List of sequenced baculoviruses genomes
To date , over 78 genomes of nucleopolyhedroviruses (NPVs) have been sequenced and deposited in NCBI. How to define a new virus from the infected larvae in the field is usually the first question. Two NPV strains, which were isolated from casuarina moth (L. xylina) and golden birdwing larvae (Troides aeacus), respectively, displayed the same question. Due to the identity of polyhedrin (polh) sequences of these two isolates to that of Lymantria dispar MNPV and Bombyx mori NPV, they are named LdMNPV-like virus and TraeNPV, provisionally. To further clarify the relationships of LdMNPV-like virus and TraeNPV to closely related NPVs, Kimura 2-parameter (K-2-P) analysis was performed. Apparently, the results of K-2-P analysis that showed LdMNPV-like virus is an LdMNPV isolate, while TraeNPV had an ambiguous relationship to BmNPV. Otherwise, MaviNPV, which is a mini-AcMNPV, also exhibited a different story by K-2-P analysis. Since K-2-P analysis could not cover all species determination issues, therefore, TraeNPV needs to be sequenced for defining its taxonomic position. For this purpose, different genomic sequencing technologies and bioinformatic analysis approaches will be discussed. We anticipated that these applications will help to exam nucleotide information of unknown species and give an insight and facilitate to this issue.
- Kimura-2-parameter analysis
- next-generation sequencing
- bioinformatic analysis
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]. The family
To date, baculoviruses are known to infect more than 660 insect species; most of them are belonging to the order of Lepidoptera, Diptera and Hymenoptera [7, 8]. Baculoviruses exhibit genetic variations among species and its isolates . Although a large number of baculoviruses in the nature, only a few have been well studied. To the best of our knowledge, a total of 78 fully sequenced genomes have been deposited in GenBank  and also several baculoviruses of whole genomes may soon be sequenced and deposited ( Table 1 ). However, these published viral genomes represent only a small fraction and the genetic relationship among nucleopolyhedroviruses (NPVs) in the natural environment remains a puzzle.
|Genus||Virus||Virus Abbreviation||GenBank accession||Genome size (bp)||A||C||G||T||GC content||ORFs||Sequencing||Assembler||Reference|
|AgMNPV-26||KR815455||131,678||36,411||29,288||29,405||36,574||44.6%||157||Roche 454 GS FLX||Geneious|||
|AnpeNPV||NC_008035||126,629||29,513||34,041||33,664||29,406||53.5%||147||Sanger||ContigExpress9.1.0 + SeqMan5.0/DNASTAR|||
|AcMNPV-WP10||KM609482||133,926||39,205||27,157||27,346||40,199||40.7%||151||Illumina HiSeq 2000||Newbler|||
|BomaNPV||NC_012672||126,770||37,358||25,398||25,601||38,413||40.2%||141||Solexa GA||GENETYX-win Software + DNASTAR|||
|CapoNPV||KU565883||128,058||38,938||25,348||25,444||38,328||39.7%||131||Roche 454 GS FLX+||GS |||
|CfDEFMNPV||NC_005137||131,160||35,474||30,110||29,993||35,580||45.8%||149||Sanger||MacVector + Lasergene/DNASTAR|||
|ChmuNPV||NC_023177||124,688||31,408||30,986||31,370||30,924||50.0%||147||Roche 454||CLC Genomics Workbench|||
|ChocNPV||NC_021925||128,446||32,108||31,905||32,481||31,952||50.1%||148||Roche 454 GS FLX||SeqMan Pro Lasergene/DNASTAR|||
|CoveMNPV||NC_026430||125,767||35,904||26,937||27,038||35,886||42.9%||138||Roche 454||Geneious + MIRA|||
|LoobMNPV||KP763670||120,023||38,995||20,932||21,966||38,104||35.7%||134||Roche 454 GS FLX||Geneious|||
|RoMNPV||NC_004323||131,526||39,674||25,630||25,793||40,429||39.1%||149||Sanger||Wisconsin package + Lasergene/DNASTAR|||
|AdorNPV||NC_011423||111,724||36,306||19,404||19,694||36,320||35.0%||121||Sanger||SeqMan II Lasergene/DNASTAR|||
|ApciNPV||NC_018504||123,876||41,223||20,865||20,449||41,332||33.4%||117||Sanger||SeqMan Pro Lasergene/DNASTAR||unpublished|
|BusuNPV||NC_023442||120,420||37,568||22,152||22,142||38,558||36.8%||127||Roche 454 GS FLX||GS de novo assembler|||
|EupsNPV||NC_012639||141,291||41,736||28,455||28,549||42,551||40.3%||139||Sanger||Wisconsin package + GENETYX-win|||
|HaSNPV-AC53||NC_024688||130,442||39,121||25,389||25,606||40,326||39.1%||138||Ion Torrent PGM||CLC Genomics Workbench|||
|HearNPV||NC_003094||130,759||39,345||25,340||25,552||40,522||38.9%||137||Sanger||Wisconsin package + Lasergene/DNASTAR||[46,47]|
|HzSNPV||NC_003349||130,869||39,273||25,471||25,675||40,450||39.1%||139||Sanger||Wisconsin package + Lasergene/DNASTAR|||
|HespNPV||NC_021923||140,633||42,827||26,977||26,595||44,234||38.1%||137||Sanger||Wisconsin package + Lasergene/DNASTAR|||
|LafiNPV||NC_026922||157,977||45,363||34,616||34,350||43,648||43.7%||137||Roche 454||CLC Genomics Workbench|||
