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Genome of Epinotia Aporema Granulovirus (Epapgv), a Polyorganotropic Fast Killing Betabaculovirus with a Novel Thymidylate Kinas

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Genome of Epinotia Aporema Granulovirus (Epapgv), a Polyorganotropic Fast Killing Betabaculovirus with a Novel Thymidylate Kinas Ferrelli et al. BMC Genomics 2012, 13:548 http://www.biomedcentral.com/1471-2164/13/548 RESEARCH ARTICLE Open Access Genome of Epinotia aporema granulovirus (EpapGV), a polyorganotropic fast killing betabaculovirus with a novel thymidylate kinase gene María Leticia Ferrelli1, Ricardo Salvador1,2, Marina Elizabeth Biedma1,4, Marcelo Facundo Berretta2, Santiago Haase1, Alicia Sciocco-Cap2, Pablo Daniel Ghiringhelli3 and Víctor Romanowski1* Abstract Background: Epinotia aporema (Lepidoptera: Tortricidae) is an important pest of legume crops in South America. Epinotia aporema granulovirus (EpapGV) is a baculovirus that causes a polyorganotropic infection in the host larva. Its high pathogenicity and host specificity make EpapGV an excellent candidate to be used as a biological control agent. Results: The genome of Epinotia aporema granulovirus (EpapGV) was sequenced and analyzed. Its circular double-stranded DNA genome is 119,082 bp in length and codes for 133 putative genes. It contains the 31 baculovirus core genes and a set of 19 genes that are GV exclusive. Seventeen ORFs were unique to EpapGV in comparison with other baculoviruses. Of these, 16 found no homologues in GenBank, and one encoded a thymidylate kinase. Analysis of nucleotide sequence repeats revealed the presence of 16 homologous regions (hrs) interspersed throughout the genome. Each hr was characterized by the presence of 1 to 3 clustered imperfect palindromes which are similar to previously described palindromes of tortricid-specific GVs. Also, one of the hrs (hr4) has flanking sequences suggestive of a putative non-hr ori. Interestingly, two more complex hrs were found in opposite loci, dividing the circular dsDNA genome in two halves. Gene synteny maps showed the great colinearity of sequenced GVs, being EpapGV the most dissimilar as it has a 20 kb-long gene block inversion. Phylogenetic study performed with 31 core genes of 58 baculoviral genomes suggests that EpapGV is the baculovirus isolate closest to the putative common ancestor of tortricid specific betabaculoviruses. Conclusions: This study, along with previous characterization of EpapGV infection, is useful for the better understanding of the pathology caused by this virus and its potential utilization as a bioinsecticide. Background (dipteran-specific NPV) [2,3]. GVs have been isolated Baculoviruses (family Baculoviridae) are rod-shaped, only from insects belonging to the order Lepidoptera enveloped, insect-specific viruses with double-stranded, and are classified in three groups according to the path- circular DNA genomes ranging in size from 80 to ology caused in their insect hosts. Type 1 pathology is 180 kb [1]. The family Baculoviridae is subdivided into characterized by an infection limited to the host’s midgut four genera: Alphabaculovirus (lepidopteran-specific and fat body resulting in a relatively slow speed of kill. nucleopolyhedrovirus, NPVs), Betabaculovirus (lepidop- Type 2 pathology is characterized by infection of most teran-specific granulovirus, GVs), Gammabaculovirus of the host’s tissues and a rapid speed of kill. There is a (hymenopteran-specific NPVs) and Deltabaculovirus third pathology with a single representative, the Harrisina brillians granulovirus, that causes an infection constrained * Correspondence: [email protected] to the midgut epithelium that results in the rapid death of 1 Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias the host [4]. Exactas, Universidad Nacional de La Plata, CONICET, La Plata, Argentina Full list of author information is available at the end of the article © 2012 Ferrelli et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ferrelli et al. BMC Genomics 2012, 13:548 Page 2 of 14 http://www.biomedcentral.com/1471-2164/13/548 A highly pathogenic granulovirus was isolated from a Analysis of the EpapGV genome sequence led to the larva of the “bean shoot borer” Epinotia aporema identification of 133 putative protein coding genes. The (Lepidoptera: Tortricidae), one of the major soybean search was restricted to open reading frames starting with pests in Argentina, and characterized at biological and a methionine codon, coding for polypeptides of at least 50 molecular levels [5]. Further characterization of its path- amino acid residues (aa) and minimal overlapping of ology demonstrated that this virus belongs to the type 2 adjacent ORFs. This information comprises 90.94% of the GVs meaning that the infection caused by EpapGV