JCVI: General Method of Rapid Smith/Birnstiel Mapping Adds for Gap Closure In Shotgun Microbial Genome Sequencing Projects: Application to Pseudomonas putida KT2440
 
 
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Weinel, C., Tummler, B., Hilbert, H., Nelson, K. E., Kiewitz, C.

General Method of Rapid Smith/Birnstiel Mapping Adds for Gap Closure In Shotgun Microbial Genome Sequencing Projects: Application to Pseudomonas putida KT2440

Nucleic Acids Res. 2001 Nov 15; 29(22): E110.

PubMed Citation

Abstract

A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of SwaI- or I-CeuI-restricted chromosomes to serve as a backbone for the quick quality control of sequence and contig assemblies. The library of PCR-generated SwaI linking probes was derived from the sequence assembly after 3- and 6-fold genome coverage. In order to support gap closure in regions with ambiguous assemblies such as the repetitive sequence of the seven ribosomal operons, high-resolution Smith/Birnstiel maps were generated by Southern hybridisation of pulsed-field gel electrophoresis-separated rare-cutter complete/frequent-cutter partial digestions with rare-cutter fragment end probes. Overall 1.5 Mb of the 6.1 Mb P.putida KT2440 genome has been subjected to high-resolution physical mapping in order to align assemblies generated from shotgun sequencing.