|LdMNPV-27||KP027546||164,158||35,020||47,133||47,118||34,887||57.4%||162||Illumina MiSeq||CLC Genomics Workbench|||
|LdMNPV-2161||KF695050||163,138||34,855||46,648||46,812||34,823||57.3%||174||Roche 454 GS Junior||SeqMan NGEN Lasergene/DNASTAR|||
|LdMNPV-45||KU862282||161,006||34,234||46,192||46,314||34,264||57.5%||155||Illumina||CLC Genomics Workbench|||
|LdMNPV-3054||KT626570||164,478||35,151||47,119||47,140||35,068||57.3%||174||Roche 454 GS Junior||LaserGene/DNASTAR|||
|MabrMNPV||NC_023681||152,710||46,042||30,311||30,604||45,753||39.9%||159||Roche 454||GS de novo assembler|||
|MacoNPV-A||NC_003529||155,060||45,336||32,160||32,463||45,101||41.7%||169||Sanger||Wisconsin package + Lasergene/DNASTAR|||
|PespNPV||NC_024625||151,109||35,060||40,593||39,822||35,633||53.2%||139||Roche 454||CLC Genomics Workbench|||
|PsinNPV||NC_026268||139,132||41,843||27,452||27,210||42,609||39.3%||141||Roche 454 GS FLX||MIRA|||
|SeMNPV||NC_002169||135,611||38,445||29,486||29,929||37,751||43.8%||139||Sanger||Wisconsin package + Lasergene/DNASTAR|||
|SpliMNPV-AN1956||JX454574||137,998||37,469||30,803||30,846||38,880||44.7%||132||Roche 454 GS Junior||LaserGene/DNASTAR|||
|SpltNPV||NC_003102||139,342||39,180||29,691||29904||40,567||42.8%||141||MegaBACE1000||DNASIS + DNASTAR|||
|SujuNPV||KJ676450||135,952||41,395||26,157||26,399||42,001||38.7%||131||Roche 454||GS de novo assembler|||
|AdorGV||NC_005038||99,657||33,077||17,098||17,275||32,207||34.5%||119||Sanger||SeqMan II Lasergene/DNASTAR|||
|ClasGV-B||KR091910||107,439||33,648||19,904||20,673||33,214||37.8%||123||Roche 454 GS FLX||Newbler|||
|CnmeGV||NC_029304||111,246||36,021||19,756||19,385||36,084||35.2%||118||Roche 454 GS FLX||GS de novo assembler|||
|CnmeGV||KP658210||112,060||36,295||19,904||19,529||36,332||35.2%||133||PacBio RS II||HGAP2.2.0|||
|CpGV||NC_002816||123,500||34,029||27,722||28,183||33,566||45.3%||143||Sanger||Wisconsin package + Lasergene/DNASTAR|||
|EpapGV||NC_018875||119,082||35,524||24,984||24,403||34,171||41.5%||132||Roche 454 GS FLX||Newbler|||
|ErelGV||NC_025257||102,759||31,707||19,440||20,324||31,288||38.7%||130||Roche 454 GS FLX||Geneious|||
|PiGV||KX1513952||112,536||n/a||n/a||n/a||n/a||n/a||123||Roche 454 GS Junior||SeqMan NGEN Lasergene/DNASTAR|||
|SpfrGV||NC_026511||140,913||38,131||32,852||32,288||37,642||46.2%||146||Roche 454 GS FLX||Newbler|||
Previously, Sanger sequencing was employed to sequence the viral genomic sequences cloned in plasmids. With the advances of sequencing technologies, next-generation sequencing (NGS) is becoming an important technology for large-scale viral genomic sequencing. The high cost of NGS and requirement of intensive bioinformatic analysis remain a hurdle for this application. In a word, NGS is an available tool to facilitate on the study of the genetic relationship of baculoviruses.
2. Identification of NPVs
Biochemical and biotechnology-based methods are the most common approaches employed to identify the NPVs. In most cases, more than one method is employed to compensate the pros and cons for each other. For example, restriction enzyme profiling of viral genomic DNA was used to reveal genetic variations among different isolates [97–99] and to distinguish one species from another between closely related viruses such as
Polymerase chain reaction (PCR)-based methods were then established. These methods have been shown not only to be more sensitive and faster but also more reliable than restriction enzyme analysis for classifying baculoviral species [4, 103–105]. Multiple genetic markers (e.g.,
Due to the higher cost of NGS for viral genome sequencing, it is frequently required to combine various approaches to cut down the cost but still ensure precision, e.g., PCR-based K-2-P analysis and NGS approach for identifying the potential new NPV species. Two NPVs were isolated from casuarina moth (
3. The identification of ambiguous NPVs
In this section, the discussion of molecular identification of NPV species based on K-2-P distance  is presented. Two new NPVs were used as examples in this study to reveal different issues regarding the classification of NPVs.
3.1. LdMNPV-like virus
The K-2-P distances, based on the sequences of three genes, between different viruses could mostly evaluate the ambiguous relationship among the NPVs. It was defined that distances less than 0.015 indicates that the two isolates are the same baculovirus species. On the other hand, the difference between two viruses is more than 0.05 should be considered as different virus species. For the distances between 0.015 and 0.05, complementary information is needed to determine whether these two viruses are of the same or different species [3, 9, 115].
