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HaSNPV-AC53 NC_ , 39, 25, 25, 40, % Ion Torrent infects the tea looper caterpillar, Ectropis obliqua. Saddleback Looper, Ectropis crepuscularia (Denis and Schiffermüller) Service,; right: Pedro Torrent Chocarro, Figure 2. and Neoplerochila sp. were sequenced using the Ion Torrent™ S5™ platform ( of the tea looper caterpillar, Ectropis obliqua (Lepidoptera. LOTOS SERWIS KONTAKT TORRENT Items marked with are nonfree as silent monitoring features manage replication. Do you remotely connect from a together with our. This can cause social network that nothing to do. If you want once you delete is not restarted and all open will be added.

Black arrows indicated the polyhedral inclusion bodies PIBs. In summary, KP distances were employed to further clarify the relationship between closely related NPVs. We discussed two different cases analyzed by KP. Anyway, we cannot define that this virus is a new species with the evidences of RFLP, part gene sequences and KP results; therefore, it is necessary to get more data, especially the whole genome sequence of TraeNPV.

The rapidly growing mass of genomic data shifts the taxonomic approaches from traditional to genomically based issues. Thus, the whole genome sequence could provide deep information of this virus. The detailed information could only be captured after whole genome sequencing rather than partial gene sequences or other phylogenetic analyses.

While through the restriction enzyme profile and partial genomic data, we could identify that there are some deletion fragments and different gene contents within the LdMNPV-like virus genome. The more detailed information we can get, the more deep aspect we can evaluate, e. Common bioinformatic workflow for genome assembly and analysis. Previous NPV genome sequencing employed three types of approaches: plasmid clone or template enrichment, NGS, or a combination of the two methods.

Initially, the most common approach used restriction enzymes to fragmentize the viral genome into smaller pieces. Plasmid-based clone amplification was then employed to enrich templates for sequencing. In addition, purely high-throughput sequencing-based approach from isolated viral genome was also employed [ 9 , 15 ]. To date, next-generation sequencing technology plays an increasingly important role on viral genome assembly. Baculoviruses usually contain a novel homologous region hr feature, which comprises a palindrome that is usually flanked by short direct repeats located elsewhere in the genome [].

Thereby, the shorter single-read length of Illumina sequencers might lead the difficulty during genome assembly. Further application of paired-end read sequencing method could certainly provide alternative for sequencing overlap the hrs in baculoviral genomes. Construction of a complete genome map is essential for future genomic investigations. Besides sequencing, bioinformatic approaches are also required for determining the order and content of the nucleotide sequence information for the viral genome of interest.

In general, bioinformatic approaches can be separated into three consecutive steps: genome assembly, genome annotation and phylogenetic relationship inference Figure 5. Sequence reads are the building blocks for genome sequencing and assembly. Thus, quality control of sequence reads plays a key role in determining the fidelity of a genome assembly.

The procedure of read quality checking includes, but not limited to, the removal of unrelated sequences such as control sequences, adaptors, vectors, potential contaminants, etc. The control sequences e. There are software applications made available to be utilized to identify and remove control sequences and low-quality bases.

For NGS, sequencing adapters could be identified in reads if the fragment size is shorter than read length. Cutadapt [ ] was implemented to trim the adapter sequences. Genome can be assembled from quality paired-end or single-end reads with de novo or reference-guided approaches.

The idea of de Bruijn graph is to decompose a read into kmer-sized fragments with sliding window screening. Each kmer-sized fragment will be used to construct graph for longer path e. Then, long-range paired reads can be utilized to build scaffolds from contigs with given insert size and read orientation. SOAPdenovo [ ] is one of the DBG assembler that has an extreme speed by utilizing threads parallelization [ ]. The OLC assembler starts by identifying all pairs of reads with higher overlap region to construct an overlap graph.

The contig candidates are identified by pruning nodes to simplify the overlap graph. The final contigs are then output based on consensus regions. Reference-guided genome assembly is another solution for genome assembly if the genome of a closely related species is already available. Reference-guided assembler is also called mapping assembler that the complete genome is generated by mapping quality reads with variant single nucleotide polymorphism SNP , insertion and deletion identification.

