PMID- 20438864
OWN - NLM
STAT- MEDLINE
DCOM- 20101105
LR  - 20211020
IS  - 1567-7257 (Electronic)
IS  - 1567-1348 (Print)
IS  - 1567-1348 (Linking)
VI  - 10
IP  - 6
DP  - 2010 Aug
TI  - Analysis of synonymous codon usage in porcine reproductive and respiratory 
      syndrome virus.
PG  - 797-803
LID - 10.1016/j.meegid.2010.04.010 [doi]
AB  - In this study, we calculated the relative synonymous codon usage (RSCU) values 
      and codon usage bias (CUB) values to implement a comparative analysis of codon 
      usage pattern of open reading frames (ORFs) which belong to the two main 
      genotypes of porcine reproductive and respiratory syndrome virus (PRRSV). By 
      analysis of synonymous codon usage values in each ORF of PRRSV, the optimal 
      codons for most amino acids were all C or G-ended codons except GAU for Asp, CAU 
      for His, UUU for Phe and CCU for Pro. The synonymous codon usage patterns in 
      different ORFs of PRRSV were different and genetically conserved. Among them, 
      ORF1a, ORF4, ORF5 and ORF7 could cluster these strains into the two main 
      serotypes (EU and US). Due to mutational pressure, compositional constraint 
      played an important role in shaping the synonymous codon usage pattern in 
      different ORFs, and the synonymous codon usage diversity in ORFs was correlated 
      with gene function. The degree of CUB for some particular amino acids under 
      strong selection pressure probably served as a potential genetic marker for each 
      ORF in PRRSV. However, gene length and translational selection in nature had no 
      effect on the synonymous codon usage pattern in PRRSV. These conclusions could 
      not only offer an insight into the synonymous codon usage pattern and 
      differentiation of gene function, but also assist in understanding the 
      discrepancy of evolution among ORFs in PRRSV.
CI  - Copyright 2010 Elsevier B.V. All rights reserved.
FAU - Liu, Yong-sheng
AU  - Liu YS
AD  - Key Laboratory of Animal Virology of Ministry of Agriculture, State Key 
      Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research 
      Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, PR 
      China.
FAU - Zhou, Jian-hua
AU  - Zhou JH
FAU - Chen, Hao-tai
AU  - Chen HT
FAU - Ma, Li-na
AU  - Ma LN
FAU - Ding, Yao-zhong
AU  - Ding YZ
FAU - Wang, Meng
AU  - Wang M
FAU - Zhang, Jie
AU  - Zhang J
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20100510
PL  - Netherlands
TA  - Infect Genet Evol
JT  - Infection, genetics and evolution : journal of molecular epidemiology and 
      evolutionary genetics in infectious diseases
JID - 101084138
RN  - 0 (Codon)
SB  - IM
MH  - Animals
MH  - Codon/analysis/genetics
MH  - DNA Mutational Analysis
MH  - Evolution, Molecular
MH  - Genome, Viral
MH  - Open Reading Frames
MH  - Phylogeny
MH  - *Point Mutation
MH  - Porcine Reproductive and Respiratory Syndrome/virology
MH  - Porcine respiratory and reproductive syndrome virus/classification/*genetics
MH  - Serotyping
MH  - Swine/*virology
PMC - PMC7106271
EDAT- 2010/05/05 06:00
MHDA- 2010/11/06 06:00
PMCR- 2010/05/01
CRDT- 2010/05/05 06:00
PHST- 2010/01/04 00:00 [received]
PHST- 2010/04/23 00:00 [revised]
PHST- 2010/04/24 00:00 [accepted]
PHST- 2010/05/05 06:00 [entrez]
PHST- 2010/05/05 06:00 [pubmed]
PHST- 2010/11/06 06:00 [medline]
PHST- 2010/05/01 00:00 [pmc-release]
AID - S1567-1348(10)00108-5 [pii]
AID - 10.1016/j.meegid.2010.04.010 [doi]
PST - ppublish
SO  - Infect Genet Evol. 2010 Aug;10(6):797-803. doi: 10.1016/j.meegid.2010.04.010. 
      Epub 2010 May 10.