Linked Life Data

12812058

Source:http://linkedlifedata.com/resource/pubmed/id/12812058

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2003-6-18
pubmed:abstractText
By using the whole genome sequences and EST data from the indica rice cultivar 93-11, a detailed relative analysis is made of the effect of some impact factors on synonymous codon usage. The results showed that the gene expression level assessed by mRNA abundance is positive relative to the "codon adaptation index" (CAI, 0.227**), and "codon preference parameter" (CPP, 0.145**), but negative relative to "effective number of codons" (ENC, -0.147**), indicating that genes with higher expression showed more significant variation in codon usage. There are significant negative correlations between gene length and CAI, CPP (r = -0.413** and -0.480** respectively), but a positive correlation between gene length and ENC(r = 0.210**), which suggested a tendency of shorter genes to higher expression of the transcriptional activity in 93-11. From the results that a higher negative correlation between GC content and ENC(r = -0.740**), but higher positive correlations between GC content and CAI, CPP (r = 0.877** and 0.832**, respectively), we can concluded that the GC content in coding region gave far more contribution to codon usage bias than that mRNA abundance and gene length. Four kinds of bases showed a three-period distribution in the translation initiation region, the bias at the first codon sites, which located +4, and +6, in the downstream of ATG being the largest. That suggested that there was a strong action of natural selection on these specific positions in the 93-11 genome. In this paper twenty-five codons defined firstly as "optimal codons" in 93-11 may provide some more useful information for rice gene-transformation.
pubmed:language
chi
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0379-4172
pubmed:author
pubmed:issnType
Print
pubmed:volume
30
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
335-40
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2003
pubmed:articleTitle
[Synonymous codon usage bias in the rice cultivar 93-11 (Oryza sativa L. ssp. indica)].
pubmed:affiliation
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou Genomics Institute, Hangzhou, China.
pubmed:publicationType
Journal Article, English Abstract, Research Support, Non-U.S. Gov't