in its nucleotide sequence (Additional File 1). The adenine of the host is polyorganotropic [6]. All this information has granulin start codon was designated nucleotide 1 and the been instrumental to formally propose its use as a sequence was numbered in the direction of granulin gene microbial control agent with great potential. In order to transcription, which defined the clockwise orientation of contribute to a more thorough characterization of the circular genome map [20]. The putative ORFs were EpapGV we set out to determine and analyze its complete numbered sequentially in this orientation. Seventy-two genome sequence. ORFs were in the same orientation as the granulin ORF, To date, close to 60 baculovirus genomes have been fully and sixty-one, in the opposite. EpapGV DNA sequence was sequenced, 12 of them belong to the Betabaculovirus searched for promoter motifs 150 bp upstream of the start- genus. Completely sequenced GVs are listed in Table 1 and ing codon of each ORF. Early promoter motifs including their pathology types are indicated. In this report, we TATA box (TATAWAW, TATAWTW, TATAW) in con- present the complete sequence and organization of the junction with CAKT initiator sequence (INR) [21] were EpapGV genome and compare them to other baculoviruses found in the upstream regions of 26 ORFs; 64 ORFs had a using genomic and phylogenetic analyses. late INR motif DTAAG [22] and 11 ORFs had both early and late elements. Results and Discussion General characteristics of the EpapGV genome Gene content The complete EpapGV genome [GenBank: JN408834] The EpapGV genome contains the 31 core genes present was covered 34 times by 454 sequencing. It consists of in all baculoviruses. The genes were also classified 119,082 bp in good agreement with the previous estimate according to their presence in different genera [23,24] of 120.1 kbp based on restriction mapping [19]. Betabacu- (Figure 1). loviruses have AT-rich genomes ranging between 54.7% A distinct feature of the EpapGV genome is that the (CpGV) and 67.6% (CrleGV). The AT content of EpapGV core gene alkaline nuclease (alk-exo, epap119) is fused genome is 58.5%. However, no correlation between these in frame with the helicase-2 ORF (epap120). This fusion data and biological properties has been found thus far. gene codes for an 886 aa polypeptide with the first 383 Table 1 Completely sequenced Betabaculovirus Virus Genome Accesion Annotated Average % id Host family Pathology Reference size (bp) number ORFs with EpapGV type EpapGV 119.082 JN408834 133 - Tortricidae II [6], this work. AdorGV 99.657 AF547984 119 41.02 Tortricidae I [7,8] AgseGV 131.680 AY522332 132 44.12 Noctuidae II Xiulian et al., 2004, unpublished ChocGV 104.710 DQ333351 116 44.39 Tortricidae nr [9] CrleGV 110.907 AY229987 128 44.25 Tortricidae II [10] CpGV 123.500 U53466 143 44.16 Tortricidae II [11] HearGV 169.794 EU255577 179 39.71 Noctuidae I [12] PhopGV 119.217 AF499596 130 42.55 Gelechiidae II Croizier et al., 2002, unpublished PiraGV 108.592 NC_013797 120 44.62 Pieridae nr [13] PlxyGV 100.999 AF270937 120 41.01 Plutellidae II [14] PsunGV 176.677 EU678671 183 40.17 Noctuidae I Li et al., 2008, unpublished SpliGV 124.121 DQ288858 136 40.96 Noctuidae nr [15,16] XcenGV 178.733 AF162221 181 39.84 Noctuidae I [17] ClanGV* 101.487 NC_015398 123 nd Notodontidae nr [18] When information is available, GV type pathology is indicated. nr: not reported. (*) The genome of Clostera anachoreta GV was published [18] after the present work was completed; it was not included in this analysis. Ferrelli et al. BMC Genomics 2012, 13:548 Page 3 of 14 http://www.biomedcentral.com/1471-2164/13/548 AcMNPV 8 10 27 23 Putative non-hr ori 29148 142 143 CpGV 1 127 128 2 3 4 5 17 31 30 29 23 22 2019 18 15 14 EpapGV 1 2345678910111213 14 1516 17 181920 2122 23 24 25 26 27 28 29 granulin rr1 rr2a pk-1hr1a hr1b iap-3hr2 dUTPase F protein hr3 hr4a hr4b pep pep pep odv-e56 odv-e18 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 AcMNPV 64 127 126 145 146 147 115 46 6 22 106/107 35 109 CpGV 13 11 10 98 7 33 35 37 39 4142 45 46 47 48 50 52 54 55 EpapGV 30 31 3233 34 35 36 37 38 39 40 4142 43 44 45 46 47 48 4950 51 52 53 gp37hr5a hr5b cathepsin chitinase hr6a hr6b early ie-1 lef-7pif-3 odv-e66 lef-2metalloproteinase p13hr7 pif-2 ubq odv-ec43 cbp 23 kD 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 AcMNPV 3637 31 138 4038 129 13 14 119 28 25 103 102 101 100 99 98 96 95 CpGV 57 58 59 60 16 62 6869 71 73 74 75 7679 80 8182 82 83 84 85 86 87 88 89 90 EpapGV 54 55 56 57 58 59 60 61 62 63 6465 66 67 68 69 70 71 72 7374 75 76 77 78 79 80 8182 83 84 85 hr11 39 K lef-11sod p74hr9 hr10 p47tmpk nudix p2438.7 lef-1 pif-1 fgf-1 lef-6dbp p48/p45 p12 bv/odv- p6.9 lef-5 38 K pif-4 helicase-1 pp31 hr8a hr8b pyrophosphatase kD
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