A noninvasive molecular approach: Exploiting species-locus-specific pcr primers in defeating numts and dna cross-contamination of cercopithecidae

M. A.B. Abdul-Latiff, N. R. Aifat, Salmah Yaakop, Badrul Munir Md. Zain

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts).

Original languageEnglish
Pages (from-to)1015-1023
Number of pages9
JournalJournal of Animal and Plant Sciences
Volume27
Issue number3
Publication statusPublished - 1 Jun 2017

Fingerprint

Cercopithecidae
cross contamination
loci
polymerase chain reaction
Macaca nemestrina
pseudogenes
Macaca fascicularis
cytochrome b
sampling
cytochrome-c oxidase
Primates
mitochondrial DNA
researchers
feces
history
new species
DNA
methodology

Keywords

  • Macaca
  • Noninvasive
  • Numts
  • Species-locus-specific primers
  • Trachypithecus

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Plant Science

Cite this

@article{3c1e1f71d5d849a39f4500e8030792d9,
title = "A noninvasive molecular approach: Exploiting species-locus-specific pcr primers in defeating numts and dna cross-contamination of cercopithecidae",
abstract = "The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts).",
keywords = "Macaca, Noninvasive, Numts, Species-locus-specific primers, Trachypithecus",
author = "Abdul-Latiff, {M. A.B.} and Aifat, {N. R.} and Salmah Yaakop and {Md. Zain}, {Badrul Munir}",
year = "2017",
month = "6",
day = "1",
language = "English",
volume = "27",
pages = "1015--1023",
journal = "Journal of Animal and Plant Sciences",
issn = "1018-7081",
publisher = "Pakistan Agricultural Scientists Forum",
number = "3",

}

TY - JOUR

T1 - A noninvasive molecular approach

T2 - Exploiting species-locus-specific pcr primers in defeating numts and dna cross-contamination of cercopithecidae

AU - Abdul-Latiff, M. A.B.

AU - Aifat, N. R.

AU - Yaakop, Salmah

AU - Md. Zain, Badrul Munir

PY - 2017/6/1

Y1 - 2017/6/1

N2 - The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts).

AB - The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts).

KW - Macaca

KW - Noninvasive

KW - Numts

KW - Species-locus-specific primers

KW - Trachypithecus

UR - http://www.scopus.com/inward/record.url?scp=85021378938&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85021378938&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:85021378938

VL - 27

SP - 1015

EP - 1023

JO - Journal of Animal and Plant Sciences

JF - Journal of Animal and Plant Sciences

SN - 1018-7081

IS - 3

ER -