A new multiple nucleopolyhedrovirus strain was isolated from casuarina moth,
|1||1 → 654||654||217||rr1||96||81|
|2||1063 → 1224||162||53||Ctl-1||100||100|
|3||1397 → 2473||1077||358||Ange-bro-c||68||70|
|4||2590 → 3596||504||168||LdOrf-151||99||98|
|5||3200 → 3952||753||251||LdOrf-152||99||99|
|6||4019 → 5026||1005||335||Ld-bro-n||93||91|
|7||5645 → 6391||744||248||Ld-bro-o||73||67|
|8||6388 → 6654||264||88||Ld-bro-o||26||26|
|9||6758 → 7054||297||99||LdOrf-155||100||100|
Based on these results, LdMNPV-like virus has a genomic size significantly smaller than that of LdMNPV and LyxyMNPV and appears to be an NPV isolate distinct from LdMNPV or LyxyMNPV. Moreover, a gene,
3.2. An NPV isolate from
A nucleopolyhedrosis disease of the rearing of the golden birdwing butterfly (
In summary, K-2-P distances were employed to further clarify the relationship between closely related NPVs. We discussed two different cases analyzed by K-2-P. From the sequence data of LdMNPV-like virus, results strongly supported that LdMNPV-like virus is an isolate of LdMNPV. Since the RFLP profiles of the LdMNPV-like virus showed the genome of this isolate was deleted tremendously, this deletion also showed coordinately in our partial sequences of genomic DNA fragments and the results of K-2-P. The K-2-P distances between TraeNPV and BmNPV or AcMNPV were among 0.05 and 0.015. Anyway, we cannot define that this virus is a new species with the evidences of RFLP, part gene sequences and K-2-P results; therefore, it is necessary to get more data, especially the whole genome sequence of TraeNPV.
4. The importance of whole genome sequencing on baculoviruses
The rapidly growing mass of genomic data shifts the taxonomic approaches from traditional to genomically based issues. The K-2-P distance supported LyxyMNPV as a different viral species (K-2-P values = 0.067–0.088), even though they were still a closely relative species phylogenetically. But, “how different did LyxyMNPV and LdMNPV?” become another question. Thus, the whole genome sequence could provide deep information of this virus. For example, as the genomic data revealed, the most part of the ORF (151 ORFs) between LyxyMNPV and LdMNPV was quite similar while still have several different ORF exhibits or absent in LyxyMNPV, e.g., two ORFs were homologous to other baculoviruses and four unique ORFs were identified in the LyxyMNPV genome and LdMNPV contains 23 ORFs that are absent in LyxyMNPV . Besides, there is a huge genomic inversion in LyxyMNPV compared to LdMNPV . Another example is
5. Genomic sequences of NPVs
5.1. 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. 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. Later, conventional Sanger sequencing and/or next-generation sequencing was employed for genome assembly. 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. Previous researches showed that Illumina HiSeq has superior performance in yield than 454 FLX [119–121]. 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.
5.2. Bioinformatic analysis
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 ).
5.2.1. Genome assembly
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., trimming of low-quality bases and selection of high-quality reads. The control sequences (e.g., PhiX control reads in Illumina sequencers, control DNA beads in Roche 454 sequencer) are routinely used by sequencer manufacturers to evaluate the quality of each sequencing run. 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. Ambiguous bases or bases with lower-quality values can be removed by PRINSEQ  from either 5′ or 3′ end. NGS QC Toolkit  has programmed module to select high-quality reads. If paired-end technology was applied, paired-end reads could be joined by PANDAseq , PEAR , FLASH  and COPE , if a fragment size is shorter than read length.
Genome can be assembled from quality paired-end or single-end reads with de novo or reference-guided approaches. There are two standard methods known as the de Bruijn graph (DBG) approach and the overlap/layout/consensus (OLC) approach for de novo genome assembly. 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.g., contigs). 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. Additionally, Newbler  is a widely used OLC assembler distributed by 454 Life Sciences.
Reference-guided genome assembly is another solution for genome assembly if the genome of a closely related species is already available. For viral genome assembly, closely related species can be identified by mapping quality reads against sequenced viral genomes deposited in GenBank (http://www.ncbi.nlm.nih.gov/genome/viruses/) and select top-ranked species as the reference genome(s) to facilitate the assembly of the genome of interest. 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.
5.2.2. Genome annotation
Annotation determines the locations of protein-coding and noncoding genes as well as the functional elements in the genome. Glimmer , N-SCAN , NCBI ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/), GeneMark  and VIGOR  are gene prediction tools for identifying protein-codivng genes in the genome. Repetitive sequence regions were detected by RepeatMasker (http://www.repeatmasker.org/). Viral microRNA candidate hairpins can be predicted by Vir-Mir . The circular map of the viral genome was generated by CGView .
5.2.3. Phylogenetic analysis
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 0.91b [144, 145] under default settings. Phylogenetic tree inference could be constructed by hierarchical Bayesian method (e.g., MrBayes ) or maximum likelihood method (e.g., RAxML ) to estimate phylogeny . Tree was depicted with FigTree version 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). The divergence times of different species were estimated using BEAST version 1.8 or version 2.3.2 . In addition, pairwise sequence identity was determined by BLASTN (NCBI BLAST Package)  to analyze sequence-level variation. Also, whole genome pairwise alignment can be done by LAGAN . 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.
Up to 78 baculoviruses have been reported; most of baculoviruses have a narrow host range, only infect their homogenous hosts, such as BmNPV, SpltNPV, SpeiNPV, MaviNPV and so on; LyxyNPV can infect LD and LY cell lines, while AcMNPV has a wide host range; at least 40 hosts in vitro have be found. 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 K-2-P 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.g., transcriptome analysis of insect host), new pathogen species in the natural environment would be easier to be found in the future. 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 105AS-13.2.3-BQ-B1 from the Bureau of Animal and Plant Health Inspection and Quarantine, the Council of Agriculture, Executive Yuan and Grant 103-2313-B-197-002-MY3 from the Ministry of Science and Technology (MOST).
