Comparative transcriptomics of eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 443-455

  Baldo, Laura ^a   Santos, M Emília ^a   Salzburger, Walter ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

454 sequencing; Astatotilapia burtoni; EST; Ophthalmotilapia ventralis; Positive selection; UTR

Indexed keywords

AFRICAN CICHLIDS; ASTATOTILAPIA BURTONI; CICHLIDAE; OPHTHALMOTILAPIA VENTRALIS; ORYZIAS; ORYZIINAE; PISCES; TILAPIA;

AFRICA; ANIMAL; ARTICLE; CICHLID; CLASSIFICATION; COMPARATIVE STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; GENOME; GENOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PHYSIOLOGY; SPECIES DIFFERENCE; UNTRANSLATED REGION;

AFRICA; ANIMALS; BASE SEQUENCE; CICHLIDS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENOME; GENOTYPE; MOLECULAR SEQUENCE DATA; PHENOTYPE; PHYLOGENY; SPECIES SPECIFICITY; UNTRANSLATED REGIONS;

EID: 80055080319     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr047     Document Type: Article

References (39)

1. Aparicio S, et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:1301-1310. (Pubitemid 34913162)
2. Cheng J, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 308:1149-1154. (Pubitemid 40696429)
3. Clabaut C, Salzburger W, Meyer A. 2005. Comparative phylogenetic analyses of the adaptive radiation of Lake Tanganyika cichlid fish: nuclear sequences are less homoplasious but also less informative than mitochondrial DNA. J Mol Evol. 61:666-681. (Pubitemid 41599903)
4. Conesa A, et al. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinfor-matics. 21:3674-3676. (Pubitemid 41264107)
5. Cooper TF, Rozen DE, Lenski RE. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc Natl Acad Sci U S A. 100:1072-1077. (Pubitemid 36183957)
6. Elmer KR, et al. 2010. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mol Ecol. 19(Suppl 1):197-211.
7. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185. (Pubitemid 28177229)
8. Fay JC, Wittkopp PJ. 2008. Evaluating the role of natural selection in the evolution of gene regulation. Heredity. 100:191-199. (Pubitemid 351156873)
9. Goldman N,Yang Z. 1994. Acodon-based modelofnucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11:725-736.
10. Johnson TC, et al. 1996. Late Pleistocene desiccation of Lake Victoria and rapid evolution of cichlid fishes. Science. 273:1091-1093.
11. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066. (Pubitemid 34851225)
12. Kobayashi N, Watanabe M, Horiike T, Kohara Y, Okada N. 2009. Extensive analysis of EST sequences reveals that all cichlid species in Lake Victoria share almost identical transcript sets. Gene. 441:187-191.
13. Koblmuller S, et al. 2008. Age and spread of the haplochromine cichlid fishes in Africa. Mol Phylogenet Evol. 49:153-169.
14. Kocher TD. 2004. Adaptive evolution and explosive speciation: the cichlid fish model. Nat Rev Genet. 5:288-298. (Pubitemid 38435624)
15. Kumar S, Subramanian S. 2002. Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A. 99:803-808. (Pubitemid 34106591)
16. Lee BY, et al. 2010. An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags. BMC Genomics. 11:278.
17. Loh YH, et al. 2008. Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biol. 9:R113.
18. Loh YH, Yi SV, Streelman T. 2011. Evolution of microRNAs and the diversification of species. Genome Biol Evol. 3:55-65.
19. Matschiner M, Hanel R, Salzburger W. 2011. On the origin and trigger of the notothenioid adaptive radiation. PLoS One. 6:e18911.
20. Muller K. 2005. SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Appl Bioinformatics. 4:65-69. (Pubitemid 41043903)
21. Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3:418-426. (Pubitemid 16010523)
22. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. 1999. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A. 96:2896-2901. (Pubitemid 29148815)
23. Rocha EP, et al. 2006. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol. 239:226-235.
24. Salzburger W. 2009. The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes. Mol Ecol. 18:169-185.
25. Salzburger W, Braasch I, Meyer A. 2007. Adaptive sequence evolution in a color gene involved in the formation of the characteristic egg-dummies of male haplochromine cichlid fishes. BMC Biol. 5:51.
26. Salzburger W, Mack T, Verheyen E, Meyer A. 2005. Out of Tanganyika: genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes. BMC Evol Biol. 5:17.
27. Salzburger W, Meyer A, Baric S, Verheyen E, Sturmbauer C. 2002. Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas. Syst Biol. 51:113-135. (Pubitemid 35169410)
28. Salzburger W, et al. 2008. Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genomics. 9:96.
29. Seehausen O. 2006. African cichlid fish: a model system in adaptive radiation research. Proc Biol Sci. 273:1987-1998. (Pubitemid 44214911)
30. Shapiro MD, et al. 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature. 428:717-723. (Pubitemid 38508276)
31. Simmons MP, Ochoterena H. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst Biol. 49:369-381.
32. Stamatakis A, Ludwig T, Meier H. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 21:456-463. (Pubitemid 40310232)
33. Steinke D, Salzburger W, Meyer A. 2006. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J Mol Evol. 62:772-784. (Pubitemid 43847227)
34. Sturmbauer C, Meyer A. 1993. Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes from Lake Tanganyika in eastern Africa. Mol Biol Evol. 10:751-768. (Pubitemid 23204794)
35. Swofford DL. 2000. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Sunderland (MA): Sinauer Associates.
36. Verheyen E, Salzburger W, Snoeks J, Meyer A. 2003. Origin of the superflock of cichlid fishes from Lake Victoria, East Africa. Science. 300:325-329. (Pubitemid 36433723)
37. Wolf JB, Kunstner A, Nam K, Jakobsson M, Ellegren H. 2009. Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol. 1:308-319.
38. Wray GA, et al. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 20:1377-1419. (Pubitemid 37086669)
39. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591. (Pubitemid 47236688)