Draft Genome Sequence of Lactobacillus plantarum Strain IPLA 88

D a Genome Sequence o Lac obacillus plan a um S ain IPLA 88 Vic o Lade o, Pa icia Al a ez-Siei o, Begoña Red uello, Bea iz del Rio, Daniel M. Lina es, M. C uz Ma in, Ma ía Fe nández, Miguel A. Al a ez Ins i u o de P oduc os Lác eos de As u ias, IPLA-CSIC, Villa iciosa, As u ias, Spain He e, we epo a 3.2-Mbp d a assembly o he genome o Lac obacillus plan a um IPLA 88. The sequence o his sou dough isola e p o ides insigh in o he adap a ion o his e sa ile species o di e en en i onmen s. Recei ed 12 June 2013 Accep ed 24 June 2013 Published 25 July 2013 Ci a ion Lade o V, Al a ez-Siei o P, Red uello B, del Rio B, Lina es DM, Ma in MC, Fe nández M, Al a ez MA. 2013. D a genome sequence o Lac obacillus plan a um s ain IPLA 88. Genome Announc. 1(4):e00524-13. doi:10.1128/genomeA.00524-13. Copy igh © 2013 Lade o e al. This is an open-access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion 3.0 Unpo ed license. Add ess co espondence o Miguel A. Al a ez, [email p o ec ed]. Lac obacillus plan a um shows g ea capaci y o adap o di e - en en i onmen s, a consequence o i s e sa ile me abolism. I is encoun e ed in se e al habi a s, including human mucosae and e men ed oods and be e ages (especially hose de i ed om eg- e ables) (1–3). Some L. plan a um s ains ha e been p oposed as p obio ics (4–6) o as agen s o elimina ing oxic compounds, such as biogenic amines (7). O e he pas decade, se e al g oups ha e ocused on he ole o L. plan a um in sou dough e men a- ion and sugges i o be an ideal s a e o ype I sou doughs (8). We epo he e he d a genome o L. plan a um IPLA 88 s ain, isola ed om an I alian ype I sou dough. To al DNA om L. plan a um s ain IPLA 88 was ex ac ed, and a genomic lib a y o 0.5 kbp was cons uc ed and subjec ed o 90-bp pai ed-end sequencing (p o iding app oxima ely 120- old co e age) using an HiSeq 1000 sys em sequence (Illumina) a he Beijing Genomics Ins i u e (China). Quali y- il e ed eads we e assembled using Vel e so wa e (h p://www.ebi.ac.uk/~ze bino / el e /), esul ing in 208 con igs anging om 208 o 205,844 bp. The o al sequence leng h is 3,254,055 bp, wi h a G⫹C con en o 44.4%. The la e is consis en (a he low end o he ange) wi h esul s epo ed o o he L. plan a um genomes (44.5 o 44.7%). Anno a ion was pe o med using he NCBI P oka yo ic Genomes Anno a ion Pipeline (PGAAP) (h p://www.ncbi.nlm.nih.go /genomes/s a ic/Pipeline.h ml) and imp o ed wi h esul s ob- ained by BLAST analysis (h p://blas .ncbi.nlm.nih.go ). The ge- nome con ains 3,116 p edic ed coding sequences. P edic ed copies o he 16S, 23S and 5S RNA genes we e ound, as well as 47 genes o RNAs. The s ain possesses genes coding o h ee alpha-amylases (L103_0182, L103_09189, and L103_13633) and one oligo-1,6- glucosidase (L103_09184) (p o iding he abili y o hyd olyze ␣ -1,6-D-glucosidic linkages in s a ch and glycogen) and o se - e al pep idases speci ic o glu amine and p oline esidues ( e y abundan in whea glu en p o eins); hese help IPLA 88 g ow and pa icipa e in sou dough e men a ion (9). No e idence o i ulence- ela ed o an ibio ic esis ance genes was ound, and no genes in ol ed in biogenic amine p oduc ion we e de ec ed. The genome did, howe e , con ain a leas h ee p ophages plus some genes in ol ed in plasmid mobiliza ion o eplica ion, and one pu a i e oxin/an i oxin plasmid s abiliza ion sys em, in ag ee- men wi h he p esence o a leas h ee plasmids (da a no shown). In compa isons wi h he genomes o o he L. plan a um s ains in public da abases, including L. plan a um WCFS1 (4), JDM1 (5), and ZJ316 (6) o human o igin and L. plan a um ST-III (10)o dai y o igin, he L. plan a um IPLA 88 genome showed 230 o 419 di e en genes, o which 157 we e unique o he s ain. This may be a e lec ion o i s di e en o igin. Al hough 65% o hese unique genes code o p o eins o unknown unc ion, some ap- pea o be ela ed o exopolysaccha ide syn hesis o o encode pep idase ac i i ies, capaci ies ha a e desi able o he de elop- men o sou dough ex u e and la o . Knowledge o he L. plan a um IPLA 88 genome sequence should help imp o e ou unde s anding o how lac ic acid bac e ia in gen- e al, and L. plan a um in pa icula , adap o di e en en i onmen s. Nucleo ide sequence accession numbe s. The esul s o his whole-genome sho gun p ojec we e deposi ed in he DDBJ/ EMBL/GenBank da abase unde he accession no. ASJE00000000. The e sion o he genome desc ibed he e has he accession num- be ASJE01000000. ACKNOWLEDGMENTS This wo k was unded by he Spanish Minis y o Economy and Compe - i i eness (AGL2010-18430). B.D.R. and D.M.L. a e bene icia ies o JAE- DOC con ac s (CSIC), and P.A.-S. is he bene icia y o a g an om he FICYT, P incipado de As u ias, Spain. We hank Pasquale Russo o kindly p o iding a a ie y o I alian sou doughs. REFERENCES 1. Siezen RJ, Tzene a VA, Cas ioni A, Wels M, Phan HT, Rademake JL, S a enbu g MJ, Klee ebezem M, Molenaa D, an Hylckama Vlieg JE. 2010. Pheno ypicandgenomicdi e si yo Lac obacillusplan a ums ainsisola ed om a ious en i onmen al niches. En i on. Mic obiol. 12:758–773. 2. Ga dne NJ, Sa a d T, Obe meie P, Caldwell G, Champagne CP. 2001. Selec ion and cha ac e iza ion o mixed s a e cul u es o lac ic acid e men a ion o ca o , cabbage, bee and onion ege able mix u es. In . J. Food Mic obiol. 64:261–275. 3. De Vuys L, V ancken G, Ra y s F, Rimaux T, Weckx S. 2009. 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