Monday, July 27, 2009
P114

Optical mapping as a means of scaffolding difficult to assemble bacterial genomes: a case study with Lactobacillus helveticus

Guillaume Barreau1, Thomas A. Tompkins2, Marcin Swiatek1, Vanessa de Carvalho2, Thodoros Topaloglou1, Hui Cai3, Jeffery R. Broadbent4, and James L. Steele3. (1) McGill University & Genome Quebec Innovation Center, 740 Dr Penfield Avenue, Rm 6103, Montreal, QC H3A 1A4, Canada, (2) R&D, Institut Rosell Inc., 6100 Royalmount, Montreal, QC H4P 2R2, Canada, (3) Department of Food Sciences, University of Wisconsin-Madison, 1605 Linden Dr., Rm. 220, Madison, WI 53706, (4) Associate Vice President for Research, Utah State University, 1450 Old Main Hill, Logan, UT 84322-1450

Obligately homofermentative Lactobacillus helveticus are found in a number of nutrient-rich environmental niches such as milk, distillers’ grains and the human vagina.  The diversity of the environments they inhabit is highly reflected in their genomic variability.  Microarray-based comparative genomic hybridization (m-CGH) of 21 strains demonstrated that only 68% of the genes were shared, and another 30% were variable (Broadbent et al 2008).  Comparison of the two sequenced genomes, L. helveticus DPC 4571 (Callanan et al 2008) and CNRZ32 (Broadbent and Steele, unpublished) exhibited very low synteny between the strains, unless they were independently aligned to the closely related Lactobacillus acidophilus NCFM.  The observed variability is due, in part, to the large number (200+) of insertion sequence (IS) elements which occur randomly throughout these genomes.  Thus, each strain of L. helveticus must be assembled de novo.  We used reads ranging from 200 to 400 base pairs obtained by pyrosequencing to assemble contigs for two probiotic strains of L. helveticus, R0052 and R0389.  Some of the libraries sequenced were paired-ends which allowed to place some contigs relatively to each other into scaffolds. However, attempts to scaffold these contigs to the existing completed genomes were unsuccessful.  Optical mapping of the genomes indicate that genome structure is highly diverse within these strains, supporting the genome content differences observed via m-CGH.  Aligning the scaffolds to the optical maps proved to be a reliable means to assemble the genomes and allow a more targeted approach to gap closure.

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