Genome-scale comparative analysis of gene fusions, genefissions, and the fungal tree of life

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 52, 2012, Pages 21402-21407

  Leonard, Guy ^a   Richards, Thomas A ^a,b  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^b UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Blastocladiomycota; Clade; Monophyly; Neofunctionalization; Systematics

Indexed keywords

ARTICLE; CONTROLLED STUDY; CONVERGENT EVOLUTION; FUNGAL GENE; FUNGUS; GENE DUPLICATION; GENE FISSION; GENE FUSION; GENE TRANSFER; GENETIC ANALYSIS; GENOME; HOMOPLASY; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL;

FUNGI; GENE FUSION; GENES, FUNGAL; GENOME, FUNGAL; GENOMIC INSTABILITY; PHYLOGENY;

FUNGI;

EID: 84871827466     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1210909110     Document Type: Article

References (40)

1. Apic G, Gough J, Teichmann SA (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 310(2):311-325. (Pubitemid 32664871)
2. Doolittle RF (1995) The multiplicity of domains in proteins. Annu Rev Biochem 64:287-314.
3. Stechmann A, Cavalier-Smith T (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297(5578):89-91. (Pubitemid 34743097)
4. Philippe H, et al. (2000) Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc Biol Sci 267(1449):1213-1221. (Pubitemid 30438420)
5. Stechmann A, Cavalier-Smith T (2003) The root of the eukaryote tree pinpointed. Curr Biol 13(17):R665-R666. (Pubitemid 37078393)
6. Richards TA, Cavalier-Smith T (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature 436(7054):1113-1118. (Pubitemid 41232283)
7. Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C (2010) The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse? Nat Rev Microbiol 8(10):743-752.
8. Stover NA, Cavalcanti AR, Li AJ, Richardson BC, Landweber LF (2005) Reciprocal fusions of two genes in the formaldehyde detoxification pathway in ciliates and diatoms. Mol Biol Evol 22(7):1539-1542. (Pubitemid 40800681)
9. Nara T, Hshimoto T, Aoki T (2000) Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257(2):209-222.
10. Wolf YI, Kondrashov AS, Koonin EV (2000) Interkingdom gene fusions. Genome Biol 1 (6):H0013.
11. Yanai I, Wolf YI, Koonin EV (2002) Evolution of gene fusions: Horizontal transfer versus independent events. Genome Biology 3(5)::research0024.
12. Kummerfeld SK, Teichmann SA (2005) Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet 21(1):25-30. (Pubitemid 40178845)
13. James TY, et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443(7113):818-822. (Pubitemid 44622687)
14. Stajich JE, et al. (2009) The fungi. Curr Biol 19(18):R840-R845.
15. James TY, et al. (2006) A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98(6):860-871. (Pubitemid 46683210)
16. Liu Y, et al. (2009) Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support. BMC Evol Biol 9:272.
17. Fitzpatrick DA, Logue ME, Stajich JE, Butler G (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 6:99.
18. Torruella G, et al. (2012) Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol 29(2):531-544.
19. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402. (Pubitemid 27359211)
20. Bateman A, et al. (2004) The Pfam protein families database. Nucleic Acids Res 32 (Database issue):D138-D141. (Pubitemid 38081623)
21. Letunic I, Copley RR, Bork P (2002) Common exon duplication in animals and its role in alternative splicing. Hum Mol Genet 11(13):1561-1567. (Pubitemid 34679256)
22. Hirt RP, et al. (1999) Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci USA 96(2):580-585. (Pubitemid 29061251)
23. Slot JC, Rokas A (2010) Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc Natl Acad Sci USA 107(22):10136-10141.
24. Conesa A, Götz S (2008) Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008:619832.
25. Doolittle WF (1999) Lateral genomics. Trends Cell Biol 9(12):M5-M8.
26. Andersson JO, Roger AJ (2002) Evolutionary analyses of the small subunit of glutamate synthase: Gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers. Eukaryot Cell 1(2):304-310. (Pubitemid 36562406)
27. Boucher Y, et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 37:283-328. (Pubitemid 38041428)
28. Lawrence JG, Ochman H (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol 10(1):1-4. (Pubitemid 34075253)
29. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784):299-304. (Pubitemid 30337055)
30. Richards TA, Leonard G, Soanes DM, Talbot NJ (2011) Gene transfer into the fungi. Fungal Biol Rev 25:98-110.
31. Marcet-Houben M, Gabaldón T (2010) Acquisition of prokaryotic genes by fungal genomes. Trends Genet 26(1):5-8.
32. Nakamura Y, Itoh T, Martin W (2007) Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. Mol Biol Evol 24(1):110-121. (Pubitemid 46026286)
33. Maddison WP, Maddison DR (2011) Mesquite: A modular system for evolutionary analysis. Version 2.75. Available at: http://mesquiteproject.org.
34. Kelkar YD, Ochman H (2012) Causes and consequences of genome expansion in fungi. Genome Biol Evol 4(1):13-23.
35. Richards TA, et al. (2009) Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21(7):1897-1911.
36. Richards TA, et al. (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci USA 108(37): 15258-15263.
37. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25 (15):1972-1973.
38. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6:29.
39. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696-704. (Pubitemid 37365050)
40. Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.