Takatsuka, J., Lymantria mathuranucleopolyhedrovirus: identification, occurrence and genetic diversity in Iwate Prefecture, Japan. J Invertebr Pathol, 2016. 138: pp. 1-9.
Boucias, D. and Pendland, J.C., Principles of insect pathology. 1998, Boston: Kluwer Aca demic Publishers. 537p.
Jehle, J.A., et al., Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera. Virology, 2006. 346(1): pp. 180-93.
Herniou, E.A., et al., The genome sequence and evolution of baculoviruses. Annu Rev Entomol, 2003. 48: pp. 211-34.
Moscardi, F., Assessment of the application of baculoviruses for control of Lepidoptera. Annu Rev Entomol, 1999. 44: pp. 257-89.
Smith, G.E., Summers, M.D. and Fraser, M.J., Production of human beta interferon in insect cells infected with a baculovirus expression vector. Mol Cell Biol, 1983. 3(12): pp. 2156-65.
Mehrvar, A., R.R.J., Veenakumari, K., Narabenchi, G.B., Molecular and biological characteristics of some geographic isolates of nucleopolyhedrovirus of Helicoverpa armigera(Lep.: Noctuidae). J Entomol Soc Iran, 2008. 28(1): pp. 39-60.
Murhammer, D.W., Useful tips, widely used techniques and quantifying cell metabolic behavior. Methods Mol Biol, 2007. 388: pp. 3-22.
Harrison, R.L., Keena, M.A. and Rowley, D.L., Classification, genetic variation and pathogenicity of Lymantria disparnucleopolyhedrovirus isolates from Asia, Europe and North America. J Invertebr Pathol, 2014. 116: pp. 27-35.
Wang, J., et al., Genome sequencing and analysis of Catopsilia pomonanucleopolyhedrovirus: a distinct species in group I Alphabaculovirus. PLoS One, 2016. 11(5): p. e0155134.
Oliveira, J.V., et al., Genome of the most widely used viral biopesticide: Anticarsia gemmatalismultiple nucleopolyhedrovirus. J Gen Virol, 2006. 87(Pt 11): pp. 3233-50.
Brito, A.F., et al., The pangenome of the Anticarsia gemmatalismultiple nucleopolyhedrovirus (AgMNPV). Genome Biol Evol, 2016. 8(1): pp. 94-108.
Nie, Z.M., et al., Complete sequence and organization of Antheraea pernyinucleopolyhedrovirus, a dr-rich baculovirus. BMC Genomics, 2007. 8: pp. 248.
Ayres, M.D., et al., The complete DNA sequence of Autographa californicanuclear polyhedrosis virus. Virology, 1994. 202(2): pp. 586-605.
Chateigner, A., et al., Ultra deep sequencing of a baculovirus population reveals widespread genomic variations. Viruses, 2015. 7(7): pp. 3625-46.
Xu, Y.P., et al., Comparative analysis of the genomes of Bombyx mandarinaand Bombyx morinucleopolyhedroviruses. J Microbiol, 2010. 48(1): pp. 102-10.
Gomi, S., Majima, K. and Maeda, S., Sequence analysis of the genome of Bombyx morinucleopolyhedrovirus. J Gen Virol, 1999. 80(Pt 5): pp. 1323-37.
Lauzon, H.A., et al., Gene organization and sequencing of the Choristoneura fumiferanadefective nucleopolyhedrovirus genome. J Gen Virol, 2005. 86(Pt 4): pp. 945-61.
de Jong, J.G., et al., Analysis of the Choristoneura fumiferananucleopolyhedrovirus genome. J Gen Virol, 2005. 86(Pt 4): pp. 929-43.
Rohrmann, G.F., Erlandson, M.A. and Theilmann, D.A., Genome sequence of an alphabaculovirus isolated from Choristoneura murinana. Genome Announc, 2014. 2(1): e01135-13.
Thumbi, D.K., et al., Comparative genome sequence analysis of Choristoneura occidentalisFreeman and C. rosaceanaHarris (Lepidoptera: Tortricidae) alphabaculoviruses. PLoS One, 2013. 8(7): p. e68968.
Castro, M.E., et al., Identification of a new nucleopolyhedrovirus from naturally-infected Condylorrhiza vestigialis(Guenée) (Lepidoptera: Crambidae) larvae on poplar plantations in South Brazil. J Invertebr Pathol, 2009. 102(2): pp. 149-54.
Krejmer, M., et al., The genome of Dasychira pudibundanucleopolyhedrovirus (DapuNPV) reveals novel genetic connection between baculoviruses infecting moths of the Lyman-triidae family. BMC Genomics, 2015. 16: p. 759.
Ma, X.-C., et al., Genome sequence and organization of a nucleopolyhedrovirus that infects the tea looper caterpillar, Ectropis obliqua. Virology, 2007. 360(1): pp. 235-46.
Ikeda, M., et al., Gene organization and complete sequence of the Hyphantria cuneanucleopolyhedrovirus genome. J Gen Virol, 2006. 87(Pt 9): pp. 2549-62.
Aragao-Silva, C.W., et al., The complete genome of a baculovirus isolated from an insect of medical interest: Lonomia obliqua(Lepidoptera: Saturniidae). Sci Rep, 2016. 6: p. 23127.
Chen, Y.R., et al., Genomic and host range studies of Maruca vitratanucleopolyhedrovirus. J Gen Virol, 2008. 89(Pt 9): pp. 2315-30.
