dorsal/arxiv
View SchemaGene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation
| Authors | Keiichi Homma, Satoshi Fukuchi, Yoji Nakamura, Takashi Gojobori, Ken Nishikawa |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0609018 |
| URL | https://arxiv.org/abs/q-bio/0609018 |
Abstract
The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been unavailable. It is desirable to select horizontally transferred genes reliably and examine their relationship to operons. We here developed a method to identify candidates of horizontally transferred genes based on minimization of gene cluster insertions/deletions. To select a benchmark set of positively horizontally transferred genes against which the candidate set can be appraised, we devised another procedure using intergenetic alignments. Comparison with the benchmark set of horizontally transferred genes demonstrated the absence of a significant number of false positives in the candidates, showing that the method identifies horizontally transferred genes with a high degree of confidence. Horizontally transferred genes constitute at least 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of which originate from other gamma-proteobacteria. Not only informational genes, but also operational genes (those involved in housekeeping) are horizontally transferred less frequently than expected. A gene-cluster analysis of Escherichia coli K-12 operons revealed that horizontal transfer produced four entire operons and expanded two operons, but deletion of intervening genes accounts for the formation of no operons. We propose that operons generally form by horizontal gene transfer. We further suggest that genes with related essential functions tend to reside in conserved operons, while genes in nonconserved operons generally confer slight advantage to the organisms and frequently undergo horizontal transfer and decay.
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"date_created": "2026-03-02T18:01:35.502000Z",
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"abstract": "The formation mechanism of operons remains controversial despite the proposal\nof many models. Although acquisition of genes from other species, horizontal\ngene transfer, is considered to occur, definitive concrete cases have been\nunavailable. It is desirable to select horizontally transferred genes reliably\nand examine their relationship to operons. We here developed a method to\nidentify candidates of horizontally transferred genes based on minimization of\ngene cluster insertions/deletions. To select a benchmark set of positively\nhorizontally transferred genes against which the candidate set can be\nappraised, we devised another procedure using intergenetic alignments.\nComparison with the benchmark set of horizontally transferred genes\ndemonstrated the absence of a significant number of false positives in the\ncandidates, showing that the method identifies horizontally transferred genes\nwith a high degree of confidence. Horizontally transferred genes constitute at\nleast 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of\nwhich originate from other gamma-proteobacteria. Not only informational genes,\nbut also operational genes (those involved in housekeeping) are horizontally\ntransferred less frequently than expected. A gene-cluster analysis of\nEscherichia coli K-12 operons revealed that horizontal transfer produced four\nentire operons and expanded two operons, but deletion of intervening genes\naccounts for the formation of no operons. We propose that operons generally\nform by horizontal gene transfer. We further suggest that genes with related\nessential functions tend to reside in conserved operons, while genes in\nnonconserved operons generally confer slight advantage to the organisms and\nfrequently undergo horizontal transfer and decay.",
"arxiv_id": "q-bio/0609018",
"authors": [
"Keiichi Homma",
"Satoshi Fukuchi",
"Yoji Nakamura",
"Takashi Gojobori",
"Ken Nishikawa"
],
"categories": [
"q-bio.PE",
"q-bio.BM"
],
"title": "Gene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation",
"url": "https://arxiv.org/abs/q-bio/0609018"
},
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"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
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"user_id": 1000002
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