Complete Genome Sequence of Probiotic Lactobacillus plantarum Strain FMNP01, Isolated from Mango Fruit Xue-Fei Li,a,b Xue-Yi Liao,a,b Yong-Feng Liu,c Li-Qiong Guo,a,b Zhi-Wei Ye,a,b Jun-Fang Lina,b Institute of Food Biotechnology, South China Agricultural University, Guangzhou, Chinaa; Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, Chinab; BGI-Shenzhen, Shenzhen, Chinac
Lactobacillus plantarum strain FMNP01 is a new strain with probiotic properties that was isolated from fresh mango from Guangzhou, China. Here, we report the complete genome of this organism. Received 14 October 2014 Accepted 17 October 2014 Published 26 November 2014 Citation Li X-F, Liao X-Y, Liu Y-F, Guo L-Q, Ye Z-W, Lin J-F. 2014. Complete genome sequence of probiotic Lactobacillus plantarum strain FMNP01, isolated from mango fruit. Genome Announc. 2(6):e01207-14. doi:10.1128/genomeA.01207-14. Copyright © 2014 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Jun-Fang Lin, [email protected]
actic acid bacteria (LAB) have a long history of use in the food industry and usually are regarded as generally safe food starters. As one of the most impotent LAB, Lactobacillus plantarum is widely distributed in plant-derived foods such as fruits, pickles, wine, and bean sauces. L. plantarum is also considered to be one of the most important probiotics because some L. plantarum strains possess a variety of health benefits such as immune enhancement (1–3). We sequenced the genome of L. plantarum strain FMNP01, which was originally isolated from fresh mango, using shotgun strategy with Illumina HiSeq2000. Here, we report the genome sequence of L. plantarum strain FMNP01. Whole-genome sequencing of L. plantarum strain FMNP01 was performed (BGI-Shenzhen, Shenzhen, China) with a shotgun strategy. A total of 513 Mb of next-generation Illumina paired-end 90-bp reads were generated by sequencing genome shotgun libraries of different fragment lengths (500 bp and 6 kb) with 155fold coverage of the genome. The assembly, performed by SOAPdenovo version 1.05 (4) with optimal assembly acquired with a key parameter K value of 39, consisted of 18 contigs and 4 scaffolds. The L. plantarum strain FMNP01 genome comprises a single circular chromosome (3,313,644 bp), with an overall G⫹C content of 44.48%. Coding sequence (CDS) prediction was carried out with Glimmer version 3.0 (5) and provided 3,147 CDSs covering 83.70% of the genome. Non-coding RNA was predicted by rRNAmmer 1.2 (6), tRNAscan-SE 1.2 (7), and Rfam 10.1 (8). There are 3,147 protein-coding genes, 16 rRNAs, 64 tRNAs, 70 minisatellite DNAs, and 3 microsatellite DNAs in the genome of L. plantarum strain FMNP01. Compared with L. plantarum strain WCFS1 (9, 10) and L. plantarum strain 16 (11), L. plantarum FMNP01 has more than 200 unique genes. These include glycosyl transferase, acetoin utilization protein, melibiose operon regulatory protein, glycosyl hydrolase, cellulose synthase, and other proteins related to carbohydrate metabolism. Interestingly, two potassium-transporting ATPase subunit proteins, involved in inorganic ion transport and metabolism, were uniquely identified in FMNP01. Furthermore, many prophage sequences and locations of FMNP01 are novel.
November/December 2014 Volume 2 Issue 6 e01207-14
In conclusion, the comparative analysis revealed that FMNP01 changed its genome to adapt the environmental niches, and the more than 200 unique genes may give it different abilities to utilize carbohydrates, transport potassium, and so on. The genome sequence gives us a basis to further elucidate the functional mechanisms of its probiotic properties. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at GenBank under the accession number JPSU00000000. The version described in this paper is version JPSU01000000. ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China (grants 31272217 and 31372116) and the Project of Science and Technology of Guangdong Province (grant 2013B010404041).
REFERENCES 1. Cebeci A, Gürakan C. 2003. Properties of potential probiotic Lactobacillus plantarum strains. Food Microbiol. 20:511–518. http://dx.doi.org/ 10.1016/S0740-0020(02)00174-0. 2. Siezen RJ, van Hylckama Vlieg JE. 2011. Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb. Cell Fact. 10(Suppl 1):S3. http://dx.doi.org/10.1186/1475-2859-10-S1-S3. 3. De Vries MC, Vaughan EE, Kleerebezem M, de Vos WM. 2006. Lactobacillus plantarum—survival, functional and potential probiotic properties in the human intestinal tract. Int. Dairy J. 16:1018 –1028. http:// dx.doi.org/10.1016/j.idairyj.2005.09.003. 4. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272. http://dx.doi.org/10.1101/gr.097261.109. 5. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009. 6. Lagesen K, Hallin P, Rødland EA, Staerfeldt H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108. http://dx.doi.org/10.1093/nar/ gkm160. 7. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 0955– 0964. http://dx.doi.org/10.1093/nar/25.5.0955. 8. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. 2009.
Li et al.
Rfam: updates to the RNA families database. Nucleic Acids Res. 37: D136 –D140. http://dx.doi.org/10.1093/nar/gkn766. 9. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, Stiekema W, Lankhorst RM, Bron PA, Hoffer SM, Groot MN, Kerkhoven R, de Vries M, Ursing B, de Vos WM, Siezen RJ. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA 100:1990 –1995. http://dx.doi.org/10.1073/pnas.0337704100.
10. Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SA. 2012. Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J. Bacteriol. 194:195–196. http:// dx.doi.org/10.1128/JB.06275-11. 11. Crowley S, Bottacini F, Mahony J, van Sinderen D. 2013. Complete genome sequence of Lactobacillus plantarum strain 16, a broad-spectrum antifungal-producing lactic acid bacterium. Genome Announc. 1(4): e00533-13. http://dx.doi.org/10.1128/genomeA.00533-13.
November/December 2014 Volume 2 Issue 6 e01207-14