WGS sequencing of Pseudomonas sp. strain DKN 2791 - SRA

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SRX20983861: WGS sequencing of Pseudomonas sp. strain DKN 2791
1 ILLUMINA (Illumina NovaSeq 6000) run: 1.1M spots, 522M bases, 173.1Mb downloads

Design: Genomic DNA libraries were prepared using the Nextera XT Library Prep Kit (Illumina, San Diego, USA) following the manufacturers protocol with the following modifications: input DNA was increased 2-fold, and PCR elongation time was increased to 45s. DNA quantification and library preparation were carried out on a Hamilton Microlab STAR automated liquid handling system (Hamilton Bonaduz AG, Switzerland). Pooled libraries were quantified using the Kapa Biosystems Library Quantification Kit for Illumina. Libraries were sequenced using an Illumina sequencer (NovaSeq 6000) using a 250bp paired end protocol. Reads were adapter trimmed using Trimmomatic 0.30 with a sliding window quality cutoff of Q15. Quality was assessed using in-house scripts combined with Samtools, BedTools and bwa-mem.

Submitted by: UC Davis

Study: Blue Soy Mutants Project

PRJNA993393 • SRP448605 • All experiments • All runs

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Two spontaneous mutants developed from the Pseudomonas carnis strain UCD_MED7 = DKN 2790 were isolated and subjected to 16S rRNA gene sequencing. A BLAST search run against reference sequences (refseq_rna) was inconclusive because a Pseudomonas carnis reference strain was not available. Another run against the nucleotide collection (nr/nt) showed high identity scores (100%) for twenty-one different entries including the whole genome shotgun sequence from Pseudomonas carnis strain UCD_MED7. Strain UCD_MED7 produced a striking blue pigment when cultured in/on soymilk, but the mutant strains did not. All three strains formed fluorescent pigments and two also formed dark, melanin-like pigments. Whole genome shotgun sequences were obtained for the two mutant strains to facilitate the discovery of genes involved in blue pigment biosynthesis. The pigment composition and biosynthetic pathway have yet to be determined.

Sample: Circular, entire, smooth-shiney, low convex, dark gray colonies, 2-4 mm in diameter after 48 hours on TSA. Gram-negative, motile bacilli.

SAMN36399053 • SRS18258984 • All experiments • All runs

Organism: Pseudomonas sp. DKN 2791

Library:

Name: 252701

Instrument: Illumina NovaSeq 6000

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 1.1M spots, 522M bases, 173.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR25237520	1,099,857	522M	173.1Mb	2023-07-11

ID:: 28417693

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