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The genome structure of Pseudomonas putida : high‐resolution mapping and microarray analysis
Author(s) -
Stjepandic´ Diana,
Weinel Christian,
Hilbert Helmut,
Koo Hean L.,
Diehl Frank,
Nelson Karen E.,
Tümmler Burkhard,
Hoheisel Jörg D.
Publication year - 2002
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1046/j.1462-2920.2002.00313.x
Subject(s) - biology , cosmid , genetics , genome , contig , sequence assembly , plasmid , whole genome sequencing , shotgun sequencing , clone (java method) , pseudomonas putida , restriction map , computational biology , genomic library , gene , base sequence , transcriptome , gene expression
Summary As part of a collaborative project aimed at sequencing and functionally analysing the entire genome of Pseudomonas putida strain KT2440, a physical clone map was produced as an initial resource. To this end, a high‐coverage cosmid library was arrayed and ordered by clone hybridizations. Restriction fragments generated by rare‐cutting enzymes and plasmids containing the rrn operon and 23S rDNA of Pseudomonas aeruginosa were used as probes and, parts of the cosmids were end‐sequenced. This provided the information necessary for merging and comparing the macro‐restriction map, cosmid clone order and sequence information, thereby assuring co‐linearity of the eventual sequence assembly with the actual genome. A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non‐coding portions.