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Cloning and Molecular Analysis of the Complete Genome of Papaya Ringspot Virus Hainan Isolate

Author: LuYaZuo
Tutor: ZhouPeng
School: South China University of Tropical Agriculture
Course: Biochemistry and Molecular Biology
Keywords: Papaya ringspot virus Genome Sequencing Homology analysis Phylogenetic analysis
CLC: S436.67
Type: Master's thesis
Year: 2007
Downloads: 108
Quote: 2
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Abstract


Papaya ringspot virus (Papaya ringspot virus) is the virus papaya production areas at home and abroad is the most widely distributed, the most serious damage, the serious harm papaya yield and quality, and reduce the value of the goods, but also endanger the gourd Branch crops. The full study cause the Fan operation melons ringspot virus disease a PRSV the Haikou isolate (PRSV-HN) genomic RNA sequencing and PRSV-HN genome nucleotide sequence and the deduced amino acid sequence structure and functional analysis of the theoretical basis for this study PRSV genetic variation, infection and pathogenesis at the molecular level. Viral RNA as a template transcribed cDNA, primers were designed using the conserved sequence, the the PRSV-HN genome segment for PCR amplification, through the objective fragment ligation, transformation, screening, sequencing and sequence assembly obtained after the separation was the coding region of sequence. Intraoperative end fast cDNA amplification method (RACE) to obtain the 5'-non-coding region sequence of the separation was complete. The genome sequence in GenBank accession number: EFl83499. Sequence analysis showed that: the PRSV-HN genome sequence of a total of 10,323 nuclear Tartars nucleotide, the 5'-and 3'-noncoding region sequence were 85 and 209 nucleotides, (excluding po1yA tail), middle 10029 nucleotides in a single open reading frame encoding a 3343 amino acid multimeric protein: the protein itself catalytic cracking 10 polypeptides, the cleavage sites adjacent polypeptide Q sequentially as: Y / N, G / G, and Q / A, Q / s, Q / G Q / G, E / G, Q / S and Q / S. Isolates of PRSV-HN has been reported in 12 PRSV whole genome sequence comparison, the results show that the number of nucleotides of the genome sequence there are some differences, 10317bp-10332bp, rich in cP gene N-terminal A District there triplets Absence. The PRSV-HN 12 PRSV genomic homology of the nucleotide sequence of polyglutamine protein encoded amino acid sequence homology of 82.3% - 89.1%, and 89.8% -93.1%. Low homology 5-UTR, only 65.9% -87.1% homology 3-UTR, 90.8% -96.6%. Pl protein is the largest towel variation of the virus-encoded protein, amino acid sequence homology is only 65.4% -80.1%, and the HC-Pro, CI and CP high homology. Take a long amino acid sequence NJ tree Containing PRSV isolate asked three evolutionarily related clusters, WW, W-1, the HA and the Mex-Vrpo are very similar, into a cluster. DEL isolate to form an independent branch. Thai-1, Thal-2, HN, and from the five isolates (YK, TW-l, TW-2, TW-3, CI) to form an evolutionary cluster. The phylogenetic tree shows that despite the DE1L isolate Americas isolate closer, but overall the Americas isolate and Asian isolates differentiation and geographic distribution of some relevance. In addition, the evolutionary tree distribution also showed no significant virus evolution direction of the P-type and W-type mesh relevance. PRSV-HN length nucleotide sequence and Thai-1 of Thai-2 and derived from the five isolates (YS, TW-l, TW-2, TW-3, CI) highest homology, however, but only 88.4% - 89.1%; evolutionary tree, PRSV-HN alone form a separate branch. Therefore, it is recommended that the PRSV-HN attributed to a different one with the Thai-l, Thai-2 as well as the five isolates from Taiwan. Department. The amino acid sequence of the coat protein of PRSV isolate PRSV-HN isolates have been reported with some made the comparison and phylogenetic tree analysis, the results showed that the highest affinity, also revealed that PRSV-HN strain YS. The P3 protein showed that the protein exists in the transmembrane, and may be associated with the spread of the virus within the host cell.

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CLC: > Agricultural Sciences > Plant Protection > Pest and Disease Control > Horticultural Crops Pest and Disease Control > Fruit tree pests and diseases > Tropical and subtropical fruit pests
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