Free Newsletters - Space News - Defense Alert - Environment Report - Energy Monitor
. Space Industry and Business News .




TECH SPACE
Big data: A method for obtaining large, phylogenomic data sets
by Staff Writers
St. Louis, MO (SPX) Jan 16, 2014


The final annotated chloroplast genome assembly of Bartsia inaequalis with the 16 overlapping primer combinations indicated. Note that the primer combinations for regions 11, 12, 13, and 16 amplify both inverted repeat A and B in a single reaction. Image courtesy Simon Uribe-Convers from: Uribe-Convers, S., J. R. Duke, M. J. Moore, and D. C. Tank. 2014. A long PCR-based approach for DNA enrichment prior to next-generation sequencing for systematic studies. Applications in Plant Sciences 2(1): 1300063. doi:10.3732/apps.1300063.

Traditional molecular systematic studies have progressed by sequencing genes one by one, a time- and cost-intensive task that has limited the amount of data a researcher could feasibly obtain. With the continual improvement of next-generation sequencing technologies, however, obtaining large molecular data sets is becoming much easier, and much cheaper. This increase in data means, in many cases, increased accuracy in reconstructing the evolutionary history of organisms.

As phylogenetic studies advance to include progressively more sequence data, new techniques are being developed to obtain such data sets. While it would be ideal to simply sequence entire genomes, this is not yet feasible across large numbers of taxa. Instead, current methods are being developed that allow researchers to target specific genomic regions of interest for the organisms being studied.

Scientists at the University of Idaho and Oberlin College have developed one such method to obtain large, phylogenomic data sets. "This method utilizes long PCR, or long-range PCR, to strategically generate DNA templates for next-generation sequencing," explains Simon Uribe-Convers, graduate student and lead author. The protocol is available for free viewing in the January issue of Applications in Plant Sciences.

Long-range PCR is a method that allows for the amplification of much larger fragments of DNA than is possible with traditional PCR-fragments larger than 40 kilobases have been reported in long PCR, versus fewer than 10 kilobases for traditional PCR. The authors of this study have developed a universal primer set across flowering plants that amplifies 3-15 kilobase fragments, which can then easily be sequenced using recently developed next-generation sequencing technologies.

Uribe-Convers and colleagues tested this approach by amplifying chloroplast genomes for 30 species across flowering plants. Surprisingly, the primers were even found to successfully amplify chloroplast regions in several pine species. To further test the compatibility of this approach with next-generation sequencing, 15 complete chloroplast genomes (often referred to as plastomes) were then sequenced.

Although this study focused on plastomes and utilized the popular Illumina sequencing platform, Uribe-Convers explains, "[t]his can easily be expanded to mitochondrial and nuclear regions, and can be used in combination with any next-generation sequencing platform. Furthermore, this approach is not restricted to plant studies, but will be useful for any organism."

With the development of new methods such as the one described by Uribe-Convers and colleagues, scientists can obtain large, phylogenomic data sets for large numbers of taxa. Long-range PCR, in concert with next-generation sequencing, provides researchers with the means to sequence entire plastomes, mitochondrial genomes, and large portions of the nuclear genome.

"This method has important implications for the way future systematic studies are conducted as it provides researchers with a way to strategically target regions of interest in their study organism, such as single-copy regions of the nuclear genome or portions of organellar genomes, to produce large data sets at low costs," says Uribe-Convers. "We want to help move the field of systematics into the realm of big data, and we hope that our approach contributes to that."

Simon Uribe-Convers, Justin R. Duke, Michael J. Moore, and David C. Tank. 2014. A long PCR-based approach for DNA enrichment prior to next-generation sequencing for systematic studies. Applications in Plant Sciences 2(1): 1300063. doi:10.3732/apps.1300063.

.


Related Links
American Journal of Botany
Space Technology News - Applications and Research






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle




Memory Foam Mattress Review
Newsletters :: SpaceDaily :: SpaceWar :: TerraDaily :: Energy Daily
XML Feeds :: Space News :: Earth News :: War News :: Solar Energy News





TECH SPACE
New computer memory can hold data 20 years without power
Singapore (UPI) Dec 30, 2013
Researchers in Singapore say they've developed new computer memory that can store more data and keep it intact 20 times longer than current magnetic memory. Engineers at the National University of Singapore say the new form of Magnetoresistive Random Access Memory technology will drastically increase storage space and ensure that fresh data stays intact, even in the case of a power fail ... read more


TECH SPACE
Starting Fire With Water

SimCity coming down from the "cloud"

GPM Completes Spacecraft Alignments

S. Asia takes 71 percent of market for ship breaking

TECH SPACE
Northrop Grumman Supports US Marine Corps Command, Control and Communications Facility for Tactical Air Operations

Rocket Rokot brings 3 Russian military-purpose satellites on orbit

US Air Force selects Raytheon's high-bandwidth satellite terminal for secure, protected communications

Military Communication Improved as 6th Boeing-built Wideband Satellite Enters Service

TECH SPACE
Vega Flight VV03 And Ariane Flight VA218

Competiveness, quality and launcher family evolution are the keywords for Arianespace in 2014 and beyond

Orbital Sciences launches second mission to space station

Cygnus Heads to Space for First Station Resupply Mission

TECH SPACE
Northrop Grumman and Trex Enterprises to Introduce Celestial Navigation to Soldier Precision Targeting Laser Systems

GPS Traffic Maps for Leatherback Turtles Show Hotspots to Prevent Accidental Fishing Deaths

China to upgrade homegrown GPS to improve accuracy

Beidou to cover world by 2020 with 30 satellites

TECH SPACE
Embraer says it met all regional jet delivery targets

Swiss could vote in May on fighter deal

US F-18 fighter crashes off Virginia coast

Lockheed Martin Receives JASSM Contract For Additional Finnish Air Force F-18 Integration

TECH SPACE
Ultra-flexible chip can be wrapped around a hair

Exfoliation method paves way for 2D materials to be used in printable photonics and electronics

Theorists Predict New State of Quantum Matter May Have Big Impact on Electronics

Low-power tunneling transistor for high-performance devices at low voltage

TECH SPACE
Charles River Analytics Develops Satellite Image Processing System for NASA

Earth may be heaver than thought due to invisible belt of dark matter

More BARREL Balloons Take to the Skies

China's HD observation satellite opens its eyes

TECH SPACE
Toxic chemicals found in children's clothes, shoes: Greenpeace

Italy's govt agrees to send in army against mafia dumps

Hong Kong suffers in smog as pollution problems rise

ADB says China and Japan should tackle pollution together




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement