Examining Ancient Inter-domain Horizontal Gene Transfer
Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes i...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2008-01-01
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| Series: | Evolutionary Bioinformatics |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=773 |
| _version_ | 1818240206979989504 |
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| author | Francisca C. Almeida Magdalena Leszczyniecka Paul B. Fisher Rob DeSalle |
| author_facet | Francisca C. Almeida Magdalena Leszczyniecka Paul B. Fisher Rob DeSalle |
| author_sort | Francisca C. Almeida |
| collection | DOAJ |
| description | Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identifi ed cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes–in the Bacteria + Archaea class (ABC-type FE3+ -siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT. |
| first_indexed | 2024-12-12T13:09:46Z |
| format | Article |
| id | doaj.art-7ac23b7ae57d4a3e8746a7788c9b1009 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-12T13:09:46Z |
| publishDate | 2008-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-7ac23b7ae57d4a3e8746a7788c9b10092022-12-22T00:23:34ZengSAGE PublishingEvolutionary Bioinformatics1176-93432008-01-014109119Examining Ancient Inter-domain Horizontal Gene TransferFrancisca C. AlmeidaMagdalena LeszczynieckaPaul B. FisherRob DeSalleDetails of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identifi ed cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes–in the Bacteria + Archaea class (ABC-type FE3+ -siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT.http://la-press.com/article.php?article_id=773horizontal gene transfernode height testeschericia coliblast |
| spellingShingle | Francisca C. Almeida Magdalena Leszczyniecka Paul B. Fisher Rob DeSalle Examining Ancient Inter-domain Horizontal Gene Transfer Evolutionary Bioinformatics horizontal gene transfer node height test eschericia coli blast |
| title | Examining Ancient Inter-domain Horizontal Gene Transfer |
| title_full | Examining Ancient Inter-domain Horizontal Gene Transfer |
| title_fullStr | Examining Ancient Inter-domain Horizontal Gene Transfer |
| title_full_unstemmed | Examining Ancient Inter-domain Horizontal Gene Transfer |
| title_short | Examining Ancient Inter-domain Horizontal Gene Transfer |
| title_sort | examining ancient inter domain horizontal gene transfer |
| topic | horizontal gene transfer node height test eschericia coli blast |
| url | http://la-press.com/article.php?article_id=773 |
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