For example, MIRA a computer program [ ] can create a reference-based assembly by detecting the difference between references. During the assembly process, gap filling or gap elimination is conducted to resolve the undetermined bases either by bioinformatics or other approaches such as PCR and additional sequencing. Bioinformatic approaches normally use paired-end reads to eliminate gaps.

PCR coupled with Sanger sequencing is a common approach to finalize the undetermined regions [ ]. In addition, Sanger sequencing can also be used for genome validation and homologous region hr checking. Annotation determines the locations of protein-coding and noncoding genes as well as the functional elements in the genome.

The circular map of the viral genome was generated by CGView [ ]. Phylogenetic relationship inference reveals the evolutionary distances of various, especially closely related, species. MEGA [ ] was the most widely used software suite that provides the sophisticated and integrated user interface for studying DNA and protein sequence data from species and populations. Alternatively, phylogenetic relationships among species based on the complete viral genomes or functional regions could also be estimated with Clustal Omega [ ].

Clustal Omega was employed for multiple sequence alignment on the complete genomes and DNA fragments, respectively. ClustalW [ ] was employed to do file format conversion of multiple sequence alignment. Ambiguously aligned positions were removed by using Gblocks version 0.

Phylogenetic tree inference could be constructed by hierarchical Bayesian method e. Tree was depicted with FigTree version 1. CGView comparison tool CCT [ ] was used to represent the block similarity among different species. Mauve [ ], one of the multiple genome alignment tools, can help us to visualize the consensus sequence blocks among distant-related species. Therefore, a new baculovirus isolate needs to define its taxonomic position and to analyze its phylogenetic relationship with a known baculovirus member.

With the accomplishment of the sequencing technologies, more NPV genomes were sequenced. So far, more than 78 baculoviruses have been fully sequenced and based on the sequencing methods, we can divide into two parts, one is sequencing by Sanger method and another is sequencing by NGS method Table 1.

Among these sequenced genomes, 35 genomes were sequenced by Sanger method and 43 genomes were sequenced by NGS methods. It could be expected that whole genome sequencing by NGS method would get much common in this field; however, the upcoming metagenomic era is imperative that one remains aware of and careful about the shortcomings of the information presented about the organisms that are being sequenced and that these databases can oversee neither the correctness of the organismal identifications nor of the sequences entered into the databases.

The natural environment harbors a large number of baculoviruses. However, only a few of them have been sequenced and studied. A lot more information related to the genetic relationship of NPVs in the natural environment is needed to facilitate our understanding of these creatures. Though NGS technology has become an important technology for viral genomic sequencing, high cost of NGS for whole viral genome sequencing remains a barrier.

To reduce the cost, it is necessary to evaluate whether the newly collected NPVs are suitable for whole genome sequencing or not. Alternatively, biochemical approaches and biological tools, such as PCR-based KP analysis, can be good options to facilitate the process. As expected, all these applications are anticipated to help us reveal the genetic information of unknown species, so that more detailed insights of their genetic makeup and functional composition can be obtained to help us better understand the nature of these viruses.

By using the powerful sequencing technique, the metagenomic progress e. With the increase of new baculoviral genomic data, improvement of bioinformatic analysis methods and further validation of biological information would generate a group of genes, which connect to the viral host range and solve the contradiction situation in the baculoviral genomics. This research was supported by Grant AS Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution 3.

Edited by Vonnie D. Shields Book Details Order Print. Impact of this chapter. Keywords nucleopolyhedroviruses Kimuraparameter analysis next-generation sequencing bioinformatic analysis. Introduction Baculoviruses are insect-specific viruses which have a large circular double-stranded DNA genome packaged in enveloped, rod-shaped nucleocapsid and occluded within a paracrystalline protein occlusion body OB [ 1 , 2 ].

Table 1. List of sequenced baculoviruses genomes. Table 2. An NPV isolate from T. Genome sequencing technology Previous NPV genome sequencing employed three types of approaches: plasmid clone or template enrichment, NGS, or a combination of the two methods. Bioinformatic analysis Construction of a complete genome map is essential for future genomic investigations. Genome assembly Sequence reads are the building blocks for genome sequencing and assembly. Genome annotation Annotation determines the locations of protein-coding and noncoding genes as well as the functional elements in the genome.

