Navigation Links
Big data: A method for obtaining large, phylogenomic data sets
Date:1/9/2014

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 PCRfragments 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 315 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."


'/>"/>
Contact: Beth Parada
apps@botany.org
American Journal of Botany
Source:Eurekalert  

Related biology news :

1. Kaiser Permanentes Robert Mangel to Speak at Rock Stars of Big Data: Register Now to Reserve Your Space
2. Discovery leads to patent for novel method of treating traumatic brain injury
3. Penn biologists establish new method for studying RNAs regulatory footprint
4. Updating air pollution measurement methods with air quality, health effects research
5. Most clinical studies on vitamins flawed by poor methodology
6. A magnetic nanoparticles-based method for DNA extraction from the saliva after stroke
7. Novel method could help bring cancer biomarkers to clinic
8. New method of DNA editing allows synthetic biologists to unlock secrets of a bacterial genome
9. New method for stabilizing hemoglobin could lead to stable vaccines, artificial blood
10. SU biologist develops method for monitoring shipping noise in dolphin habitat
11. UCSB biomedical scientist discovers a new method to increase survival in sepsis
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Big data: A method for obtaining large, phylogenomic data sets
(Date:6/1/2016)... YORK , June 1, 2016 ... Technology in Election Administration and Criminal Identification to Boost ... to a recently released TechSci Research report, " Global ... By Region, Competition Forecast and Opportunities, 2011 - 2021", ... 24.8 billion by 2021, on account of growing security ...
(Date:5/12/2016)... , May 12, 2016 WearablesResearch.com , ... published the overview results from the Q1 wave of ... recent wave was consumers, receptivity to a program where ... with a health insurance company. "We were ... share," says Michael LaColla , CEO of Troubadour ...
(Date:4/28/2016)... First quarter 2016:   , Revenues amounted to ... of 2015 The gross margin was 49% (27) ... operating margin was 40% (-13) Earnings per share rose ... was SEK 249.9 M (21.2) , Outlook   ... The operating margin for 2016 is estimated to exceed ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... ... June 24, 2016 , ... While the majority of commercial spectrophotometers and fluorometers ... the 6000i models are higher end machines that use the more unconventional z-dimension of ... beam from the bottom of the cuvette holder. , FireflySci has developed several ...
(Date:6/23/2016)... , June 23, 2016 /PRNewswire/ - FACIT has ... Ontario biotechnology company, Propellon Therapeutics Inc. ... and commercialization of a portfolio of first-in-class WDR5 ... targets such as WDR5 represent an exciting class ... in precision medicine for cancer patients. Substantial advances ...
(Date:6/23/2016)... , June, 23, 2016  The Biodesign Challenge (BDC), ... new ways to harness living systems and biotechnology, announced ... (MoMA) in New York City . ... participating students, showcased projects at MoMA,s Celeste Bartos Theater ... Antonelli , MoMA,s senior curator of architecture and design, ...
(Date:6/23/2016)... , June 23, 2016 Apellis Pharmaceuticals, ... 1 clinical trials of its complement C3 inhibitor, ... and multiple ascending dose studies designed to assess ... of subcutaneous injection in healthy adult volunteers. ... either as a single dose (ranging from 45 ...
Breaking Biology Technology: