Quantification of insect genome divergence

Trends in Genetics

Volumn 23, Issue 1, 2007, Pages 16-20

  Zdobnov, Evgeny M ^a   Bork, Peer ^b,c  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA; GENE IDENTIFICATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME; HONEYBEE; HYMENOPTERA; LEPIDOPTERA; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; QUANTITATIVE GENETICS; SEQUENCE ANALYSIS; SHORT SURVEY; SILKWORM; SYNTENY; TRIBOLIUM;

ANIMALS; GENOME; GENOMICS; INSECT PROTEINS; INSECTS; MODELS, GENETIC; PHYLOGENY; SYNTENY; VARIATION (GENETICS);

HEXAPODA; VERTEBRATA;

EID: 33845670418     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2006.10.004     Document Type: Short Survey

References (25)

1. Grimaldi D., and Engel M. Evolution of the Insects (2005), Cambridge University Press
2. Zdobnov E.M., et al. Consistency of genome-based methods in measuring Metazoan evolution. FEBS Lett. 579 (2005) 3355-3361
3. Eyras E., et al. Gene finding in the chicken genome. BMC Bioinformatics 6 (2005) 131
4. Brent M.R., and Guigo R. Recent advances in gene structure prediction. Curr. Opin. Struct. Biol. 14 (2004) 264-272
5. Snyder M., and Gerstein M. Genomics. Defining genes in the genomics era. Science 300 (2003) 258-260
6. Ciccarelli F.D., et al. Complex genomic rearrangements lead to novel primate gene function. Genome Res. 15 (2005) 343-351
7. Zdobnov E.M., et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298 (2002) 149-159
8. Whiting M.F. Phylogeny of the holometabolous insect orders based on 18S ribosomal DNA: when bad things happen to good data. EXS 92 (2002) 69-83
9. Raible F., et al. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science 310 (2005) 1325-1326
10. Savard J., et al. Genome-wide acceleration of protein evolution in flies (Diptera). BMC Evol. Biol. 6 (2006) 7
11. Savard, J. et al. (2006) Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res. DOI:10.1101/gr.5204306 (www.genome.org)
12. Hillier L.W., et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432 (2004) 695-716
13. Nadeau J.H., and Taylor B.A. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. U. S. A. 81 (1984) 814-818
14. Negre B., et al. Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res. 15 (2005) 692-700
15. Miller J.R. The Wnts. Genome Biol (2002) 3 REVIEWS3001
16. Xia Q., et al. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306 (2004) 1937-1940
17. Holt R.A., et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298 (2002) 129-149
18. Drysdale R.A., and Crosby M.A. FlyBase: genes and gene models. Nucleic Acids Res. 33 (2005) D390-D395
19. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
20. Salamov A.A., and Solovyev V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10 (2000) 516-522
21. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
22. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
23. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
24. Schmidt H.A., et al. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 (2002) 502-504
25. Jones D.T., et al. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282