Evolutionary Genomics Leads the Way

Evolutionary Genomics and Systems Biology

Volumn , Issue , 2010, Pages 1-16

  Penny, David ^a   Collins, Lesley J ^a  

^a MASSEY UNIVERSITY   (New Zealand)

Author keywords

Evolutionary genomics "next generation sequencing (NGS)"; Evolutionary genomics leading the way; Genomes from deeply diverging eukaryotes and ancestral eukaryote nature

Indexed keywords

EID: 80053617478     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470570418.ch1     Document Type: Chapter

References (55)

1. AMARAL, P.P.,DINGER, M.E.,MERCER, T.R., and MATTICK, J.S., 2008. The eukaryotic genome as an RNA machine. Science 319: 1787-1789.
2. ANDERSON, P. and KEDERSHA, N., 2006. RNA granules. J. Cell Biol. 172: 803-808.
3. ANDERSSON, S.G.E., 2006. The bacterial world gets smaller. Science 314: 259-260.
4. BLOMBERG, S.P. and GARLAND, T., 2002. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. J. Evol. Biol. 15: 899-910.
5. BOORE, J.L., 2006. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol. Evol. 21: 439-446.
6. CAETANO-ANOLLÉS, G., KIM, H.S., and MITTENTHAL, J.E., 2007. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc. Natl. Acad. Sci. USA 104: 9358-9363.
7. CHEAH, M.T.,WACHTER, A., SUDARSAN, N., and BREAKER, R.R., 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447: 497-507.
8. CLARK, A.G., EISEN, M.B., SMITH, D.R., et al., 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
9. COLLINS, L.J. and PENNY, D., 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol. Biol. Evol. 22: 1053-1066.
10. COLLINS, L.J., and CHEN, X.S. 2009. Ancestral RNA: the RNA biology of the eukaryote ancestor. RNA Biol. 6: 1-8.
11. COLLINS, L.J., KURLAND, C.G., BIGGS, P., and PENNY, D., 2009. The modern RNP world of eukaryotes. J. Hered., 100: 597-604.
12. COSTA, F.F., 2007. Non-coding RNAs: lost in translation? Gene 386: 1-10.
13. DAGAN, T., ARTZY-RANDRUP, Y., and MARTIN, W., 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc. Natl. Acad. Sci. USA 105: 10039-10044.
14. D'ANGELO, M.A. and HETZER M.W., 2008 Structure, dynamics and function of the nuclear pore complexes. Trends Cell Biol. 18: 456-466.
15. EMBLEY, T.M. and MARTIN, W., 2006. Eukaryote evolution, changes and challenges. Nature 440: 623-630.
16. FORTERRE, P., 1995. Thermoreduction, a hypothesis for the origin of prokaryotes. CR Acad. Sci. Paris Life Sci. 318: 415-422.
17. FREYHULT, E.K., BOLLBACK, J.P., and GARDNER, P.P., 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res. 17: 117-125.
18. GOODMAN, M. et al., 1962. Immunochemistry of primates and primate evolution. Ann. NY Acad. Sci. 102: 219-234.
19. HARTMAN, H. and FEDOROV, A., 2002. The origin of the eukaryotic cell: a genomic investigation. Proc. Natl. Acad. Sci. USA 99: 1420-1425.
20. HENZ, S.R., HUSON, D.H., AUCH, A.F., NIESELT-STRUWE, K., and SCHUSTER, S.C., 2005. Whole-genome prokaryote phylogeny. Bioinformatics 21: 2329-2335.
21. HOPPER, A.K., 2006. Cellular dynamics of small RNAs. Crit. Rev. Biochem. Mol. Biol. 41: 3-19.
22. IRIMIA, M., RUKOV, J.L., PENNY, D., and ROY, S.W., 2007. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol. Biol. 7: 188.
23. JEFFARES, D.C., POOLE, A.M., and PENNY, D., 1998. Relics from the RNA world. J. Mol. Evol. 46: 18-36.
24. JEFFARES, D.C., MOURIER, T., and PENNY, D., 2006. The biology of intron gain and loss. Trends Genet. 22: 16-22.
25. JEFFARES, D.C., PENKETT, C.J., and BaHLER, J., 2008. Selection against introns in rapidly regulated genes. Trends Genet. 24: 375-378.
26. JEFFROY, O., BRINKMANN, H., DELSUC, F., and PHILIPPE, H., 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22: 225-231.