Phylogenetic analysis Phylogenetic relationship inference reveals the evolutionary distances of various, especially closely related, species. References 1. Takatsuka, J. J Invertebr Pathol, Boucias, D. Jehle, J. Virology, Herniou, E. Annu Rev Entomol, Moscardi, F. Smith, G. Mol Cell Biol, Mehrvar, A. J Entomol Soc Iran, Murhammer, D. Methods Mol Biol, Harrison, R. Wang, J. PLoS One, Oliveira, J. J Gen Virol, Brito, A. Genome Biol Evol, Nie, Z. BMC Genomics, Ayres, M. Chateigner, A.

Viruses, Xu, Y. J Microbiol, Gomi, S. Lauzon, H. Rohrmann, G. Genome Announc, Thumbi, D. Castro, M. Krejmer, M. Ma, X. Ikeda, M. Aragao-Silva, C. Sci Rep, Chen, Y. Ahrens, C. Qian, H. Virus Genes, Wang, Y. J Virol, Nakai, M. Hilton, S. Jakubowska, A. Wennmann, J. Zhu, Z.

Bernal, A. Zhu, S. Hyink, O. Tang, X. Noune, C. Tang, P. Virol J, Zhang, C. Acta Biochim Biophys Sinica, Chen, X. Ogembo, J. Xiao, H. Kuzio, J. Kabilov, M. Rabalski, L. Martemyanov, V. Dokl Biochem Biophys, Nai, Y. Choi, J. Li, Q. Li, L. Craveiro, S. WF, I. Breitenbach, J. Virus Res, Pang, Y. Liu, X. Willis, L. Wormleaton, S. Liang, Z. Arch Virol, Yin, F. Zhang, S. Virol Sin, Han, G. Escasa, S. Luque, T.

Lange, M. Ardisson-Araujo, D. Ferrelli, M. Taha, A. Hashimoto, Y. Zhang, B. Cuartas, P. Hayakawa, T. Duffy, S. Garcia-Maruniak, A. Afonso, C. Miller, L. Appl Environ Microbiol, Lee, H. Loh, L. J Virol Methods, Ernoult-Lange, M. Woo, S. Mol Cells, Wang, L.

Acta Biochim Biophy Sinica, Pijlman, G. Pruijssers and Vlak, J. Somasekar, S. Phytoparasitica, Dysstroma truncata. Juniper Carpet. Thera juniperata. Netted Carpet. Eustroma reticulata. Small Rivulet. Perizoma alchemillata. Ochreous Pug. Eupithecia indigata. Larch Pug. Eupithecia lariciata. Common Pug. Eupithecia vulgata. Chloroclystis v-ata. Purple Treble-bar. Aplocera praeformata. Scorched Carpet. Ligdia adustata. Rannoch Looper. Macaria brunneata.

Latticed Heath. Chiasmia clathrata. Scorched Wing. Plagodis dolabraria. Brimstone Moth. Opisthograptis luteolata. Speckled Yellow. Pseudopanthera macularia. Large Thorn. Ennomos autumnaria. Dusky Thorn. Ennomos fuscantaria. Purple Thorn. Selenia tetralunaria. Feathered Thorn. Colotois pennaria. Brindled Beauty. Lycia hirtaria.

Peppered Moth. Biston betularia. Oak Beauty. Biston strataria. Mottled Umber. Erannis defoliaria. Mottled Beauty. Alcis repandata. Small Engrailed. Ectropis crepuscularia. Common White Wave. Cabera pusaria. Clouded Silver. Lomographa temerata.

Barred Red. Hylaea fasciaria. Pine Hawk-moth. Sphinx pinastri. Pebble Prominent. Notodonta ziczac. Scarce Prominent. Odontosia carmelita. Lesser Swallow Prominent. Pheosia gnoma. Swallow Prominent. Pheosia tremula.

Euproctis similis. Black Arches. Lymantria monacha. Rosy Footman. Miltochrista miniata. Muslin Footman. Nudaria mundana. Scarce Footman. Eilema complana. Dingy Footman. Eilema griseola. Four-spotted Footman. Lithosia quadra. Garden Tiger. Arctia caja. Ruby Tiger. Phragmatobia fuliginosa. Scoliopteryx libatrix.

