Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 186-194

  Koestler, Tina ^a   Ebersberger, Ingo ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

Gene cluster; HMG; MAT locus; Plesiomorphy; Sex determination; Shared synteny.

Indexed keywords

ANIMALIA; EUKARYOTA; MICROSPORIDIA; ZYGOMYCETES;

FUNGAL PROTEIN;

ARTICLE; CLASSIFICATION; EVOLUTION; FUNGAL GENE; GENETICS; MICROSPORIDIA; MOLECULAR GENETICS; PHYLOGENY;

BIOLOGICAL EVOLUTION; FUNGAL PROTEINS; GENES, MATING TYPE, FUNGAL; MICROSPORIDIA; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 79954732034     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr009     Document Type: Article

References (35)

1. Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL. 2008. InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 36:D263-D266. (Pubitemid 351149733)
2. Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H. 2005. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol.54:743-757. (Pubitemid 43142294)
3. Butler G, et al. 2004. Evolution of the MAT locus and its Ho endonuclease in yeast species. Proc Natl Acad Sci U S A. 101: 1632-1637. (Pubitemid 38234206)
4. Cavalier-Smith T. 1986. The kingdoms of organisms. Nature 324: 416-417. (Pubitemid 17184156)
5. Chen F, Mackey AJ, Vermunt JK, Roos DS. 2007. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One. 2:e383.
6. Corradi N, Keeling PJ. 2009. Microsporidia: a journey through radical taxonomical revisions. Fungal Biol Rev. 23:1-8.
7. Dietrich FS, et al. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307. (Pubitemid 38452185)
8. Dyer PS. 2008a. Evolutionary biology: genomic clues to original sex in fungi. Curr Biol. 18:R207-R209. (Pubitemid 351329609)
9. Dyer PS. 2008b. Evolutionary biology: microsporidia sex-a missing link to fungi. Curr Biol. 18:R1012-R1014.
10. Gill EE, Fast NM. 2006. Assessing the microsporidia-fungi relationship: combined phylogenetic analysis of eight genes. Gene 375:103-109. (Pubitemid 43817397)
11. Haber JE. 1998. Mating-type gene switching in Saccharomyces cerevisiae. Annu Rev Genet. 32:561-599. (Pubitemid 29045325)
12. Haqq CM, King CY, Donahoe PK, Weiss MA. 1993. SRY recognizes conserved DNA sites in sex-specific promoters. Proc Natl Acad Sci U S A. 90:1097-1101. (Pubitemid 23053958)
13. Hennig W. 1966. Phylogenetic systematics. Urbana (IL): University of Illinois Press.
14. Idnurm A, Walton FJ, Floyd A, Heitman J. 2008. Identification of the sex genes in an early diverged fungus. Nature 451:193-196.
15. James TY, et al. 2006. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443:818-822. (Pubitemid 44622687)
16. Katinka MD, et al. 2001. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:450-453. (Pubitemid 34173726)
17. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518. (Pubitemid 40360980)
18. Keeling P. 2009. Five questions about microsporidia. PLoS Pathog. 5:e1000489.
19. Keeling PJ. 2003. Congruent evidence from alpha-tubulin and betatubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet Biol. 38:298-309. (Pubitemid 36398176)
20. Keeling PJ, Luker MA, Palmer JD. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol Biol Evol. 17:23-31. (Pubitemid 30056989)
21. Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12:656-664.
22. Koestler T, von Haeseler A, Ebersberger I. 2010. FACT: functional annotation transfer between proteins with similar feature architectures. BMC Bioinformatics. 11:417.
23. Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109. (Pubitemid 38658218)
24. Lee SC, et al. 2008. Microsporidia evolved from ancestral sexual fungi.Curr Biol. 18:1675-1679.
25. Lee SC, et al. 2010. Evolution of the sex-related locus and genomicfeatures shared in microsporidia and fungi. PLoS One. 5:e10539.
26. Lee SC, Ni M, Li W, Shertz C, Heitman J. 2010. The evolution of sex: a perspective from the fungal kingdom. Microbiol Mol Biol Rev 74:298-340.
27. Lengeler KB, et al. 2002. Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes. Eukaryot Cell. 1:704-718. (Pubitemid 36557730)
28. Letunic I, Doerks T, Bork P. 2009. SMART 6: recent updates and new developments. Nucleic Acids Res. 37:D229-D232.
29. Remm M, Storm CE, Sonnhammer EL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 314:1041-1052. (Pubitemid 34073068)
30. Schuster-Bockler B, Schultz J, Rahmann S. 2004. HMM Logos for visualization of protein families. BMC Bioinformatics. 5:7.
31. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogeneticanalyses with thousands of taxa and mixed models. Bioinformatics. 22:2688-2690. (Pubitemid 44642609)
32. Swanson WJ, Vacquier VD. 2002. The rapid evolution of reproductive proteins. Nat Rev Genet. 3:137-144. (Pubitemid 34506597)
33. Thomarat F, Vivares CP, Gouy M. 2004. Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes. J Mol Evol. 59:780-791. (Pubitemid 40100874)
34. Thomas JO, Travers AA. 2001. HMG1 and 2, and related " architectural"DNA-binding proteins. Trends Biochem Sci. 26:167-174 (Pubitemid 32197576)
35. Vossbrinck CR, Maddox JV, Friedman S, Debrunner-Vossbrinck BA, Woese CR. 1987. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature. 326:411-414. (Pubitemid 17053774)