Description:
HT1006 is a set of 1006 E. coli K-12 genes currently annotated in EcoGene that represent the 1053 genes predicted to be inherited by horizontal transfer by Davids (2008).
Details:
Using a gene by gene similarity comparison of five genomes and codon correspondence analysis, Davids (2008) identified and then refined three non-overlapping gene sets as core (2158 genes), non-core (1044 genes, reduced to 971) and HGT (HT, 1053 genes). These 1053 HT genes minus the IS and prophage genes (which are grouped separately) are the current "HT genes" (horizontally transmitted) predictions annotated with blue buttons on the bottom of the GenePages.
The 1053 genes in the HGT set of Davids (2008) are based on Genbank U00096 bnumbers which have since been updated.
42 of the 1053 genes are multiple instances of 7 different IS element transposase genes from five different IS elements: IS1, IS2, IS5, IS30 and IS186. These 42 instances are reduced to 7 genes in EcoGene. One aditional ISZ'-encoded pseudogene insZ' is added for a total of 8 different IS-encoded HT gene sequences. Thus 34/43 of these 1053 predictions are considered as redundant sequences in EcoGene and are not represented in this gene set, leaving 1053 - 34 = 1019 HT genes predicted by Davids (2008).
The 1019 remaining genes are then mapped to 1006 genes in the current set of genes annotated in EcoGene. This net loss of 13 genes is due to the process of DNA sequence correction and subsequent reannotation that combine 2 old ORFs into one new ORF or split one old ORF into two new ORFs.
EcoGene also has annotated IS3, IS4, IS150 and several other pseudogene fragments related to transposases. These are also HT genes but they are listed separately with the Topic-related gene set of IS-encoded genes and pseudogenes.
Since the prophage and IS genes are already grouped into EcoTopics, a full set of the HT genes can be downloaded by getting all three prophage, IS and HT gene sets. HT1006 includes the IS and prophage genes identified by Davids (2008), but they are removed from the gene set associated with the curated HT superTopic "Horizontal Gene Transfer" to avoid double counting them since all prophage and IS sequences are already considered as HT elements. This includes 7 IS genes and one IS pseudogene (out of 17 total in EcoGene) and 58 prophage genes and pseudogenes (out of 222 total in EcoGene).
Additional MG1655 HT predictions from previous publications will be added and compared to the results of this recent study and the HT genes annotated in EcoGene are a composite from these studies to provide a curated set of HT gene set predictions as well as including any HT individual publication's results as gene sets in subTopics associated specifically with that publication.
The EcoGene HT prediction gene set are linked to this TopicPage at the bottom of the GenePages as well as in the EcoTopic menu.
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