The sequencing library was prepared using TruSeq Nano DNA Kit and sequenced with HiSeq 2500 System (2 × 100 paired-end) at Macrogen Inc. (Seoul, Republic of Korea). The resulting reads were filtered and trimmed to remove short and low-quality regions/reads and then assembled using CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) with default parameters. The read mapping and genome annotation was performed using Geneious 7.1.8 [86 (link)]. ORFs were annotated using BLASTx search against the NCBI non-redundant protein database. Maximum likelihood (ML) tree reconstruction was performed with FastTree using the default options [87 (link)] on alignments of terminase genes and complete genomes (without gaps) from pbunaviruses (21 isolates/species). The branch support values were estimated with the Shimodaira-Hasegawa test [88 (link)]. The pairwise genome comparison was performed using PASC [50 (link)]. The genome of selected species and strains were compared using MAUVE [89 (link)] and plotted using genoPlotR package [90 (link)] available for R.
Truseq nano dna kit
Manufactured by Macrogen
The TruSeq Nano DNA kit is a sample preparation kit designed for next-generation sequencing. It is used for fragmenting and preparing DNA samples for sequencing on Illumina platforms.
Automatically generated - may contain errors
Lab products found in correlation
Genejet kit, by Thermo Fisher Scientific (2 mentions)
Qubit fluorimeter, by Thermo Fisher Scientific (2 mentions)
Hiseq4000 machine, by Macrogen (2 mentions)
Clc genomics workbench, by Qiagen (1 mentions)
Hiseq 2500 system, by Macrogen (1 mentions)
Hiseq x, by Illumina (1 mentions)
Miseq platform, by Illumina (1 mentions)
6 protocols using truseq nano dna kit
1
Phylogenetic Analysis of Pbunaviruses
2
Gut Microbiome Sequencing in Mouse Diets
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Sequencing was performed by Macrogen (Seoul, Korea) using paired-end sequencing with read length 101 nucleotides using TruSeq Nano DNA kit sample library preparation protocol (Part #15041110 Rev. A) on a HiSeq 25000 System (Part #15011190 Rev. V HCS 2.2.70). For each of the six samples from mice fed the A1 and A2 diets, 8 to 12 million reads were obtained. The data was annotated using the Centrifuge software and a mapping threshold of 80 nucleotides minimum match length was apply to filter poor confidence matches [40 (link)]. Results were analysed with the R packages Phyloseq [41 (link)] and DESeq2 version 1.2.10 [42 ,43 (link)].
3
Hybrid Genome Assembly of Microorganism
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Genomic DNA was extracted using the GeneJET Kit (Thermo Scientific) and quantified using a Qubit fluorimeter (Invitrogen). Illumina sequencing (100 bp paired-end) was performed by Macrogen Inc. (Korea) using the TruSeq Nano DNA kit and a Hiseq4000 machine. FastQC v0.11.9 (7 ) and Trimmomatic v0.36 (8 (link)) were used for quality check and trimming. Nanopore libraries prepared with the Native Barcoding Expansion (EXP-NBD104) and the 1D Ligation Sequencing (SQK-LSK109) kits were run on a MinION device and FLO-MIN106 (R9.4) flow cells. After base-calling with Guppy v5.0.7, the raw nanopore reads were corrected, trimmed, and assembled using Canu v2.3 (9 (link)). Hybrid assemblies were performed using Unicycler v0.4.9b (10 (link)) with the short and long reads plus the Canu assembly as input. The assemblies were evaluated using QUAST v5.0.2 (11 (link)) and CheckM (12 (link)), and annotated with RAST v2.0 (13 (link)).
4
Hybrid Genome Assembly of Microorganism
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Genomic DNA was extracted using the GeneJET Kit (Thermo Scientific) and quantified using a Qubit fluorimeter (Invitrogen). Illumina sequencing (100 bp paired-end) was performed by Macrogen Inc. (Korea) using the TruSeq Nano DNA kit and a Hiseq4000 machine. FastQC v0.11.9 (7 ) and Trimmomatic v0.36 (8 (link)) were used for quality check and trimming. Nanopore libraries prepared with the Native Barcoding Expansion (EXP-NBD104) and the 1D Ligation Sequencing (SQK-LSK109) kits were run on a MinION device and FLO-MIN106 (R9.4) flow cells. After base-calling with Guppy v5.0.7, the raw nanopore reads were corrected, trimmed, and assembled using Canu v2.3 (9 (link)). Hybrid assemblies were performed using Unicycler v0.4.9b (10 (link)) with the short and long reads plus the Canu assembly as input. The assemblies were evaluated using QUAST v5.0.2 (11 (link)) and CheckM (12 (link)), and annotated with RAST v2.0 (13 (link)).
5
Complete Chloroplast Genome Sequencing
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The DNA library was constructed with the TruSeq Nano DNA Kit (Macrogen, Seoul, South Korea) and sequenced on the Illumina HiSeq X platform (Illumina, San Diego, CA) following manufacturer protocol. Sequencing generated 54,033,292 raw paired-end reads (150 bp) that were then assembled in NOVOPlasty 4.1 (Dierckxsens et al. 2017 (link)). The selected seed sequence was complete chloroplast genome of Q. glaucoides (Yang et al. 2021 (link); MG678003). Checking the assembled plastome, 2,850,980 reads were mapped in Geneious Prime 2022.2.2 (Kearse et al. 2012 (link)), resulting in a coverage of 4111× (Figure S1 ). Additionally, the plastome was annotated in Geneious and manually corrected for start and stop codons, as well as intron/exon boundaries. The complete chloroplast genome sequence of Q. turbinella was submitted to GenBank of the National Center for Biotechnology Information (NCBI, accession number OQ835463). The gene graphical map of the chloroplast genome structure and schematic maps of the cis-splicing genes and trans-splicing genes were illustrated using the CPGView (http://www.1kmpg.cn/cpgview ; Liu et al. 2023 (link)).
6
DNA Library Preparation and Illumina Sequencing
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A library was prepared from the extracted DNA by Macrogen using the TruSeq Nano DNA kit with a 350 bp insert size. This was then sequenced on an illumina MiSeq platform with 100 bp paired end reads.
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