Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites

Molecular Biology and Evolution

Volumn 21, Issue 7, 2004, Pages 1422-1427

  Castillo Davis, Cristian I ^a   Bedford, Trevor B C ^a   Hartl, Daniel L ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Gene duplication; Genome evolution; Intron gain loss; Malaria

Indexed keywords

NUCLEOTIDE; PROTEIN;

ARTICLE; DUPLICATE GENE; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC SELECTION; GENETIC TRANSCRIPTION; INTRON; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; ORTHOLOGY; PLASMODIUM; PLASMODIUM FALCIPARUM; PLASMODIUM YOELII; SPECIES DIFFERENTIATION;

ANIMALS; EVOLUTION, MOLECULAR; GENES, DUPLICATE; HUMANS; INTRONS; MALARIA; MICE; PLASMODIUM FALCIPARUM; PLASMODIUM YOELII; PROTOZOAN PROTEINS;

PLASMODIUM FALCIPARUM; PLASMODIUM YOELII; PROTOZOA; RODENTIA;

EID: 3042599701     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh143     Document Type: Article

References (37)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bozdech, Z., M. Llinás, B. L. Pulliam, E. D. Wong, J. Zhu, and J. L. DeRisi. 2003. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 1:001-016.
3. Calderwood, M. S., L. Gannoun-Zaki, T. E. Wellems, and K. W. Deitsch. 2003. Plasmodium falciparum var genes are regulated by two regions with separate promoters, one upstream of the coding region and a second within the intron. J. Biol. Chem. 278:34125-34132.
4. Carlton, J. M., S. V. Angiuoli, B. B. Suh et al. (41 co-authors). 2002. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419:512-519.
5. Castillo-Davis, C. I., D. L. Hartl, and G. Achaz. 2004. cis-regulatory and protein evolution in orthologous and duplicate genes (submitted).
6. Castillo-Davis, C. I., S. L. Mekhedov, D. L. Hartl, E. V. Koonin, and F. A. Kondrashov. 2002. Selection for short introns in highly expressed genes. Nat. Genet. 31:415-418.
7. Fedorova, L., and A. Fedorov. 2003. Introns in gene evolution. Genetica 118:123-131.
8. Gardner, M. J., N. Hall, E. Fung et al. (42 co-authors). 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498-511.
9. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-726.
10. Horrocks, P., K. Dechering, and M. Lanzer. 1998. Control of gene expression in Plasmodium falciparum. Mol. Biochem. Parasitol. 95:171-181.
11. Hughes, A. L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci. 256:119-124.
12. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
13. Jongwutiwes, S., C. Putaporntip, R. Friedman, and A. L. Hughes. 2002. The extent of nucleotide polymorphism is highly variable across a 3-kb region on Plasmodium falciparum chromosome 2. Mol. Biol. Evol. 19:1585-1590.
14. Kent, W. J., and A. M. Zahler. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10:1115-1125.
15. Kondrashov, F. A., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. 2002. Selection in the evolution of gene duplications. Genome Biol. 3:research 0008.1-0008.9.
16. Le Roch, K. G., Y. Zhou, P. L. Blair et al. (8 co-authors). 2003. Discover of gene function by expression profiling of the malaria parasite life cycle. Science 301:1503-1508.
17. Llopart, A., J. M. Comeron, F. G. Brunet, D. Lachaise, and M. Long. 2002. Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc. Natl. Acad. Sci. USA 99:8121-8126.
18. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
19. Maniatis, T., and R. Reed. 2002. An extensive network of cupling among gene expression machines. Nature 416:499-506.
20. Moriyama, E. N., D. A. Petrov, and D. L. Hartl. 1998. Genome size and intron size in Drosophila. Mol. Biol. Evol. 15:770-773.
21. Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
22. Nembaware, V., K. Crum, J. Kelso, and C. Seoighe. 2002. Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res. 12:1370-1376.
23. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Heidelberg.
24. Ohta, T. 1987. Simulating evolution by gene duplication. Genetics 115:207-213.
25. Patankar, S., A. Munasinghe, A. Shoaibi, L. M. Cummings, and D. F. Wirth. 2001. Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malaria parasite. Mol. Cell 12:3114-3125.
26. Perkins, S. L., and J. J. Schall. 2002. A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J. Parasitol. 88:972-978.
27. Rogozin I. B., Y. I. Wolf, A. V. Sorokin, B. G. Mirkin, and E. V. Koonin. 2003. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol. 13:1512-1517.
28. Roy, S. W., A. Fedorov, and W. Gilbert. 2003. Large-scale comparison of intron positions in mammalian genes show intron loss but no gain. Proc. Natl. Acad. Sci. USA 99:984-989.
29. Tarrío, R., F. Rodríguez-Trelles, and F. J. Ayala. 1998. New Drosophila introns originate by duplication. Proc. Natl. Acad. Sci. USA 95:1658-1662.
30. Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
31. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
32. Wagner, A. 2002. Asymmetric functional divergence of duplicate genes in yeast. Mol. Biol. Evol. 19:1760-1768.
33. Walsh, J. B. 1995. How often do duplicated genes evolve new functions? Genetics 139:421-428.
34. Yang, Z. 2000. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus. A. J. Mol. Evol. 51:423-432.
35. Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
36. Zhang, P., Z. Gu, and W.-H. Li. 2003. Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol. 4:R56.
37. Zhou, Z., M. J. Luo, K. Straesser, J. Katahira, E. Hurt, and R. Reed. 2000. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 407:401-405.