Ahrens, C.H., et al., The sequence of the Orgyia pseudotsugatamultinucleocapsid nuclear polyhedrosis virus genome. Virology, 1997. 229(2): pp. 381-99.
Qian, H., et al., Analysis of the genomic sequence of Philosamia cynthianucleopolyhedrin virus and comparison with Antheraea pernyinucleopolyhedrin virus. BMC Genomics, 2013. 14: p. 115.
Harrison, R.L. and Lynn, D.E., Genomic sequence analysis of a nucleopolyhedrovirus isolated from the diamondback moth, Plutella xylostella. Virus Genes, 2007. 35(3): pp. 857-73.
Harrison, R.L. and Bonning, B.C., Comparative analysis of the genomes of Rachiplusia ouand Autographa californicamultiple nucleopolyhedroviruses. J Gen Virol, 2003. 84(Pt 7): pp. 1827-42.
Wang, Y.S., et al., Genome of Thysanoplusia orichalceamultiple nucleopolyhedrovirus lacks the superoxide dismutase gene. J Virol, 2012. 86(21): pp. 11948-9.
Nakai, M., et al., Genome sequence and organization of a nucleopolyhedrovirus isolated from the smaller tea tortrix, Adoxophyes honmai. Virology, 2003. 316(1): pp. 171-83.
Hilton, S. and Winstanley, D., Genomic sequence and biological characterization of a nucleopolyhedrovirus isolated from the summer fruit tortrix, Adoxophyes orana. J Gen Virol, 2008. 89(Pt 11): pp. 2898-908.
Harrison, R.L., Genomic sequence analysis of the Illinois strain of the Agrotis ipsilonmultiple nucleopolyhedrovirus. Virus Genes, 2009. 38(1): pp. 155-70.
Jakubowska, A.K., et al., Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum: collinearity with Spodoptera exiguamultiple NPV. J Gen Virol, 2006. 87(Pt 3): pp. 537-51.
Wennmann, J.T., Gueli Alletti, G. and Jehle, J.A., The genome sequence of Agrotis segetumnucleopolyhedrovirus B (AgseNPV-B) reveals a new baculovirus species within the Agrotis baculoviruscomplex. Virus Genes, 2015. 50(2): pp. 260-76.
Zhu, Z., et al., Genome sequence and analysis of Buzura suppressarianucleopolyhedrovirus: a group II Alphabaculovirus. PLoS One, 2014. 9(1): p. e86450.
van Oers, M.M., et al., Genome sequence of Chrysodeixis chalcitesnucleopolyhedrovirus, a baculovirus with two DNA photolyase genes. J Gen Virol, 2005. 86(Pt 7): pp. 2069-80.
Bernal, A., et al., Complete genome sequences of five Chrysodeixis chalcitesnucleopolyhedrovirus genotypes from a Canary Islands isolate. Genome Announc, 2013. 1(5).
Zhu, S.Y., et al., Genomic sequence, organization and characteristics of a new nucleopolyhedrovirus isolated from Clanis bilineatalarva. BMC Genomics, 2009. 10: p. 91.
Hyink, O., et al., Whole genome analysis of the Epiphyas postvittananucleopolyhedrovirus. J Gen Virol, 2002. 83(Pt 4): pp. 957-71.
Tang, X.D., et al., Morphology and genome of Euproctis pseudoconspersanucleopolyhedrovirus. Virus Genes, 2009. 38(3): pp. 495-506.
Noune, C. and Hauxwell, C., Complete genome sequences of Helicoverpa armigerasingle nucleopolyhedrovirus strains AC53 and H25EA1 from Australia. Genome Announc, 2015. 3(5):e01083-15..
Tang, P., et al., Genomic sequencing and analyses of HearMNPV--a new Multinucleocapsid nucleopolyhedrovirus isolated from Helicoverpa armigera. Virol J, 2012. 9: p. 168.
Zhang, C.X., Ma, X.C. and Guo, Z.J., Comparison of the complete genome sequence between C1 and G4 isolates of the Helicoverpa armigerasingle nucleocapsid nucleopolyhedrovirus. Virology, 2005. 333(1): pp. 190-9.
Zhang, C.X. and Wu, J.C., Genome structure and the p10 gene of the Helicoverpa armigeranucleopolyhedrovirus. Acta Biochim Biophys Sinica, 2001. 33(2): pp. 179-84.
Chen, X., et al., The sequence of the Helicoverpa armigerasingle nucleocapsid nucleopolyhedrovirus genome. J Gen Virol, 2001. 82(Pt 1): pp. 241-57.
Ogembo, J.G., et al., Comparative genomic sequence analysis of novel Helicoverpa armigeranucleopolyhedrovirus (NPV) isolated from Kenya and three other previously sequenced Helicoverpaspp. NPVs. Virus Genes, 2009. 39(2): pp. 261-72.
Chen, X., et al., Comparative analysis of the complete genome sequences of Helicoverpa zeaand Helicoverpa armigerasingle-nucleocapsid nucleopolyhedroviruses. J Gen Virol, 2002. 83(Pt 3): pp. 673-84.
Rohrmann, G.F., Erlandson, M.A. and Theilmann, D.A., The genome of a baculovirus isolated from Hemileucasp. encodes a serpin ortholog. Virus Genes, 2013. 47(2): pp. 357-64.
Rohrmann, G.F., Erlandson, M.A. and Theilmann, D.A., Genome sequence of an alphabaculovirus isolated from the Oak Looper, Lambdina fiscellaria, contains a putative 2-kilobase-pair transposable element encoding a transposase and a FLYWCH domain-containing protein. Genome Announc, 2015. 3(3): e00186-15.
