Conversion events in gene clusters

Giltae Song, Chih Hao Hsu, Cathy Riemer, Yu Zhang, Hie Kim, Federico Hoffmann, Louxin Zhang, Ross C. Hardison, Eric D. Green, Webb Miller

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments. Results: To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (-globin and -globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at http://www.bx.psu.edu/miller-lab. Conclusions: These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.

Original languageEnglish (US)
Article number226
JournalBMC Evolutionary Biology
Volume11
Issue number1
DOIs
StatePublished - Aug 1 2011

Fingerprint

multigene family
gene
history
interferons
chemokines
cytochrome P-450
primate
ligand
cytochrome
genomics
Primates
genome
phylogenetics
phylogeny
methodology
analysis
method

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics

Cite this

Song, G., Hsu, C. H., Riemer, C., Zhang, Y., Kim, H., Hoffmann, F., ... Miller, W. (2011). Conversion events in gene clusters. BMC Evolutionary Biology, 11(1), [226]. https://doi.org/10.1186/1471-2148-11-226
Song, Giltae ; Hsu, Chih Hao ; Riemer, Cathy ; Zhang, Yu ; Kim, Hie ; Hoffmann, Federico ; Zhang, Louxin ; Hardison, Ross C. ; Green, Eric D. ; Miller, Webb. / Conversion events in gene clusters. In: BMC Evolutionary Biology. 2011 ; Vol. 11, No. 1.
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Song, G, Hsu, CH, Riemer, C, Zhang, Y, Kim, H, Hoffmann, F, Zhang, L, Hardison, RC, Green, ED & Miller, W 2011, 'Conversion events in gene clusters', BMC Evolutionary Biology, vol. 11, no. 1, 226. https://doi.org/10.1186/1471-2148-11-226

Conversion events in gene clusters. / Song, Giltae; Hsu, Chih Hao; Riemer, Cathy; Zhang, Yu; Kim, Hie; Hoffmann, Federico; Zhang, Louxin; Hardison, Ross C.; Green, Eric D.; Miller, Webb.

In: BMC Evolutionary Biology, Vol. 11, No. 1, 226, 01.08.2011.

Research output: Contribution to journalArticle

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Song G, Hsu CH, Riemer C, Zhang Y, Kim H, Hoffmann F et al. Conversion events in gene clusters. BMC Evolutionary Biology. 2011 Aug 1;11(1). 226. https://doi.org/10.1186/1471-2148-11-226