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Description of selected scaffolds |
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| Scaffold |
No of trp genes in the scaffold |
Gene order |
Comments |
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| CH027495 |
6 |
EGD(CF)B |
Lack of trpA gene Gap of unsequenced DNA between trpB and those genes that are unrelated to trp genes may contain gene trpA. |
| CH027608 |
5 |
DCFBA |
Lack of trpE and trpG genes. However, the region between trpD and genes unrelated to trp is missing. |
| CH011919 |
5 |
EGDCBA |
Lack of a trpF gene There is a gap in the sequence between two neighboring contigs that contain E-G-D-C on the one hand and B-A on the other. Until the connecting pieces are found in both these cases, no decision can be made as to whether the missing genes are separate from the other trp genes. |
| CH005689 |
5 |
EGDFB |
Lacks both trpC and trpA. While the absence of trpC is not in doubt because trpD is adjacent to trpF, and on the same contig, trpA is probably missing due to the incompleteness of the sequence. |
| CH026313 |
4 |
DCFB |
Lack of trpE trpG and trpA genes. Not definite that this is a split operon because of gaps between trpD/trpB and their neighboring genes. Moreover the gap between trpD and trpC challenge the correctness of assembly |
| AACY01051805 AACY01049273 |
7 |
EGDCFBA |
Shewanella oneidensis, SAR-1 and SAR-2 |
| CH004526 CH004459 |
Split operon: 4 and 3 |
EGDC FBXA |
One interesting feature of the trp genes of Burkholderia SAR-1 should be mentioned: in all previously known genomes of Burkholderia sp., the split-operons contain F→B→X→A where "X" is unrelated to known trp genes. The sequence from the Sargasso Sea metagenome of SAR-1 Burkholderia-like sequences contains an F→X→A split operon. The computer program used by Venter and colleagues failed to identify a trpB gene within the sequence. However when a search was made using the Burkholderia trpB sequence as a probe, a trpB gene was detected between trpF and X, as is true for all other Burkholderia species and there were no non-trp genes between trpF and trpB. |
Kagan et al. Genome Biology 2008 9:R20 doi:10.1186/gb-2008-9-1-r20 |
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