PMID- 32179080
OWN - NLM
STAT- MEDLINE
DCOM- 20210603
LR  - 20210603
IS  - 1872-8359 (Electronic)
IS  - 0167-7012 (Linking)
VI  - 172
DP  - 2020 May
TI  - A simple 18S rDNA approach for the identification of cultured eukaryotic 
      microalgae with an emphasis on primers.
PG  - 105890
LID - S0167-7012(19)30673-6 [pii]
LID - 10.1016/j.mimet.2020.105890 [doi]
AB  - Any forms of valorization of microorganisms would require accurate identity 
      recognition to ensure repeatability, reproducibility and quality assurance. This 
      study aimed to evaluate the effectiveness of different primers for identifying 
      cultured eukaryotic microalgae using a simple 18S rDNA approach. A total of 34 
      isolated microalgae and one culture collection were utilized in the search for an 
      effective molecular identification method for microalgae. Ammonium formate was 
      applied to marine microalgae prior to DNA extraction. The microalgal DNA was 
      extracted using a commercial kit and subjected directly to PCR amplification 
      using four different published 18S rDNA primers. The DNA sequences were analysed 
      using Basic Local Alignment Search Tool (BLAST) and phylogenetic trees to 
      determine the microalgae identity. The identity was further validated with 
      conventional morphological taxonomic identification, and the relationship of 
      microalgal morphology and genetic materials was also determined. The microalgal 
      DNA was successfully amplified, including marine species without prior cleaning. 
      In addition, the ss5 + ss3 primer pair was found to be an ideal primer set among 
      the tested primers for identifying microalgae. Overall, molecular identification 
      showed relative matching with morphological identification (82.86%). This study 
      is important because it serves as a platform to develop a standardized eukaryotic 
      microalgae identification method. In addition, this method could help to ease the 
      eukaryotic microalgae identification process and enrich the current reference 
      databases such as GenBank.
CI  - Copyright (c) 2020 Elsevier B.V. All rights reserved.
FAU - Khaw, Yam Sim
AU  - Khaw YS
AD  - Marine Biotechnology Laboratory, Institute of Bioscience, Universiti Putra 
      Malaysia, 43400 Serdang, Selangor, Malaysia.
FAU - Khong, Nicholas Mun Hoe
AU  - Khong NMH
AD  - Marine Biotechnology Laboratory, Institute of Bioscience, Universiti Putra 
      Malaysia, 43400 Serdang, Selangor, Malaysia; School of Pharmacy, Monash 
      University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, 
      Malaysia.
FAU - Shaharuddin, Noor Azmi
AU  - Shaharuddin NA
AD  - Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, 
      Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
FAU - Yusoff, Fatimah Md
AU  - Yusoff FM
AD  - Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 
      43400 Serdang, Selangor, Malaysia; International Institute of Aquaculture and 
      Aquatic Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.. 
      Electronic address: fatimahyus@gmail.com.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200313
PL  - Netherlands
TA  - J Microbiol Methods
JT  - Journal of microbiological methods
JID - 8306883
RN  - 0 (DNA, Ribosomal)
RN  - 0 (RNA, Ribosomal, 18S)
SB  - IM
MH  - Base Sequence
MH  - DNA, Ribosomal/*genetics
MH  - Eukaryota/classification/*genetics/*isolation & purification
MH  - Microalgae/classification/*genetics/*isolation & purification
MH  - Phylogeny
MH  - Polymerase Chain Reaction/methods
MH  - RNA, Ribosomal, 18S/genetics
MH  - Reproducibility of Results
OTO - NOTNLM
OT  - 18S rRNA gene
OT  - Cultured microalgae
OT  - Eukaryotic
OT  - Molecular identification
OT  - PCR amplification
OT  - Primer
COIS- Declaration of Competing Interest The authors declare no conflict of interest.
EDAT- 2020/03/18 06:00
MHDA- 2021/06/04 06:00
CRDT- 2020/03/18 06:00
PHST- 2019/08/14 00:00 [received]
PHST- 2020/02/22 00:00 [revised]
PHST- 2020/03/10 00:00 [accepted]
PHST- 2020/03/18 06:00 [pubmed]
PHST- 2021/06/04 06:00 [medline]
PHST- 2020/03/18 06:00 [entrez]
AID - S0167-7012(19)30673-6 [pii]
AID - 10.1016/j.mimet.2020.105890 [doi]
PST - ppublish
SO  - J Microbiol Methods. 2020 May;172:105890. doi: 10.1016/j.mimet.2020.105890. Epub 
      2020 Mar 13.