Truseq dna ht sample prep kit

The complete genome sequence of L. salivarius FFIG58 was reported recently [23 (link)]. Seven additional FFIG strains were selected for complete genome sequencing in this work. Single colonies of the selected L. salivariusFFIG strains cultured on MRS (Oxoid, Cambridge, UK) agar plates were inoculated separately into MRS broth and incubated at 37 °C for 12 h. The isolation of the genomic DNA was performed by using a lysozyme lysis buffer (75 mM NaCl, 20 mM EDTA, 20 mM Tris-HCl, pH 7.5, 10 mg/mL lysozyme), the chloroform-isoamyl alcohol separation, and isopropanol precipitation method as described previously [23 (link),24 (link)]. The genomic DNA samples were sequenced with an Illumina HiSeq platform using the 2 × 300-bp paired-end read length-sequencing protocol. The paired-end sequencing libraries were prepared using the TruSeq DNA HT Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The paired-end reads were filtered with PrinSeq-lite (v.0.20.4) and assembled with A5-miseq (v.201690825) with default parameters [23 (link)].
Sequencing results were analyzed using various software programs at their default settings, unless otherwise specified. Gene prediction and annotation were performed using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (v.4.12) [25 (link)] and Rapid Annotations using Subsystems Technology (RAST) [26 (link)].

Wasp specimens were sampled at Santa Maria City, latitude 34.95303 and longitude − 120.43572 parasitizing Drosophila flies - Leptopilina boulardi parasites several Drosophila species while Braconidae species is a restricted parasite of Drosophila species from the flavopilosa group - a highly specialized species group that uses flowers as unique breeding sites [29 (link)–31 (link)]. It is important to emphasize that we tried to identify the Braconidae wasp at the lowest taxonomic level possible, but after contacting specialized taxonomists it was not possible to reach species identification. Therefore, we will call this species from now on as braconid or Braconidae wasp although it is closely related to the Aphidius genus in a previous COI analysis [29 (link)–31 (link)]). Genomic DNA was prepared with TruSeq DNA HT Sample Prep Kit (Illumina) according to the manufacturer’s instructions and sequenced in a Solexa-Illumina HiSeq 2000 New Generation Sequencing (NGS) device using a single-end approach of read length of 100 bp [29 (link)].

A total of 13 paired tumor and adjacent normal tissues underwent either whole-genome or whole-exome sequencing (Supplementary Table 6). Genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA), and the quality of DNA was tested by using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Whole-genome sequencing for seven of the paired samples was previously reported [13 (link)], and the data were obtained with an average depth of 65× coverage for tumor samples and 42× coverage for control samples. For the remaining six paired samples, sequencing libraries were prepared using a TruSeq DNA HT sample prep kit (Illumina, San Diego, CA, USA), and whole-exome enrichment was performed using SureSelect human all exon kits (Agilent) according to the manufacturer’s instructions. Paired-end sequencing (2 × 150 bp) was performed on a HiSeq 2500 sequencing platform (Illumina), as described in our previous study [13 (link)], acquiring the data with an average depth of 70× coverage for tumor samples and 67× coverage for control samples.

All of the E. coli isolates were whole-genome sequenced using an Illumina HiSeq platform. However, for the purposes of this study, WGS analyses were conducted for only 4 isolates belonging to ST127. Genomic DNA was extracted using a TIANamp Bacteria DNA Kit (Tiangen, China) and the paired-end sequencing libraries were constructed using Nextera XT DNA Sample Preparation Kits or a TruSeq DNA HT Sample Prep Kit (Illumina, USA), following the manufacturers’ instructions.
The quality of the short-reads was analyzed using fastQC, and low quality reads were trimmed using the Trimmomatic software package (58 ). The trimmed reads were de novo assembled using SPAdes (26 (link)).

Microbial DNA was extracted from morning stools (200 mg) with the QIAamp DNA Stool Mini Kit (Qiagen, Hilden, Germany) according to the manufactures’ instructions. The DNA library was established using a TruSeq DNA HT Sample Prep Kit and sequenced by the Illumina Hiseq 2000 at BGI-Shenzhen. By removing low quality bases and human genome, the high-quality sequences were mapped using the published gene catalog database of the human gut microbiome [26 (link)]. Microbial diversity was determined, and taxa were identified as described previously [27 (link), 28 (link)]. Functional orthologs (KOs) were predicted against the KEGG gene database (v79) by BLASTP with the highest scoring annotated hits. The relative abundances of phyla, genera, species and KOs were calculated from the relative abundances of their respective genes.

Microbial DNA was extracted from stool samples (200 mg) by the phenol/chloroform/isoamyl alcohol method (63 (link)). Fecal metagenomes were sequenced in high-quality fecal DNA samples. The DNA library was prepared using a TruSeq DNA HT Sample Prep Kit (Illumina) and sequenced by the Illumina Hiseq 2000 at BGI-Shenzhen. Removing low-quality bases and human genome left 83.59% of the high-quality sequences, and these were mapped using the published gene catalog database of the human gut microbiome (64 (link)). Microbial diversity was determined and taxa were identified as described previously (65 (link), 66 (link)). Functional orthologs (KOs) were predicted against the Kyoto Encyclopedia of Genes and Genomes (KEGG) gene database (v79) by BLASTP (http://www.ncbi.nlm.nih.gov/blast/) with the highest scoring annotated hits. The relative abundances of phyla, genera, species, and KOs were calculated from the relative abundances of their respective genes.