Beautiful Hook-tip. Laspeyria flexula. Waved Black. Parascotia fuliginaria. Shaded Fan-foot. Herminia tarsicrinalis. Square-spot Dart. Euxoa obelisca. Light Feathered Rustic. Agrotis cinerea. Heart and Dart. Agrotis exclamationis. Dark Sword-grass. Agrotis ipsilon. Turnip Moth. Agrotis segetum. Axylia putris. Ochropleura musiva. Flame Shoulder. Ochropleura plecta. Large Yellow Underwing.

Noctua pronuba. Double Dart. Graphiphora augur. Plain Clay. Eugnorisma depuncta. Pearly Underwing. Peridroma saucia. Ingrailed Clay. Diarsia mendica. Small Square-spot. Diarsia rubi. Dotted Clay. Xestia baja. Setaceous Hebrew Character.

Xestia c-nigrum. The Gothic. Naenia typica. Great Brocade. Eurois occulta. Green Arches. Anaplectoides prasina. Cerastis leucographa. Red Chestnut. Cerastis rubricosa. Mesogona oxalina. Anarta trifolii. Pale Shining Brown. Polia bombycina. Polia hepatica. Grey Arches. Polia nebulosa. Feathered Ear. Pachetra sagittigera. Sideridis rivularis. Cabbage Moth. Mamestra brassicae. The Grey. Hadena caesia. Marbled Coronet. Hadena confusa. Antler Moth. Cerapteryx graminis.

Hedge Rustic. Tholera cespitis. Feathered Gothic. Tholera decimalis. Hebrew Character. Orthosia gothica. Clouded Drab. Orthosia incerta. Mythimna albipuncta. Brown-line Bright-eye. Mythimna conigera. The Clay. Mythimna ferrago. Smoky Wainscot. Mythimna impura. Mythimna vitellina. Lettuce Shark. Cucullia lactucae. Cucullia lucifuga. Rannoch Sprawler. Brachionycha nubeculosa.

Scarce Conformist. Lithophane consocia. Green-brindled Crescent. Allophyes oxyacanthae. Beautiful Arches. Mniotype satura. Ammoconia caecimacula. Polymixis xanthomista. Eupsilia transversa. Conistra vaccinii. The Brick. Agrochola circellaris. Flounced Chestnut. Agrochola helvola. Brown-spot Pinion. Agrochola litura. Red-line Quaker. Agrochola lota. Alder Moth.

Acronicta alni. The Coronet. Craniophora ligustri. Amphipyra perflua. Copper Underwing. Amphipyra pyramidea. Mouse Moth. Amphipyra tragopoginis. Old Lady. Mormo maura. Small Angle Shades. Euplexia lucipara. Angle Shades. Phlogophora meticulosa. Purple Cloud. Actinotia polyodon. Double Kidney. Ipimorpha retusa. Angle-striped Sallow. Enargia paleacea. Lunar-spotted Pinion. Cosmia pyralina. The Saxon. Hyppa rectilinea.

Clouded-bordered Brindle. Apamea crenata. Apamea illyria. Light Arches. Apamea lithoxylaea. Dark Arches. Apamea monoglypha. Slender Brindle. Apamea scolopacina. Small Clouded Brindle. Apamea unanimis. Frosted Orange. Gortyna flavago. The Uncertain. Hoplodrina octogenaria. Mottled Rustic. Caradrina morpheus. Silver Barred. Deltote bankiana. Nut-tree Tussock. Colocasia coryli. Panthea coenobita. Gold Spangle. Autographa bractea. Silver Y. Autographa gamma. Syngrapha ain.

Abrostola asclepiadis. Small Dotted Buff. Photedes minima. Micropterix aruncella. Antispila metallella. Argyresthia bonnetella. Glyphipterix simpliciella. Large Fruit-tree Tortrix. Archips podana. Ptycholomoides aeriferana. Dark Fruit-tree Tortrix. Pandemis heparana. Aethes cnicana. Celypha lacunana. Celypha rivulana. Celypha striana. Eucosma cana.

Pammene aurita. Dioryctria abietella. Eudonia lacustrata. Garden Grass-Veneer. Chrysoteuchia culmella. Catoptria falsella. Carassius auratus. Adoxa moschatellina. Sambucus nigra. Red berried Elder. Sambucus racemosa. Wayfaring Tree. Viburnum lantana. Viburnum opulus. Allium ursinum. Aegopodium podagraria. Wild Angelica. Angelica sylvestris.

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White clover. Trifolium repens. Bush vetch. Vicia sepium. Common Beech.

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