ErelGV genomic DNA was sequenced with the 454 Genome Sequencer (GS) FLX™ Standard (Roche) at the Centro de Genômica de Alto Desempenho do Distrito Federal (Brasília, Brazil). The genome was assembled de novo using Geneious 6.0 [62 (link)] and confirmed using restriction enzyme digestion profile. The annotation was performed using Geneious 6.0 to identify the open reading frames (ORFs) that started with a methionine codon (ATG) encoding at least 50 amino acids and blastp [63 (link)] to identify homologues.
454 genome sequencer flx standard
Manufactured by Roche
Sourced in Brazil
The 454 Genome Sequencer (GS) FLX™ Standard is a high-throughput DNA sequencing system developed by Roche. It utilizes a sequencing-by-synthesis approach to generate DNA sequences. The system is capable of producing DNA sequences in a parallel manner, allowing for rapid and efficient genome analysis. The core function of the 454 Genome Sequencer (GS) FLX™ Standard is to perform DNA sequencing, enabling researchers to study genetic information and DNA-based biological processes.
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Lab products found in correlation
5 protocols using 454 genome sequencer flx standard
1
ErelGV Genome Sequencing and Annotation
2
DNA Purification from Occlusion Bodies
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Occlusion bodies (OBs) from dead L. obliqua larvae were purified and dissolved in an alkaline solution for DNA purification, all according to previously published protocol to O’Reilly et al.42 . The quantity and quality of the isolated DNA was determined by electrophoresis on 0.8% agarose gel (data not shown). The DNA was submitted to genome sequencing throughout the pyrosequencing technique performed by the 454 Genome Sequencer (GS) FLX™ Standard (Roche) at Macrogen Inc (Seoul, Republic of Korea).
3
Sequencing and Annotation of DisaGV Genome
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DisaGV genomic DNA was sequenced with the 454 Genome Sequencer (GS) FLX™ Standard (Roche) at the Centro de Genômica de Alto Desempenho do Distrito Federal (Brasília, Brazil). The genome was assembled de novo using Geneious 7.0 [47 (link)] and confirmed by comparing the restriction endonuclease fragment pattern from digestion of viral DNA to the fragment pattern generated from the assembled sequence. The annotation was performed using Geneious 7.0 to identify the ORFs that started with a methionine codon (ATG) encoding at least 50 amino acids and blastp to identify homologs. Specific primers were designed to amplify and sequence, by Sanger method, all regions in the genome with low coverage (<10 x).
4
PeluSNPV Genome Assembly and Annotation
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PeluSNPV genomic DNA was sequenced with a 454 Genome Sequencer (GS) FLX™ Standard (Roche) at the ‘Centro de Genômica de Alto Desempenho do Distrito Federal’ (Center of High-Performance Genomic, Brasilia, Brazil). The genome was assembled de novo using Geneious 7.0 (http://www.geneious.com )49 (link) and the in silico-predicted restriction enzyme digestion profile was compared to the profiles presented in the Fig. S1B . One homologous region with low coverage was amplified (PeluOrf-7 F GGG TCA TAC ATC GTA TCA CCA AGC G and Pelu-p74 R CAT CTT ATC GGT TGG CGT ACG TGA C), cloned into pCRII (Invitrogen), and sequenced by the Sanger method (GENEWIZ®, Inc., USA). The open reading frames (ORFs) that started with a methionine codon (ATG) and encoded polypeptides of at least 50 amino acids were identified with Genious 7.049 (link) and annotated using BLASTP50 (link). We considered an acceptable overlap of less than 50% of the ORF residing within the neighbor ORFs. Both Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html )51 (link) and Geneious 7.049 (link) programs were used to locate homologous regions (hrs) and direct repeats (drs).
5
De novo sequencing and annotation of DijuNPV
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DijuNPV genomic DNA was sequenced with two different high-throughput sequencing approaches: the 454 Genome Sequencer (GS) FLX™ Standard (Roche) at the ‘Centro de Genômica de Alto Desempenho do Distrito Federal’ (Center of High-Performance Genomic, Brasilia, Brazil) and the Illumina HiSeq™ 2000 platform at Macrogen Inc. (Seoul, Republic of Korea). The 454 sequencing data was assembled de novo using Geneious 9.0 [21 (link)], and the in silico-predicted restriction enzyme digestion profile was compared to Ribeiro et al. [13 ]. The open reading frames (ORFs) that started with a methionine codon (ATG) and encoded polypeptides of at least 50 amino acids were identified with Geneious 9.0 and annotated using BLASTX [22 (link)]. An acceptable overlap of less than 50% of the ORF within the neighbor ORFs was considered using a more liberal ORF annotation criterion based on Ref. [23 (link)]. Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html ) [24 (link)] implemented in Geneious 9.0 was used to locate repeat regions. The genomic DNA sequence was submitted to the GenBank with the accession number MK558262.
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