PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

Big data: A method for obtaining large, phylogenomic data sets

New approach combines long-range PCR and next-generation sequencing, allowing systematists to sequence large portions of the genome

2014-01-09
(Press-News.org) Contact information: Beth Parada
apps@botany.org
American Journal of Botany
Big data: A method for obtaining large, phylogenomic data sets New approach combines long-range PCR and next-generation sequencing, allowing systematists to sequence large portions of the genome

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."

INFORMATION:

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.

Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal focusing on new tools, technologies, and protocols in all areas of the plant sciences. It is published by the Botanical Society of America, a nonprofit membership society with a mission to promote botany, the field of basic science dealing with the study and inquiry into the form, function, development, diversity, reproduction, evolution, and uses of plants and their interactions within the biosphere. APPS is available as part of BioOne's Open Access collection.

For further information, please contact the APPS staff at apps@botany.org.



ELSE PRESS RELEASES FROM THIS DATE:

SHY hypothesis explains that sleep is the price we pay for learning

2014-01-09
SHY hypothesis explains that sleep is the price we pay for learning MADISON — Why do animals ranging from fruit flies to humans all need to sleep? After all, sleep disconnects them from their environment, puts them at risk and keeps them from seeking ...

Red blood cells take on many-sided shape during clotting

2014-01-09
Red blood cells take on many-sided shape during clotting Penn Medicine researchers find new role in stemming bleeding and preventing obstruction of blood flow, explaining need for speed in busting harmful clots PHILADELPHIA - Red blood ...

National Academy of Inventors 2013 Conference showcased global innovation

2014-01-09
National Academy of Inventors 2013 Conference showcased global innovation Innovators gathered from around the world to honor academic invention TAMPA, Fla. (Jan. 9, 2014) – The current special issue of Technology and Innovation- Proceedings of the National ...

T2 and collaborators announce discovery of novel clot structure biology enabled by T2HemoStat

2014-01-09
T2 and collaborators announce discovery of novel clot structure biology enabled by T2HemoStat T2HemoStat detection of novel clot behavior could direct therapeutic choices for stroke and heart attack victims Lexington, MA, January 9, 2014 – T2 ...

Stanford researcher's work provides glimpse into health of most-extreme runners

2014-01-09
Stanford researcher's work provides glimpse into health of most-extreme runners STANFORD, Calif. — For some runners, a marathon is not enough. Participation in so-called ultramarathons — defined as any distance beyond the standard 26.2-mile marathon ...

Study: 2-sizes-too-small 'Grinch' effect hampers heart transplantation success

2014-01-09
Study: 2-sizes-too-small 'Grinch' effect hampers heart transplantation success 22 years of data suggest need for new heart-size matching strategy to improve outcomes Baltimore, MD – January 8, 2014 – Current protocols for matching donor hearts to recipients ...

Epilepsy drug taken in pregnancy found safe in preschool child development

2014-01-09
Epilepsy drug taken in pregnancy found safe in preschool child development MINNEAPOLIS – A new study finds that the epilepsy drug levetiracetam appears not to be associated with thinking, movement and language problems for preschool children born to mothers who ...

2 million years ago, human relative 'Nutcracker Man' lived on tiger nuts

2014-01-09
2 million years ago, human relative 'Nutcracker Man' lived on tiger nuts An Oxford University study has concluded that our ancient ancestors who lived in East Africa between 2.4 million-1.4 million years ago mainly ate tiger nuts (grass bulbs) supplemented ...

Cardiologists urged to reduce inappropriate radiation exposure

2014-01-09
Cardiologists urged to reduce inappropriate radiation exposure Radiation from cardiology procedures equals more than 50 chest X-rays per person each year Sophia Antipolis, 9 January 2014: Cardiologists are being urged to reduce patient radiation exposure ...

New study finds upper-airway electronic stimulation effective for obstructive sleep apnea

2014-01-09
New study finds upper-airway electronic stimulation effective for obstructive sleep apnea UH Case Medical Center one of US and European clinical trial sites showing marked improvements for sleep apnea sufferers CLEVELAND: Results published ...

LAST 30 PRESS RELEASES:

Intra-arterial tenecteplase for acute stroke after successful endovascular therapy

Study reveals beneficial microbes that can sustain yields in unfertilized fields

Robotic probe quickly measures key properties of new materials

Climate change cuts milk production, even when farmers cool their cows

Frozen, but not sealed: Arctic Ocean remained open to life during ice ages

Some like it cold: Cryorhodopsins

Demystifying gut bacteria with AI

Human wellbeing on a finite planet towards 2100: new study shows humanity at a crossroads

Unlocking the hidden biodiversity of Europe’s villages

Planned hydrogen refuelling stations may lead to millions of euros in yearly losses

Planned C-sections increase the risk of certain childhood cancers

Adults who have survived childhood cancer are at increased risk of severe COVID-19

Drones reveal extreme coral mortality after bleaching

New genetic finding uncovers hidden cause of arsenic resistance in acute promyelocytic leukemia

Native habitats hold the key to the much-loved smashed avocado’s future

Using lightning to make ammonia out of thin air

Machine learning potential-driven insights into pH-dependent CO₂ reduction

Physician associates provide safe care for diagnosed patients when directly supervised by a doctor

How game-play with robots can bring out their human side

Asthma: patient expectations influence the course of the disease

UNM physician tests drug that causes nerve tissue to emit light, enabling faster, safer surgery

New study identifies EMP1 as a key driver of pancreatic cancer progression and poor prognosis

XPR1 identified as a key regulator of ovarian cancer growth through autophagy and immune evasion

Flexible, eco-friendly electronic plastic for wearable tech, sensors

Can the Large Hadron Collider snap string theory?

Stuckeman professor’s new book explores ‘socially sustainable’ architecture

Synthetic DNA nanoparticles for gene therapy

New model to find treatments for an aggressive blood cancer

Special issue of Journal of Intensive Medicine analyzes non-invasive respiratory support

T cells take aim at Chikungunya virus

[Press-News.org] Big data: A method for obtaining large, phylogenomic data sets
New approach combines long-range PCR and next-generation sequencing, allowing systematists to sequence large portions of the genome