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Genome Strustures And Field Infestation Levels Of Three New Viruses In Adelphocoris Suturalis

Posted on:2018-03-07Degree:MasterType:Thesis
Country:ChinaCandidate:X L LiFull Text:PDF
GTID:2323330515997471Subject:Agricultural Entomology and Pest Control
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Adelphocoris suturalis Jakovlev(Hemipetera:Miridae)is one of the most crucial agricultural pests in Southern China whose host range is wide and feeding habits is cryptic.At present,A.suturalis has been widely researched from ecological and physiological perspectives.However,there have been no reports on the microorganisms(e.g.,viruses)infecting these mirid bugs that might be used to control these pests.This study used Illumina HiSeq 2000 high-throughput sequencing technology to analysis the three samples of adults of A.suturalis.Following data clean-up,a total of 23.28 gigabases(Gb)of clean data were obtained by RNA-seq,producing a total of 134722 contigs,including 107486 unigenes,the average length of the sequence was 797.79 bp,N50 was 1568 bp.Using functional annotation,several viral genes were obtained,and the main results are as follows:1 The complete genome of a novel virus in A.suturalis was determined by RNA-seq,named Adelphocoris suturalis-associated virus 1(ASV1),which has a single-stranded RNA genome of 10845 nucleotides in length and contains five putative open reading frames(ORFs).ORF1 encodes a polypeptide of 2592 amino acids(aa)and contains four conserved domains: a viral RNA methyltransferase domain,an FtsJ-like methyltransferase domain,a viral RNA helicase domain and an RNA-dependent RNA polymerase domain.ORF2,ORF3,ORF4 and ORF5 encode polypeptides of 190,461,103 and 159 aa,respectively,of which only ORF5 contains a conserved domain,the Tobacco mosaic virus-coat superfamily.Preliminary,the NCBI Blastx results indicated that ASV1 and Paprika mild mottle virus(a plant virus)showed high homology,however,no ASV1 was found in host plant and the rusult of virus' transmission experiment suggested that it might not be a plan virus.Then,the second phylogenetic analysis with the deduced amino acid sequences indicated that ASV1 clusters with the Drosophila Boutonnet virus.The similar genomic structure and high bootstrap value in the maximum-likelihood tree suggests that ASV1(possibly along with Boutonnet virus)could be considered the prototype of a new taxon of unclassified insect viruses.The prevalence of ASV1 infection in wild populations of A.suturalis was at a low level(6.60%,14 positive in 212 samples).2 Adelphocoris suturalis-associated virus 2(ASV2)was the second novel virus which was found in A.suturalis.ASV2 has a single-stranded RNA genome of 9417 nucleotides in length and contains four putative open reading frames(ORFs)and encode polypeptides of 2697,106,169 and 61 aa,respectively.Then,only ORF1 contains 3 domains: a viral RNA methyltransferase,a viral(superfamily 1)RNA helicase,and an RNA-dependent RNA polymerase domain.phylogenetic analysis with the deduced amino acid sequences indicated that ASV2 was the same to ASV1 clusters with the Drosophila Boutonnet virus.The similar genomic structure and high bootstrap value in the maximum-likelihood tree suggests that ASV2 was the same to ASV1 could be considered the prototype of a new taxon of unclassified insect viruses.In addition,the prevalence of ASV2 infection in wild populations of A.suturalis was at a low level(1.42%,3 positive in 212 samples).3 The third virus found in A.suturalis named Adelphocoris suturalis-associated virus 3(ASV3).The length of ASV3's single-stranded RNA genome was 9922 nucleotides,and ASV3 contains six putative open reading frames(ORFs)which encode polypeptides of 322,233,719,1662,68 and 123 aa,respectively,and included 5 domains.ORF2 has a Picornavirus capsid protein domain_like,ORF3 has a Picornavirus capsid protein domain_like and a CRPV capsid protein like,ORF4 has a viral(superfamily 1)RNA helicase and an RNA dependent RNA polymerase.Phylogenetic analysis with the deduced amino acid sequences indicated that ASV3 clusters with the Sanxia water strider virus 7(Iflaviridae:iflavirus).The similar genomic structure and high bootstrap value in the maximum-likelihood tree suggests that ASV3 was one kind of insect virus.the prevalence of ASV3 infection in wild populations of A.suturalis was also at a low level(6.60%,14 positive in 212 samples).4 In summary,three complete genomes of new virus was found in a.suturalis by RNA-seq.Phylogenetic analysis and phylogenetic tree of the ASV1 and ASV2 showed that their taxonomic status was still pending.However,the taxonomic status of ASV3 was an insect virus(Iflaviridae:iflavirus).
Keywords/Search Tags:Adelphocoris suturalis, RNA-Seq, Infection rates of virus, Phylogenetic analysis, Analysis of gene structure
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