The Yeast Gene Order Browser: Combining Curated Homology and Syntenic Context Reveals Gene Fate in Polyploid Species

Overview

Journal Genome Res

Specialty Genetics

Date 2005 Sep 20

PMID 16169922

Citations 412

Authors

Kevin P Byrne

Kenneth H Wolfe

Affiliations

Soon will be listed here.

Abstract

We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts. The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny). We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome duplication (ohnologs), and present near-exhaustive lists of the ohnolog pairs retained in S. cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404).

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References

Kashkush K, Feldman M, Levy A . Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics. 2002; 160(4):1651-9. PMC: 1462064. DOI: 10.1093/genetics/160.4.1651. View

Wong S, Butler G, Wolfe K . Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc Natl Acad Sci U S A. 2002; 99(14):9272-7. PMC: 123130. DOI: 10.1073/pnas.142101099. View

Kurtzman C, Robnett C . Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res. 2003; 3(4):417-32. DOI: 10.1016/S1567-1356(03)00012-6. View

Hittinger C, Rokas A, Carroll S . Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci U S A. 2004; 101(39):14144-9. PMC: 521130. DOI: 10.1073/pnas.0404319101. View

LUNDIN L . Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics. 1993; 16(1):1-19. DOI: 10.1006/geno.1993.1133. View

Wolfe K, Shields D . Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997; 387(6634):708-13. DOI: 10.1038/42711. View

Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J . Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003; 301(5629):71-6. DOI: 10.1126/science.1084337. View

Sherman D, Durrens P, Beyne E, Nikolski M, Souciet J . Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. Nucleic Acids Res. 2003; 32(Database issue):D315-8. PMC: 308825. DOI: 10.1093/nar/gkh091. View

Goffeau A, Barrell B, Bussey H, Davis R, Dujon B, Feldmann H . Life with 6000 genes. Science. 1996; 274(5287):546, 563-7. DOI: 10.1126/science.274.5287.546. View

10.

Fischer G, Neuveglise C, Durrens P, Gaillardin C, Dujon B . Evolution of gene order in the genomes of two related yeast species. Genome Res. 2001; 11(12):2009-19. DOI: 10.1101/gr.212701. View

11.

Wolfe K . Robustness--it's not where you think it is. Nat Genet. 2000; 25(1):3-4. DOI: 10.1038/75560. View

12.

Yang Z, Nielsen R . Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 2000; 17(1):32-43. DOI: 10.1093/oxfordjournals.molbev.a026236. View

13.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander E . Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003; 423(6937):241-54. DOI: 10.1038/nature01644. View

14.

Dietrich F, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S . The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004; 304(5668):304-7. DOI: 10.1126/science.1095781. View

15.

Llorente B, Malpertuy A, Neuveglise C, De Montigny J, Aigle M, Artiguenave F . Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Lett. 2001; 487(1):101-12. DOI: 10.1016/s0014-5793(00)02289-4. View

16.

Souciet J, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E . Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 2001; 487(1):3-12. DOI: 10.1016/s0014-5793(00)02272-9. View

17.

Wolfe K . Evolutionary genomics: yeasts accelerate beyond BLAST. Curr Biol. 2004; 14(10):R392-4. DOI: 10.1016/j.cub.2004.05.015. View

18.

Kellis M, Birren B, Lander E . Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004; 428(6983):617-24. DOI: 10.1038/nature02424. View

19.

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I . Genome evolution in yeasts. Nature. 2004; 430(6995):35-44. DOI: 10.1038/nature02579. View

20.

Keogh R, Seoighe C, Wolfe K . Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast. 1998; 14(5):443-57. DOI: 10.1002/(SICI)1097-0061(19980330)14:5<443::AID-YEA243>3.0.CO;2-L. View