27. KEELING, P.J. et al., 2005. The tree of eukaryotes. Trends Ecol. Evol. 20: 670-676.
28. KURLAND, C.G.,COLLINS, L.J., and PENNY, D., 2006. Genomics and the irreducible nature of eukaryote cells. Science 312: 1011-1014.
29. LAN, R. and REEVES, P.R., 2000. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8: 396-401.
30. LEVY, S. and STRAUSBERG, R.L., 2008. Individual genomes diversity. Nature 456: 49-50.
31. LI, W.H. and SAUNDERS, M.A., 2005. The chimpanzee and us. Nature 437: 50-51.
32. LOCKHART, P.J., LARKUM, A.W.D., STEEL, M.A., WADDELL, P.J., and PENNY, D., 1996. Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93: 1930-1934.
33. LYNCH, M., 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123.
34. MALLET, J., 2008. Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos. Trans. R. Soc. B 363: 2971-2986.
35. MATERA, A.G., TERNS, R.M., and TERNS, M.P., 2007. Noncoding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol. 8: 209-220.
36. MINAJIGIA, A. and FRANCKLYN, C.S., 2008. RNA-assisted catalysis in a protein enzyme: the 20-hydroxyl of tRNAThr A76 promotes aminoacylation by threonyltRNA synthetase. Proc. Natl. Acad. Sci. USA 105: 17748-17753.
37. MONTANGE, R.K. and BATEY, R.T., 2008. Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys. 37: 117-133.
38. MORAN, N.A. and BAUMANN, P., 2000.Bacterial endosymbionts in animals. Curr. Opin. Microbiol. 3: 270-275.
39. MOSSEL, E. and STEEL, M., 2004. A phase transition for a random cluster model on phylogenetic trees. Math. Biosci. 187: 189-203.
40. MUFFATO, M. and CROLLIUS, H.R., 2008. Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time. Bioessays 30: 122-134.
41. MUNROE, S.H. and ZHU, J., 2006. Overlapping transcripts, double-stranded RNA and antisense regulation: a genomic perspective. Cell. Mol. Life Sci. 63: 2102-2118.
42. OCHMAN, H. and DAVALOS, L.M., 2006. The nature and dynamics of bacterial genomes. Science 311: 1730-1733.
43. PENNY, D., 2005. An interpretive review of the origin of life research. Biol. Philos. 20: 633-671.
44. PENNY, D. and PHILLIPS, M.J., 2004. The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution. Trends Ecol. Evol. 19: 516-522.
45. PHILLIPS, M.J., DELSUC, F., and PENNY, D., 2004. Genomescale phylogeny: sampling and systematic errors are both important. Mol. Biol. Evol. 21: 1455-1458.
46. PRECHTL, J., KNEIP, C., LOCKHART, P., WENDEROTH, K., and MAIER, U.G., 2004. Intracellular spheroid bodies of Rhopalodia gibba have nitrogen-fixing apparatus of cyanobacterial origin. Mol. Biol. Evol. 21: 1477-1481.
47. REDON, R., et al., 2006. Global variation in copy number in the human genome. Nature 444: 444-454.
48. ROGER, A.J. and HUG, L.A., 2006. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Philos. Trans. R Soc. Lond. B Biol. Sci. 361: 1039-1054.
49. ROY, S.W., 2006. Intron-rich ancestors. Trends Genet. 22: 468-471.
50. ROY, S.W. and IRIMIA, M., 2008. Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res. 36: 1703-1712.
51. SCHUSTER, S.C., 2008. Next-generation sequencing transforms today's biology. Nat. Methods 5: 16-8.
52. VALDIVIA-GRANDA, W., 2008. The next meta-challenge for bioinformatics. Bioinformation 2: 358-62.
53. WAGNER, A., 2005. Energy constraints on the evolution of gene expression. Mol. Biol. Evol. 22: 1365-1374.
54. WANG, J., et al., 2008. The diploid genome sequence of an Asian individual. Nature 456: 60-65.
55. WOODHAMS, M.D., STADLER, P.F., PENNY, D., and COLLINS, L.J., 2007. RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol. Biol. 7: S13.