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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 12, 2009 |
| Title |
Genomes of DPC5364, DPC5365, DPC5352, DPC5367, DPC5360, DPC5394, DPC5607, CNRZ32, DPC5389 vs DPC4571 |
| Platform organism |
Lactobacillus helveticus DPC 4571 |
| Sample organisms |
Lactobacillus helveticus; Lactobacillus helveticus CNRZ32; Lactobacillus helveticus DPC 4571 |
| Experiment type |
Genome variation profiling by array
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| Summary |
Genomic rearrangement, often driven by insertion sequence (IS) elements, is one of the major processes in the evolution of prokaryotes. Sequence analysis of 16S rRNA of Lactobacillus helveticus, an organism that evolved in a dairy environment and Lactobacillus acidiophilus an organism that evolved associated with the gastrointestinal tract (GIT) demonstrated 98.4% identity suggesting that they divergently evolved from a common ancestor. Moreover, complete genome sequence analysis of both organisms has demonstrated a remarkable degree of gene synteny (75% homologous genes) despite the presence of an exceptionally high number and diversity of IS elements in the Lb. helveticus genome. Array based comparative genomic hybridization (aCGH) performed on nine strains of Lb. helveticus revealed sixteen clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered IS were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65 and ISLhe63). These findings contribute to the overall viewpoint on a versatile character of IS elements and the role they may play in bacterial genome plasticity.
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| Overall design |
2164 ORFs of Lb. helvetiucs DPC4571 spotted on the array in duplicate. Two arrays per each strain.
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| Contributor(s) |
Kaleta P, O`Callaghan J, Fitzgerald GF, Raftis E, O`Toole P, Beresford TP, Ross PR |
| Citation(s) |
19880644 |
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| Submission date |
Jun 11, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Pawel Kaleta |
| E-mail(s) |
[email protected]
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| Phone |
003532542607
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| Organization name |
TEAGASC
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| Department |
Biotechnology
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| Street address |
Moorepark
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| City |
Fermoy |
| State/province |
Co Cork |
| ZIP/Postal code |
00000 |
| Country |
Ireland |
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| Platforms (1) |
| GPL8703 |
Ocimum OciChip CA010_Teagasc, Lactobacillus helveticus 2K array |
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| Samples (9)
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| GSM415891 |
Lb. helveticus DPC5364 replicates 1,2 |
| GSM415892 |
Lb. helveticus DPC5365 replicates 1,2 |
| GSM415893 |
Lb. helveticus DPC5352 replicates 1,2 |
| GSM415894 |
Lb. helveticus DPC5367 replicates 1,2 |
| GSM415895 |
Lb. helveticus DPC5360 replicates 1,2 |
| GSM415896 |
Lb. helveticus DPC5394 replicates 1,2 |
| GSM415897 |
Lb. helveticus DPC5607 replicates 1,2 |
| GSM415898 |
Lb. helveticus CNRZ32 replicates 1,2 |
| GSM415899 |
Lb. helveticus DPC5389 replicates 1,2 |
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| Relations |
| BioProject |
PRJNA116181 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE16553_RAW.tar |
10.5 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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