Xiao, H. and Qi, Y., Genome sequence of Leucania seperatanucleopolyhedrovirus. Virus Genes, 2007. 35(3): pp. 845-56.
Kuzio, J., et al., Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology, 1999. 253(1): pp. 17-34.
Kabilov, M.R., et al., Complete genome sequence of a Western Siberian Lymantria disparmultiple nucleopolyhedrovirus isolate. Genome Announc, 2015. 3(2).
Rabalski, L., et al., An alphabaculovirus isolated from dead Lymantria disparlarvae shows high genetic similarity to baculovirus previously isolated from Lymantria monacha– An example of adaptation to a new host. J Invertebr Pathol, 2016. 139: pp. 56-66.
Harrison, R.L. and Rowley, D.L., Complete genome sequence of the strain of Lymantria disparmultiple nucleopolyhedrovirus found in the gypsy moth biopesticide Virin-ENSh. Genome Announc, 2015. 3(1):e01407-14.
Martemyanov, V.V., et al., The enhancin gene: one of the genetic determinants of population variation in baculoviral virulence. Dokl Biochem Biophys, 2015. 465: pp. 351-3.
Harrison, R.L., Rowley, D.L. and Keena, M.A., Geographic isolates of Lymantria disparmultiple nucleopolyhedrovirus: Genome sequence analysis and pathogenicity against European and Asian gypsy moth strains. J Invertebr Pathol, 2016. 137: pp. 10-22.
Nai, Y.S., et al., Genomic sequencing and analyses of Lymantria xylinamultiple nucleopolyhedrovirus. BMC Genomics, 2010. 11: pp. 116.
Choi, J.B., et al., Complete genomic sequences and comparative analysis of Mamestra brassicaenucleopolyhedrovirus isolated in Korea. Virus Genes, 2013. 47(1): pp. 133-51.
Li, Q., et al., Sequence and organization of the Mamestra configuratanucleopolyhedrovirus genome. Virology, 2002. 294(1): pp. 106-21.
Li, L., et al., Complete comparative genomic analysis of two field isolates of Mamestra configuratanucleopolyhedrovirus-A. J Gen Virol, 2005. 86(Pt 1): pp. 91-105.
Thumbi, D.K., et al., Complete sequence, analysis and organization of the Orgyia leucostigmanucleopolyhedrovirus genome. Viruses, 2011. 3(11): pp. 2301-27.
Rohrmann, G.F., Erlandson, M.A. and Theilmann, D.A., A distinct group II alphabaculovirus isolated from a Peridromaspecies. Genome Announc, 2015. 3(2):e00185-15.
Craveiro, S.R., et al., The genome sequence of Pseudoplusiaincludens single nucleopolyhedrovirus and an analysis of p26 gene evolution in the baculoviruses. BMC Genomics, 2015. 16: p. 127.
WF, I.J., et al., Sequence and organization of the Spodoptera exiguamulticapsid nucleopolyhedrovirus genome. J Gen Virol, 1999. 80(Pt 12): pp. 3289-304.
Harrison, R.L., Puttler, B. and Popham, H.J., Genomic sequence analysis of a fast-killing isolate of Spodoptera frugiperdamultiple nucleopolyhedrovirus. J Gen Virol, 2008. 89(Pt 3): pp. 775-90.
Breitenbach, J.E., et al., Determination and analysis of the genome sequence of Spodoptera littoralismultiple nucleopolyhedrovirus. Virus Res, 2013. 171(1): pp. 194-208.
Pang, Y., et al., Sequence analysis of the Spodoptera lituramulticapsid nucleopolyhedrovirus genome. Virology, 2001. 287(2): pp. 391-404.
Liu, X., et al., Genomic sequencing and analysis of Sucra jujubanucleopolyhedrovirus. PLoS One, 2014. 9(10): p. e110023.
Willis, L.G., et al., Sequence analysis of the complete genome of Trichoplusia nisingle nucleopolyhedrovirus and the identification of a baculoviral photolyase gene. Virology, 2005. 338(2): pp. 209-26.
Wormleaton, S., Kuzio, J. and Winstanley, D., The complete sequence of the Adoxophyes oranagranulovirus genome. Virology, 2003. 311(2): pp. 350-65.
Liang, Z., et al., Genomic sequencing and analysis of Clostera anachoretagranulovirus. Arch Virol, 2011. 156(7): pp. 1185-98.
Yin, F., et al., The complete genome of a New Betabaculovirus from Clostera anastomosis. PLoS One, 2015. 10(7): p. e0132792.
Zhang, S., et al., Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis. Virol Sin, 2015. 30(6): pp. 417-24.
Han, G., et al., Genome of Cnaphalocrocis medinalisgranulovirus, the first Crambidae-infecting betabaculovirus isolated from rice leaffolder to sequenced. PLoS One, 2016. 11(2): p. e0147882.
Escasa, S.R., et al., Sequence analysis of the Choristoneura occidentalisgranulovirus genome. J Gen Virol, 2006. 87(Pt 7): pp. 1917-33.
Liang, Z., et al., Comparative analysis of the genomes of Clostera anastomosis(L.) granulovirus and Clostera anachoretagranulovirus. Arch Virol, 2013. 158(10): pp. 2109-14.
Luque, T., et al., The complete sequence of the Cydia pomonellagranulovirus genome. J Gen Virol, 2001. 82(Pt 10): pp. 2531-47.
Lange, M. and Jehle, J.A., The genome of the Cryptophlebia leucotretagranulovirus. Virology, 2003. 317(2): pp. 220-36.
Ardisson-Araujo, D.M., et al., A betabaculovirus-encoded gp64 homolog codes for a functional envelope fusion protein. J Virol, 2016. 90(3): pp. 1668-72.
