Conversion events in gene clusters

BMC Evolutionary Biology

Research Article

Hie Lim Kim¹  Giltae Song¹  Ross C Hardison¹  Webb Miller¹  Yu Zhang¹  Cathy Riemer¹  Chih-Hao Hsu²  Federico Hoffmann³  Louxin Zhang⁴  Eric D Green⁵ 

[1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 16802, University Park, PA, USA;Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), 20892, Bethesda, MD, USA;Department of Biochemistry and Molecular Biology, Mississippi State University, 39760, Mississippi State, MS, USA;Department of Mathematics, National University of Singapore, 117543, Singapore;NIH Intramural Sequencing Center (NISC) and Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, 50 South Drive, 20892, Bethesda, MD, USA;

关键词: Primary Species;    Conversion Event;    Outgroup Species;    Paralogous Pair;    Paralogous Region;   

DOI  :  10.1186/1471-2148-11-226

 received in 2011-03-09, accepted in 2011-07-28,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundGene 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.ResultsTo 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 (α-globin and β-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.ConclusionsThese studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.

【 授权许可】

CC BY   
© Song et al; licensee BioMed Central Ltd. 2011