Featured Research

from universities, journals, and other organizations

GenSeq: Updated nomenclature for genetic sequences to solve taxonomic determination issues

Date:
November 1, 2013
Source:
Pensoft Publishers
Summary:
An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. Verifying the taxonomic identity of the voucher specimens that are the source of genetic materials has become increasingly difficult but remains vitally important; this new nomenclatural system for DNA sequences helps remedy this issue.

This image illustrates the logic of the GenSeq nomenclature.
Credit: Prosanta Chakrabarty; CC-BY 3.0

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the "Genetypes" naming system, which some have been reluctant to adopt because of the use of the "type" suffix in the terminology. The study was published in the open access journal Zookeys.

Related Articles


The use of genetic sequences has been increasing with each passing year but unfortunately, the separation between voucher specimens and genetic sequences is similarly growing. With increasing frequency, the link between the genetic sequences being used in analyses and the organisms from which they came is not being reported. The taxonomic determination remains solely the responsibility of the submitter of the sequences. Erroneous identifications are difficult to discover, and the perpetuation of the error in subsequent uses of the sequence data is nearly impossible to stop.

In the new nomenclature, genetic sequences are labeled "genseq," followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types -- "genseq-1," secondary types -- "genseq-2," collection-vouchered topotypes -- "genseq-3," collection-vouchered non-types -- "genseq-4," and non-types that lack specimen vouchers but have photo vouchers -- "genseq-5."

To demonstrate use of the new nomenclature, the authors of the study review recently published news species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications.

"Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data,"explains one of the authors Dr. Prosanta Chakrabarty, Museum of Natural Science, Louisiana State University. "We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made."


Story Source:

The above story is based on materials provided by Pensoft Publishers. The original story is licensed under a Creative Commons License. Note: Materials may be edited for content and length.


Journal Reference:

  1. Prosanta Chakrabarty, Melanie Warren, Lawrence Page, Carole Baldwin. GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources. ZooKeys, 2013; 346: 29 DOI: 10.3897/zookeys.346.5753

Cite This Page:

Pensoft Publishers. "GenSeq: Updated nomenclature for genetic sequences to solve taxonomic determination issues." ScienceDaily. ScienceDaily, 1 November 2013. <www.sciencedaily.com/releases/2013/11/131101112414.htm>.
Pensoft Publishers. (2013, November 1). GenSeq: Updated nomenclature for genetic sequences to solve taxonomic determination issues. ScienceDaily. Retrieved October 25, 2014 from www.sciencedaily.com/releases/2013/11/131101112414.htm
Pensoft Publishers. "GenSeq: Updated nomenclature for genetic sequences to solve taxonomic determination issues." ScienceDaily. www.sciencedaily.com/releases/2013/11/131101112414.htm (accessed October 25, 2014).

Share This



More Plants & Animals News

Saturday, October 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Deep Sea 'mushroom' Could Be Early Branch on Tree of Life

Deep Sea 'mushroom' Could Be Early Branch on Tree of Life

Reuters - Innovations Video Online (Oct. 24, 2014) Miniature deep sea animals discovered off the Australian coast almost three decades ago are puzzling scientists, who say the organisms have proved impossible to categorise. Academics at the Natural History of Denmark have appealed to the world scientific community for help, saying that further information on Dendrogramma enigmatica and Dendrogramma discoides could answer key evolutionary questions. Jim Drury has more. Video provided by Reuters
Powered by NewsLook.com
Black Bear Cub Goes Sunday Shopping

Black Bear Cub Goes Sunday Shopping

Reuters - Light News Video Online (Oct. 23, 2014) Price check on honey? Bear cub startles Oregon drugstore shoppers. Rough Cut (no reporter narration). Video provided by Reuters
Powered by NewsLook.com
Dances With Wolves in China's Wild West

Dances With Wolves in China's Wild West

AFP (Oct. 23, 2014) One man is on a mission to boost the population of wolves in China's violence-wracked far west. The animal - symbol of the Uighur minority there - is under threat with a massive human resettlement program in the region. Duration: 00:41 Video provided by AFP
Powered by NewsLook.com
Breakfast Debate: To Eat Or Not To Eat?

Breakfast Debate: To Eat Or Not To Eat?

Newsy (Oct. 23, 2014) Conflicting studies published in the same week re-ignited the debate over whether we should be eating breakfast. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins