosis
8. Science, Innovation, and Partnerships for Sustainability -- Symposium May 16-18
9. Discovery of a new family of key mitochondrial proteins for the function and viability of the brain
10. New treatment for irritability in autism
11. Ability to estimate quantity increases in first 30 years of life
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:3/27/2017)... , March 27, 2017  Catholic Health Services ... Management Systems Society (HIMSS) Analytics for achieving Stage ... Model sm . In addition, CHS previously earned ... hospitals using an electronic medical record (EMR). ... high level of EMR usage in an outpatient ...
(Date:3/24/2017)... 24, 2017 Research and Markets has announced ... Analysis & Trends - Industry Forecast to 2025" report to ... The ... a CAGR of around 15.1% over the next decade to reach ... analyzes the market estimates and forecasts for all the given segments ...
(Date:3/23/2017)... 2017 Research and Markets has announced the ... Trends - Industry Forecast to 2025" report to their offering. ... The Global ... of around 8.8% over the next decade to reach approximately $14.21 ... market estimates and forecasts for all the given segments on global ...
Breaking Biology News(10 mins):
(Date:9/21/2017)... (PRWEB) , ... September 21, 2017 , ... ... scaffold technology, today announced the election of Paul Hermes, Entrepreneur in Residence at ... , Biorez has developed a proprietary, tissue-engineered scaffold for anterior cruciate ligament ...
(Date:9/20/2017)... (PRWEB) , ... September 20, 2017 , ... ... pathology, and Huron Digital Pathology , a provider of whole slide imaging ... Pathology Visions conference . The workshop, entitled “Successfully Deploying a Best-in-Class Strategy for ...
(Date:9/19/2017)... ... September 19, 2017 , ... ... the most dangerous step of sample prep for metals digestion—the addition of acids ... at an affordable price. The system is ideal for any laboratory performing their ...
(Date:9/19/2017)... Washington, D.C. (PRWEB) , ... September 19, 2017 ... ... care during an biological outbreak is about to be eliminated, said Lyle Probst, ... makes ExcitePCR’s FireflyDX™ technologies different than other pathogen detection solutions, Probst ...
Breaking Biology Technology: