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                  155072.pdf (publisher's version ) (Open Access)Here, we describe the draft genome sequence and annotation of Lactobacillus plantarum strain Lp90, the first sequenced genome of a L. plantarum strain isolated from wine. This strain has a noticeable ropy phenotype and showed potential probiotic properties. The genome consists of 3,324,076 bp (33 contigs) and contains 3,155 protein coding genes, 34 pseudogenes, and 84 RNA genes

Bayjanov, J.

Caggianiello, G.

Capozzi, V.

Cattivelli, L.

Hijum, S.A. van

Lamontanara, A.

Michelotti, V.

Orrù, L.

Renckens, B.

Spano, G.

English

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Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated
from Wine
Antonella Lamontanara,a Graziano Caggianiello,b Luigi Orrù,a Vittorio Capozzi,b Vania Michelotti,a Jumamurat R. Bayjanov,c
Bernadet Renckens,c Sacha A. F. T. van Hijum,c,d Luigi Cattivelli,a Giuseppe Spanob
Consiglio Per la Ricerca e Sperimentazione in Agricoltura (CRA) Genomics Research Centre, Fiorenzuola d’Arda, Italya; Department of Agriculture, Food and Environment
Sciences, University of Foggia, Foggia, Italyb; Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen,
The Netherlandsc; NIZO food research, Ede, The Netherlandsd
Here, we describe the draft genome sequence and annotation of Lactobacillus plantarum strain Lp90, the first sequenced genome
of a L. plantarum strain isolated from wine. This strain has a noticeable ropy phenotype and showed potential probiotic proper-
ties. The genome consists of 3,324,076 bp (33 contigs) and contains 3,155 protein coding genes, 34 pseudogenes, and 84 RNA
genes.
Received 27 January 2015 Accepted 2 February 2015 Published 12 March 2015
Citation Lamontanara A, Caggianiello G, Orrù L, Capozzi V, Michelotti V, Bayjanov JR, Renckens B, van Hijum SAFT, Cattivelli L, Spano G. 2015. Draft genome sequence of
Lactobacillus plantarum Lp90 isolated from wine． Genome Announc 3(2):e00097-15. doi:10.1128/genomeA.00097-15.
Copyright © 2015 Lamontanara et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Giuseppe Spano, giuseppe.spano@unifg.it.
Lactobacillus plantarum is a bacterial species found in many dif-ferent ecological niches such as vegetables,meat, fish, anddairy
products as well as in the gastrointestinal tract (1). L. plantarum is
one of the dominant bacteria in fermented foods such as sauer-
kraut, pickles, olives, wine, sourdough, and kimchi (1). Some
strains are claimed to provide a health benefit and aremarketed as
probiotics (2). Here, we report the genome sequence of L. planta-
rum strain Lp90, a strain isolated from “Nero di Troia,” a typical
Apulian (South of Italy) wine and in particular, from the same
terroir of six Oenococcus oeni strains whose genomes have been
recently sequenced (3, 4). This strain is characterized by a distinc-
tive ropy phenotype, which was ascribed to its capacity to over-
produce exopolysaccharides (EPS) (5), and by potential probiotic
proprieties (unpublished results). This strain was already charac-
terized in a previous study onphenotypic and genomic diversity of
L. plantarum strains isolated from various environmental niches
(6) and in three studies dedicated to Lp90 genes coding for small
heat shock proteins (7–9). It is the first L. plantarum genome se-
quenced coming from a strain of wine origin. Twomicrograms of
genomic DNA was subjected to library preparation using the
TruSeq DNA sample prep kit FC-121-1001 according to theman-
ufacturer’s instructions. Whole-genome sequencing of Lp90 was
performed using the Illumina GAIIx platform.
Prior to assembly, raw reads were filtered using the PRINSEQ
v0.20.3 software (10). After filtering, a total of 16,574,199 paired-
end reads ranging from 75 to 115 bp in length were obtained. The
genome sequence was de novo assembled using the Ray v2.2.0
assembly program (11) with default parameters and using a Kmer
size of 71. The assembly resulted in 33 contigs with an N50 length
of 207,479 bp. The size of the shortest contig was 354 bp, while the
length of the longest contig was 489,345 bp. The genome is
3,324,076 bp long with a GC content of 44.32%. Genome annota-
tion was performed using the Rapid Annotation using Subsystem
Technology (RAST) server (12). Functional annotations were re-
fined by aligning the protein sequences to the Cluster of Ortholo-
gousGroups (COG) database (13) using BLASTp and by using the
functionality of InterProScan v5.0 in Blast2GO (14) searching for
matches against the PRINTS (v42.0), Pfam (v27.0), and TI-
GRFAMs (v13.0) databases. The TMHMM (v2.0) and Phobius
(v1.01) prediction search tools were used, respectively, to predict
transmembrane domains and the presence of signal peptides. Of
the 3,273 predicted genes, 3,155 were protein-coding genes, 34
were identified to be pseudogenes, while 84 were RNA-coding
genes (70 tRNAs and 14 rRNAs).
Nucleotide sequence accession number. The whole-genome
shotgun project has been deposited at DDBJ/EMBL/GenBank un-
der the accession number JIBX00000000.
ACKNOWLEDGMENTS
This research was partially supported by a grant from the project
PON02_00186_3417512, “S.I. Mi.S.A.,” and by the Apulian Region in the
framework of the “OenoMicroManagement” project (PIF—Progetti In-
tegrati di Filiera no. 94750304571).
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Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine

Here, we describe the draft genome sequence and annotation of Lactobacillus plantarum strain Lp90, the first sequenced genome of a L. plantarum strain isolated from wine. This strain has a noticeable ropy phenotype and showed potential probiotic properties. The genome consists of 3,324,076 bp (33 contigs) and contains 3,155 protein coding genes, 34 pseudogenes, and 84 RNA genes

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Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine

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