Genome sequence comparison and scenarios for gene rearrangements: a test case

Genomics
S HannenhalliPavel A Pevzner

Abstract

As large portions of related genomes are being sequenced, methods for comparing complete or nearly complete genomes, as opposed to comparing individual genes, are becoming progressively more important. A major, widespread phenomenon in genome evolution is the rearrangement of genes and gene blocks. There is, however, no consistent method for genome sequence comparison combined with the reconstruction of the evolutionary history of highly rearranged genomes. We developed a schema for genome sequence comparison that includes three successive steps: (i) comparison of all proteins encoded in different genomes and generation of genomic similarity plots; (ii) construction of an alphabet of conserved genes and gene blocks; and (iii) generation of most parsimonious genome rearrangement scenarios. The approach is illustrated by a comparison of the herpesvirus genomes that constitute the largest set of relatively long, complete genome sequences available to date. Herpesviruses have from 70 to about 200 genes; comparison of the amino acid sequences encoded in these genes results in an alphabet of about 30 conserved genes comprising 7 conserved blocks that are rearranged in the genomes of different herpesviruses. Algorithms to analyze rear...Continue Reading

Citations

May 14, 2009·Journal of Molecular Evolution·Rainer Merkl, Arnim Wiezer
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D SankoffG Burger
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Dannie Durand, David Sankoff
Dec 3, 1999·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D Sankoff, M Blanchette
Oct 26, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Rose HobermanDannie Durand
Sep 24, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Géraldine JeanMacha Nikolski
Jan 1, 1997·Microbial & Comparative Genomics·T Sicheritz-Pontén, S G Andersson
May 5, 2009·Genome Research·Hao Zhao, Guillaume Bourque
Jan 13, 2001·Genome Research·M M AlbàP Kellam
Nov 4, 2008·Journal of Bacteriology·Pavel S NovichkovEugene V Koonin
Oct 24, 2000·Journal of Virology·D J McGeochA C Ralph
Aug 3, 2001·Journal of Virology·E A HerniouD R O'Reilly
Nov 2, 2001·Journal of Virology·L M IyerE V Koonin
Nov 9, 2006·BMC Evolutionary Biology·Hanno Hinsch, Sridhar Hannenhalli
Dec 9, 2003·Proceedings of the National Academy of Sciences of the United States of America·Aoife McLysaghtBrandon S Gaut
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·C Seoighe, K H Wolfe
May 11, 2000·Proceedings of the National Academy of Sciences of the United States of America·M G Montague, C A Hutchison
Nov 5, 2002·Annual Review of Entomology·Elisabeth A HerniouDavid R O'Reilly
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Priscila BillerJoão Meidanis
Feb 23, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Pedro Feijão, João Meidanis
Nov 16, 2005·Annual Review of Genetics·Eugene V Koonin
Jan 1, 1997·Nature Genetics·J H Nadeau, D Sankoff
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D Sankoff, M Blanchette
Dec 21, 2019·Journal of Integrative Bioinformatics·Christophe GuyeuxJean-François Couchot
Mar 22, 2000·The Journal of General Virology·T J SadlerJ Kalmakoff
Nov 22, 2018·BMC Systems Biology·Christophe GuyeuxMichel Salomon
Dec 6, 2005·Journal of Theoretical Biology·Guido FritzschPeter F Stadler
Feb 24, 2006·Virus Research·Jing LiuArcady Mushegian
Sep 21, 2002·Genetics·Elizabeth Ann Housworth, John Postlethwait

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