Iranian Journal of Virology
مجله ویروس شناسی ایران
Iran J Virol
Medical Sciences
http://journal.isv.org.ir
1
admin
1735-5680
2588-5030
10.21859/isv
en
jalali
1399
3
1
gregorian
2020
6
1
14
1
online
1
fulltext
en
Genetic Diversity of Coat Protein Gene of Peanut Stunt Virus (PSV); Its Evolution Governed by Mutation and Natural Selection
تخصصي
Special
پژوهشي
Original article
<div style="border-bottom:solid windowtext 1.0pt; border-top:solid windowtext 1.0pt; border-left:none; border-right:none; padding:1.0pt 0in 1.0pt 0in"><span style="font-size:12pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b><span style="font-size:10.0pt">Background and Aims: </span></b><i><span style="font-size:10.0pt"><span style="color:black">Peanut stunt virus</span></span></i><span style="font-size:10.0pt"><span style="color:black"> is a member of the genus <i>Cucumovirus</i> in the family <i>Bromoviridae</i>, and causes economic yield losses mostly in legume plants worldwide. The synonymous codon usage patterns, which provide significant information about the evolutionary changes that</span></span><span style="font-size:10.0pt"> influenced viral survival rates and fitness have not been reported for PSV.</span></span></span></span><br>
<span style="font-size:12pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b><span style="font-size:10.0pt">Materials and Methods: </span></b><span style="font-size:10.0pt">The complete coat protein (CP) gene sequences of 73 PSV isolates worldwide, including Iranian isolates from the GenBank database were used for codon usage bias -CUB analysis. To clarify the genetic diversity of PSV, CP sequences were aligned using CLUSTALX2. Maximum Likelihood (ML) tree was reconstructed using 34 representatives of each group by MEGAX using the K2+G+I method with 1000 Bootstrap replicates. <span style="color:black">The CodonW 1.4.2 package was used for assessing the nucleotide mixtures at the 3rd codon position (A3, C3, T3, and G3%). The Emboss explorer (</span>http://www.bioinformatics.nl/emboss-explorer/<span style="color:black">) was used for calculating GC content at the first, second, and third codon positions (GC1s, GC2s, GC3s), where the average of GC1 and GC2s is indicated by GC1,2s. </span>The codon usage data for the different hosts were obtained from the codon usage database (available at https://hive.biochemistry.gwu.edu/review/codon)</span><span style="font-size:10.0pt">.</span></span></span></span><br>
<span style="font-size:12pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b><span style="font-size:10.0pt">Results:</span></b><span style="font-size:10.0pt"> Phylogenetic analyses using CP sequences clustered the PSV isolates into two main groups (GI & GII), in which subgroups I to V isolates fell in GI however, a new subgroup VI isolates cluster in GII. High nucleotide diversity in the PSV CP gene of new subgroup VI may indicate the recent expansion of these isolates. <span style="color:black">The average of codon adaptation index (CAI) analyses shows that the host adaptation was highest for subgroup VI, followed by V, II, III, I, and IV subgroups, respectively. A constant and conserved genomic composition CP coding sequences were inferred by low codon usage bias. Nucleotide composition analysis indicates t</span>he frequency of amino acid coded by U/C ended optimal codon. This unequal use of nucleotides composition </span><span style="font-size:10.0pt">with </span><span style="font-size:10.0pt"><span style="color:black">parity rule 2 (PR2) and the effective number of codons (ENC) plots indicates that the combination of mutation pressure and natural selection are deriving the codon usage patterns in the CP gene but the role of selection pressure is more important. </span></span><span style="font-size:10.0pt">Principal component analysis (PCA) demonstrated that the majority of PSV isolates from subgroups I to V clustered near the origin, which might be due to these isolates being older with a common origin.</span></span></span></span><br>
<span style="font-size:12pt"><span style="unicode-bidi:embed"><span new="" roman="" style="font-family:" times=""><b><span style="font-size:10.0pt">Conclusion: </span></b><span style="font-size:10.0pt">Our findings showed that overall codon usage bias within PSV CP gene sequences is slightly biased. The evolution of PSV perhaps reflects a dynamic process of mutation and natural selection to adapt their codon usage to different environments and hosts. This research makes an essential contribution to the understanding of plant virus evolution and<span style="color:black"> reveals novel information about their evolutionary fitness. This</span> study shows the high nucleotide diversity among CP gene sequences of PSV isolates and proposes a new subgroup VI</span><span style="font-size:10.0pt">.</span></span></span></span></div>
PSV, codon usage patterns, mutation pressure, natural selection, host adaptation
53
59
http://journal.isv.org.ir/browse.php?a_code=A-10-1-100&slc_lang=en&sid=1
Reza
Pourrahim
10031947532846006513
10031947532846006513
Yes
Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.
Mohammad Reza
Rezapanah
10031947532846006514
10031947532846006514
No
Insect Molecular Virology laboratory, BioControl Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran. Iranian Network for Research in Viral Diseases, Tehran, Iran.
Shirin
Farzadfar
10031947532846006515
10031947532846006515
No
Plant Virus Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.