DocumentCode :
3632360
Title :
RNA Secondary Structure and Sequence Variability of the 3´ End of Strawberry Mild Yellow Edge Virus Genome
Author :
Lili Li;Hong-Yi Yang
Author_Institution :
Coll. of Horticulture, Shenyang Agric. Univ., Shenyang, China
fYear :
2009
fDate :
6/1/2009 12:00:00 AM
Firstpage :
1
Lastpage :
4
Abstract :
The specific segment in 3´ terminal region of strawberry mild yellow edge virus (SMYEV) genome was amplified by 3´ rapid amplification of cDNA ends (RACE). Ten Chinese isolates were sequenced. Sequence analysis of coat protein gene showed nucleotide and deduced amino acid identities ranged from 76.8 to 100% and 86.4 to 100%, respectively. Phylogenetic analysis showed that all isolates of SMYEV fell into four clades. To a certain extent, the clades were related to the geological distribution of SMYEV. Isolates SY02 and SY03, derived from Fragaria pentaphylla and F.xananassa cv. Changhong 2, respectively, had a far relationship with other isolates and fell into one clade. They were likely to be the special isolates that only existed in China. The 3´ untranslated region (UTR) of SMYEV RNA was predicted to contain four stem-loop structures. RNA secondary structure analysis of the 3´ UTR of 28 SMYEV isolates revealed that the isolates fell into three distinct groups. It was related to the clustering of isolates as resulting from phylogenetic analysis. Several optimal and sub-optimal forms of 3´ UTR of potexviruses with lowest free-energy secondary structure were predicted. The conserved hexannucleotide motif and characteristic of secondary structure of potexviruses were also analyzed.
Keywords :
"RNA","Genomics","Bioinformatics","Educational institutions","Viruses (medical)","Phylogeny","Forestry","Production","Capacitive sensors","Conducting materials"
Publisher :
ieee
Conference_Titel :
Bioinformatics and Biomedical Engineering , 2009. ICBBE 2009. 3rd International Conference on
ISSN :
2151-7614
Print_ISBN :
978-1-4244-2901-1
Electronic_ISBN :
2151-7622
Type :
conf
DOI :
10.1109/ICBBE.2009.5163357
Filename :
5163357
Link To Document :
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