Genome sequencing of the Lactobacillus fabifermentans T30PCM01 isolat... - SRA

SRX365193: Genome sequencing of the Lactobacillus fabifermentans T30PCM01 isolated from grape marcs
1 ILLUMINA (Illumina MiSeq) run: 1.4M spots, 539.4M bases, 323.8Mb downloads

Design: Growth of cells and DNA preparation. For the isolation of L. Fabifermentans chromosomal DNA, an overnight culture was grown in in 100 ml of M-17 broth at 37°C. Cells were harvested by centrifugation and the pellet was resuspended in 10 ml of a TE solution (10 mM Tris-hydrochloride, 1 mM EDTA,pH 7.5) containing lysozyme (0.5 mg/ml). The suspension was incubated at 37°C for 30 min. Afterwards the cells were collected and resuspended in 4 ml of TE (50 mM Tris-hydrochloride, 20 mM EDTA, pH 8) containing 1% SDS. The suspension was mix gently by intermittent inversion and, to ensure complete lysis, was kept at 65°C for 20 min. Afterwards 2 ml of KAc 5 M were added to the lysate and the solution was maintained at 0°C for 30 min. After centrifuging at 12000xg for 30 minutes at 4°C the supernatant was recovered and DNA was precipitated using ethanol. The pellet was air-dried and resuspended in 1 ml of TE (10 mM). Sample was treated with RNAse A (0.2 mg/ml) for 30 min at 37°C and treated with proteinase K (0.3 mg/ml) for 30min at 56°C. DNA was precipitated by adding an isovolume of isopropanol and pelleted by centrifugation. Pellet was air-dried and resuspended in nuclease free water.Finally the DNA was purified using phenol-chloroform. Genomic DNA quantification and purity were determined using Nanodrop and Qubit. Absence of degradation was verified with agarose gel electrophoresis using a 0.8% gel. Genomic DNA was sequenced at the Ramaciotti Centre for Gene Function Analysis (UNSW-Sydney) using the Illumina MiSeq Benchtop Sequencer. Sequencing produced 1413271 paired-end reads of 250+250 basi. Lybraries were produced using the “Nextera XT” kit, the DNA insert size was between ~350 bp up to 1.5 kbp. Sequence quality and conversion to fastaq format was performed using the FASTX-Toolkit version 0.0.13. Assembly was performed both on the quality trimmed and quality-filtered sequences and on the original sequences. The best result in terms of N50, maximum scaffold size and number of scaffolds were obtained on the original (not-filtered) sequences. End-trimming was performed using quality threshold “13” and quality filtering was performed selecting only the sequences having less that 10% of the sequence with quality lower than 13. Finally all the sequences shorter than k-mer length used for assembly were discarded. Short reads were assembled using the ABySS software (ver. 1.3.6) with the shortPaired procedure and a kmer of 63. Assembly generated 93 scaffolds larger than 1000 bases, the remaining scaffold were discarded.

Submitted by: UNIVERSITY OF PADUA

Study: Lacticaseibacillus fabifermentans T30PCM01 Genome sequencing and assembly

PRJNA219157 • SRP031487 • All experiments • All runs

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Lactobacillus fabifermentans T30PCM01 was isolated from grape marcs of the Prosecco vineyard in Fregona (Treviso) (Italy)

Sample: Lactobacillus fabifermentas T30PCM01

SAMN02356208 • SRS491573 • All experiments • All runs

Organism: Lactiplantibacillus fabifermentans T30PCM01

Library:

Name: Lfabifermentans-paired-end

Instrument: Illumina MiSeq

Strategy: WGA

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward251 reverse

Runs: 1 run, 1.4M spots, 539.4M bases, 323.8Mb

Run	# of Spots	# of Bases	Size	Published
SRR1012908	1,413,271	539.4M	323.8Mb	2014-06-24

ID:: 522027

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