The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis.
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.
Stjepandić
Diana
D
Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D-69120 Heidelberg, Germany. d.stjepandic@dkz.de
Weinel
Christian
C
Hilbert
Helmut
H
Koo
Hean L
HL
Diehl
Frank
F
Nelson
Karen E
KE
Tümmler
Burkhard
B
Hoheisel
Jörg D
JD
D003001:Cloning, Molecular; D020451:Contig Mapping; D003360:Cosmids / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D015723:Gene Library; D016680:Genome, Bacterial; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016958:Pseudomonas putida / Q000235:genetics*; D012407:rRNA Operon / Q000235:genetics
D004269:DNA, Bacterial