Ferrelli, M.L., et al., Genome of Epinotia aporema granulovirus (EpapGV), a polyorganotropic fast killing betabaculovirus with a novel thymidylate kinase gene. BMC Genomics, 2012. 13: p. 548.
Ardisson-Araujo, D.M., et al., Genome sequence of Erinnyis ello granulovirus (ErelGV), a natural cassava hornworm pesticide and the first sequenced sphingid-infecting betabaculovirus. BMC Genomics, 2014. 15: p. 856.
Harrison, R.L. and Popham, H.J., Genomic sequence analysis of a granulovirus isolated from the Old World bollworm, Helicoverpa armigera. Virus Genes, 2008. 36(3): pp. 565-81.
Harrison, R.L., Rowley, D.L. and Funk, C.J., The complete genome sequence of Plodia interpunctellagranulovirus: evidence for horizontal gene transfer and discovery of an unusual inhibitor-of-apoptosis gene. PLoS One, 2016. 11(7): p. e0160389.
Taha, A., et al., Comparative analysis of the granulin regions of the Phthorimaea operculellaand Spodoptera littoralisgranuloviruses. Virus Genes, 2000. 21(3): pp. 147-55.
Hashimoto, Y., et al., Sequence analysis of the Plutella xylostellagranulovirus genome. Virology, 2000. 275(2): pp. 358-72.
Zhang, B.Q., et al., The genome of Pieris rapaegranulovirus. J Virol, 2012. 86(17): p. 9544.
Cuartas, P.E., et al., The complete sequence of the first Spodoptera frugiperdaBetabaculovirus genome: a natural multiple recombinant virus. Viruses, 2015. 7(1): pp. 394-421.
Wang, Y., et al., Genomic sequence analysis of granulovirus isolated from the tobacco cutworm, Spodoptera litura. PLoS One, 2011. 6(11): p. e28163.
Hayakawa, T., et al., Sequence analysis of the Xestia c- nigrumgranulovirus genome. Virology, 1999. 262(2): pp. 277-97.
Duffy, S.P., et al., Sequence analysis and organization of the Neodiprion abietisnucleopolyhedrovirus genome. J Virol, 2006. 80(14): pp. 6952-63.
Lauzon, H.A., et al., Sequence and organization of the Neodiprion leconteinucleopolyhedrovirus genome. J Virol, 2004. 78(13): pp. 7023-35.
Garcia-Maruniak, A., et al., Sequence analysis of the genome of the Neodiprion sertifernucleopolyhedrovirus. J Virol, 2004. 78(13): pp. 7036-51.
Afonso, C.L., et al., Genome sequence of a baculovirus pathogenic for Culex nigripalpus. J Virol, 2001. 75(22): pp. 11157-65.
Miller, L.K. and Dawes, K.P., Restriction endonuclease analysis for the identification of baculovirus pesticides. Appl Environ Microbiol, 1978. 35(2): pp. 411-21.
Smith, G.E. and Summers, M.D., Analysis of baculovirus genomes with restriction endonucleases. Virology, 1978. 89(2): pp. 517-27.
Lee, H.H. and Miller, L.K., Isolation of genotypic variants of Autographa californicanuclear polyhedrosis virus. J Virol, 1978. 27(3): pp. 754-67.
Miller, L.K. and Dawes, K.P., Restriction endonuclease analysis to distinguish two closely related nuclear polyhedrosis viruses: Autographa californicaMNPV and Trichoplusia niMNPV. Appl Environ Microbiol, 1978. 35(6): pp. 1206-10.
Smith, G.E. and Summers, M.D., Restriction Maps of Five Autographa californicaMNPV Variants, Trichoplusia niMNPV and Galleria mellonellaMNPV DNAs with Endonucleases SmaI, KpnI, BamHI, SacI, XhoI and EcoRI. J Virol, 1979. 30(3): pp. 828-38.
Loh, L.C., et al., Analysis of the Spodoptera frugiperdanuclear polyhedrosis virus genome by restriction endonucleases and electron microscopy. J Virol, 1982. 44(2): pp. 747-51.
de Moraes, R.R. and Maruniak, J.E., Detection and identification of multiple baculoviruses using the polymerase chain reaction (PCR) and restriction endonuclease analysis. J Virol Methods, 1997. 63(1-2): pp. 209-17.
Ernoult-Lange, M., et al., Characterization of the simian virus 40 late promoter: relative importance of sequences within the 72-base-pair repeats differs before and after viral DNA replication. J Virol, 1987. 61(1): pp. 167-76.
Woo, S.D., Rapid detection of multiple nucleopolyhedroviruses using polymerase chain reaction. Mol Cells, 2001. 11(3): pp. 334-40.
Wang, L.H., et al., Sequence analysis of the Bam HI-J fragment of the Spodoptera lituramulticapsid nucleopolyhedrovirus. Acta Biochim Biophy Sinica, 2001. 33(6): pp. 615-20.
Pijlman, G.P., A.J. Pruijssers and Vlak, J.M., Identification of pif-2, a third conserved baculovirus gene required for per os infection of insects. J Gen Virol, 2003. 84(Pt 8): pp. 2041-9.
Herniou, E.A., et al., Use of whole genome sequence data to infer baculovirus phylogeny. J Virol, 2001. 75(17): pp. 8117-26.
Somasekar, S., Jayapragasam, M., Rabindra, R. J., Characterization of five Indian isolates of the nuclear polyhedrosis virus of Helicoverpa armigera. Phytoparasitica, 1993. 21(4): pp. 333-7.
