PMID- 24069432
OWN - NLM
STAT- MEDLINE
DCOM- 20140615
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 8
IP  - 9
DP  - 2013
TI  - Identification of reference genes for qRT-PCR analysis in Yesso scallop 
      Patinopecten yessoensis.
PG  - e75609
LID - 10.1371/journal.pone.0075609 [doi]
LID - e75609
AB  - BACKGROUND: Bivalves comprise around 30,000 extant species and have received much 
      attention for their importance in ecosystems, aquaculture and evolutionary 
      studies. Despite the increasing application of real-time quantitative reverse 
      transcription PCR (qRT-PCR) in gene expression studies on bivalve species, little 
      research has been conducted on reference gene selection which is critical for 
      reliable and accurate qRT-PCR analysis. For scallops, systematic evaluation of 
      reference genes that can be used among tissues or embryo/larva stages is lacking, 
      and beta-actin (ACT) is most frequently used as qRT-PCR reference gene without 
      validation. RESULTS: In this study, 12 commonly used candidate reference genes 
      were selected from the transcriptome data of Yesso scallop 
      (Patinopectenyessoensis) for suitable qRT-PCR reference genes identification. The 
      expression of these genes in 36 tissue samples and 15 embryo/larva samples under 
      normal physiological conditions was examined by qRT-PCR, and their expression 
      stabilities were evaluated using three statistic algorithms, geNorm, NormFinder, 
      and comparative ∆Ct method. Similar results were obtained by the three approaches 
      for the most and the least stably expressed genes. Final comprehensive ranking 
      for the 12 genes combing the results from the three programs showed that, for 
      different tissues, DEAD-box RNA helicase (HELI), ubiquitin (UBQ), and 60S 
      ribosomal protein L16 (RPL16) were the optimal reference genes combination, while 
      for different embryo/larva stages, gene set containing Cytochrome B (CB), 
      Cytochrome C (CC), Histone H3.3 (His3.3), and Glyceraldehyde-3-phosphate 
      dehydrogenase (GAPDH) were recommended for qRT-PCR normalization. ACT was among 
      the least stable genes for both adult tissues and embryos/larvae. CONCLUSIONS: 
      This work constitutes the first systematic analysis on reference genes selection 
      for qRT-PCR normalization in scallop under normal conditions. The suitable 
      reference genes we recommended will be useful for the identification of genes 
      related to biological processes in Yesso scallop, and also in the reference gene 
      selection for other scallop or bivalve species.
FAU - Feng, Liying
AU  - Feng L
AD  - Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, 
      College of Marine Life Sciences, Ocean University of China, Qingdao, China.
FAU - Yu, Qian
AU  - Yu Q
FAU - Li, Xue
AU  - Li X
FAU - Ning, Xianhui
AU  - Ning X
FAU - Wang, Jing
AU  - Wang J
FAU - Zou, Jiajun
AU  - Zou J
FAU - Zhang, Lingling
AU  - Zhang L
FAU - Wang, Shi
AU  - Wang S
FAU - Hu, Jingjie
AU  - Hu J
FAU - Hu, Xiaoli
AU  - Hu X
FAU - Bao, Zhenmin
AU  - Bao Z
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20130919
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - Animals
MH  - Bivalvia/*genetics
MH  - *Gene Expression Profiling
MH  - Gene Expression Regulation
MH  - Organ Specificity
MH  - RNA Stability
MH  - Real-Time Polymerase Chain Reaction
MH  - Transcriptome
PMC - PMC3777977
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2013/09/27 06:00
MHDA- 2014/06/16 06:00
PMCR- 2013/09/19
CRDT- 2013/09/27 06:00
PHST- 2013/04/24 00:00 [received]
PHST- 2013/08/15 00:00 [accepted]
PHST- 2013/09/27 06:00 [entrez]
PHST- 2013/09/27 06:00 [pubmed]
PHST- 2014/06/16 06:00 [medline]
PHST- 2013/09/19 00:00 [pmc-release]
AID - PONE-D-13-16999 [pii]
AID - 10.1371/journal.pone.0075609 [doi]
PST - epublish
SO  - PLoS One. 2013 Sep 19;8(9):e75609. doi: 10.1371/journal.pone.0075609. eCollection 
      2013.