Hox Genes pp 3-18 | Cite as

Discovery and Classification of Homeobox Genes in Animal Genomes

  • Ferdinand Marlétaz
  • Jordi Paps
  • Ignacio Maeso
  • Peter W. H. Holland
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1196)

Abstract

The diversification of homeobox genes is of great interest to evolutionary and developmental biology. To generate a catalogue of all homeobox genes within species of interest, it is necessary to sequence complete genomes. It is now possible for small research projects and individual laboratories to determine near-complete genome sequences of animal species. We provide bioinformatic methods for assembling draft genome sequences from any animal species, including read filtering and error correction, plus methods for extracting and classifying all homeobox sequences.

Key words

Metazoa Genomics Genome assembly Homeodomain Phylogeny Gene family Molecular evolution 

Notes

Acknowledgements

The authors’ research is funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007–2013)/ERC grant [268513]11.

References

  1. 1.
    Duboule D, Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J 8:1497PubMedCentralPubMedGoogle Scholar
  2. 2.
    Graham A, Papalopulu N, Krumlauf R (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367–378PubMedCrossRefGoogle Scholar
  3. 3.
    de Rosa R, Grenier JK, Andreeva T et al (1999) Hox genes in brachiopods and priapulids and protostome evolution. Nature 399:772–776PubMedCrossRefGoogle Scholar
  4. 4.
    Garcia-Fernández J, Holland PWH (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563–566PubMedCrossRefGoogle Scholar
  5. 5.
    Amores A, Force A, Yan YL et al (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711–1714PubMedCrossRefGoogle Scholar
  6. 6.
    Pendleton JW, Nagai BK, Murtha MT et al (1993) Expansion of the Hox gene family and the evolution of chordates. Proc Natl Acad Sci U S A 90:6300–6304PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Zhong Y-F, Holland PWH (2011) HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology. Evol Dev 13:567–568PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Bürglin TR (2011) Homeodomain subtypes and functional diversity. Subcell Biochem 52:95–122PubMedCrossRefGoogle Scholar
  9. 9.
    Holland PWH, Booth HAF, Bruford EA (2007) Classification and nomenclature of all human homeobox genes. BMC Biol 5:47PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Liu Y, Schröder J, Schmidt B (2013) Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 29(3):308–315PubMedCrossRefGoogle Scholar
  11. 11.
    Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Marçais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764–770PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688–2690PubMedCrossRefGoogle Scholar
  16. 16.
    Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Compeau PEC, Pevzner PA, Tesler G (2011) How to apply de Bruijn graphs to genome assembly. Nat Biotechnol 29:987–991PubMedCrossRefGoogle Scholar
  18. 18.
    Li R, Zhu H, Ruan J et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272PubMedCentralPubMedCrossRefGoogle Scholar
  19. 19.
    Simpson JT, Wong K, Jackman SD et al (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123PubMedCentralPubMedCrossRefGoogle Scholar
  20. 20.
    Yandell M, Ence D (2012) A beginner’s guide to eukaryotic genome annotation. Nat Rev Genet 13:329–342PubMedCrossRefGoogle Scholar
  21. 21.
    Stanke M, Keller O, Gunduz I et al (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34(Web Server issue):W435–W439PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17(4):540–552PubMedCrossRefGoogle Scholar
  24. 24.
    Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704PubMedCrossRefGoogle Scholar
  25. 25.
    Ronquist F, Teslenko M, van der Mark P et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Lartillot N, Lepage T, Blanquart S (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286–2288PubMedCrossRefGoogle Scholar
  27. 27.
    Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Ferdinand Marlétaz
    • 1
  • Jordi Paps
    • 1
  • Ignacio Maeso
    • 1
  • Peter W. H. Holland
    • 1
  1. 1.Department of ZoologyUniversity of OxfordOxfordUK

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