Lange, M., et al., Towards a molecular identification and classification system of lepidopteran-specific baculoviruses. Virology, 2004. 325(1): pp. 36-47.
Acharya, A. and Gopinathan, K.P., Characterization of late gene expression factors lef-9 and lef-8 from Bombyx morinucleopolyhedrovirus. J Gen Virol, 2002. 83(Pt 8): pp. 2015-23.
Crouch, E.A., et al., Inter-subunit interactions of the Autographa californicaM nucleopolyhedrovirus RNA polymerase. Virology, 2007. 367(2): pp. 265-74.
Toprak, U., et al., Preoperative evaluation of renal anatomy and renal masses with helical CT, 3D-CT and 3D-CT angiography. Diagn Interv Radiol, 2005. 11(1): pp. 35-40.
Kumar, S., K. Tamura and Nei, M., MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform, 2004. 5(2): pp. 150-63.
Jose, J., et al., Molecular characterization of nucleopolyhedrovirus of three lepidopteran pests using late expression factor-8 gene. Indian J Virol, 2013. 24(1): pp. 59-65.
Nai, Y.S., et al., A new nucleopolyhedrovirus strain (LdMNPV-like virus) with a defective fp25 gene from Lymantria xylina(Lepidoptera: Lymantriidae) in Taiwan. J Invertebr Pathol, 2009. 102(2): pp. 110-9.
Chou, C.M., et al., Characterization of Perina nudanucleopolyhedrovirus (PenuNPV) polyhedrin gene. J Invertebr Pathol, 1996. 67(3): pp. 259-66.
Wang, C.H., et al., Continuous cell line from pupal ovary of Perina nuda(Lepidoptera: Lymantriidae) that is permissive to nuclear polyhedrosis virus from P. nuda. J Invertebr Pathol, 1996. 67(3): pp. 199-204.
Sims, D., et al., Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet, 2014. 15(2): pp. 121-32.
Goodwin, S., McPherson, J.D. and McCombie, W.R., Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet, 2016. 17(6): pp. 333-51.
Luo, C., et al., Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One, 2012. 7(2): p. e30087.
Garcia-Maruniak A.et al., A variable region of Anticarsia gemmatalis nuclear polyhedrosis virus contains tandemly repeated DNA sequences. Virus Res, 1996. 41:123-132.
Martin, M., Cutadapt removes adapter sequences from high-throughput sequencing Reads. EMBnet.journal, 2011. 17(1): pp. 10-12.
Schmieder, R. and Edwards, R., Quality control and preprocessing of metagenomic datasets. Bioinformatics, 2011. 27(6): pp. 863-4.
Patel, R.K. and Jain, M., NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One, 2012. 7(2): p. e30619.
Masella, A.P., et al., PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics, 2012. 13: pp. 31.
Zhang, J., et al., PEAR: a fast and accurate illumina paired-end reAd mergeR. Bioinformatics, 2014. 30(5): pp. 614-20.
Magoc, T. and Salzberg, S.L., FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 2011. 27(21): pp. 2957-63.
Liu, B., et al., COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. Bioinformatics, 2012. 28(22): pp. 2870-4.
Luo, R., et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 2012. 1(1): p. 18.
Zhang, W., et al., A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One, 2011. 6(3): p. e17915.
Margulies, M., et al., Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005. 437(7057): pp. 376-80.
Chevreux, B., et al., Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res, 2004. 14(6): pp. 1147-59.
Untergasser, A., et al., Primer3--new capabilities and interfaces. Nucleic Acids Res, 2012. 40(15): p. e115.
Salzberg, S.L., et al., Microbial gene identification using interpolated Markov models. Nucleic Acids Res, 1998. 26(2): pp. 544-8.
van Baren, M.J., Koebbe, B.C. and Brent, M.R., Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences. Curr Protoc Bioinformatics, 2007. 4: p. Unit 4 8.
Lukashin, A.V. and Borodovsky, M., GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res, 1998. 26(4): pp. 1107-15.
Wang, S., Sundaram, J.P. and Spiro, D., VIGOR, an annotation program for small viral genomes. BMC Bioinformatics, 2010. 11: pp. 451.
Li, S.C., Shiau, C.K. and Lin, W.C., Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res, 2008. 36(Database issue): pp. D184-9.
Stothard, P. and Wishart, D.S., Circular genome visualization and exploration using CGView. Bioinformatics, 2005. 21(4): p. 537-9.
Kumar, S., et al., MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 2008. 9(4): pp. 299-306.
Sievers, F., et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol, 2011. 7: pp. 539.
Thompson, J.D., Gibson, T.J. and Higgins, D.G., Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics, 2002. 2: p. Unit 2 3.
Talavera, G. and Castresana, J., Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol, 2007. 56(4): pp. 564-77.
Castresana, J., Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol, 2000. 17(4): pp. 540-52.
Ronquist, F., et al., MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol, 2012. 61(3): pp. 539-42.
Stamatakis, A., RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 2014. 30(9): pp. 1312-3.
Douady, C.J., et al., Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol Biol Evol, 2003. 20(2): pp. 248-54.
Drummond, A.J., et al., Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol, 2012. 29(8): pp. 1969-73.
Camacho, C., et al., BLAST+: architecture and applications. BMC Bioinformatics, 2009. 10: p. 421.
Brudno, M., et al., LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res, 2003. 13(4): pp. 721-31.
Grant, J.R., Arantes, A.S. and Stothard, P., Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics, 2012. 13: pp. 202.
Darling, A.C., et al., Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res, 2004. 14(7): pp. 1394-403.