Skip to main content

Comparative Genomics: An Introduction: Sequencing Projects and Model Organisms

  • Chapter
Comparative Genomics

Abstract

At its most literal the term means comparing genomes. This immediately brings to mind DNA and protein sequences and inevitably comparison with the human genome. However, Comparative genomics is more than that. It applies to the comparison of any organism at a variety of levels: DNA or protein sequences, mapping positions and maps, function and evolution. The aim is to decipher how genes function and provide an understanding of the link between genotype and phenotype. Often this is with particular reference to a set of heritable characters or disease, as these are clearly more attractive funding possibilities (even more so when human studies enter into the experimental equation). With livestock, such as cattle, sheep, pigs, fish etc, which are of great economic importance to any country, there are clear commercial requirements to being able to understand the inheritance patterns of advantageous characters and also disease. However, any commercial applications are underpinned by a vast array of academic or “basic” research.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abdulla, S., S. Beck, M. Belich, A. Jackson, T. Nakamura and J. Trowsdale. Divergent intron arrangement in the MB1/LMP7 proteasome gene pair. Immunogenetics. 1996;44: 254–258.

    Article  PubMed  CAS  Google Scholar 

  • Adams, M.D. et al The Genome sequence of Drosophila melanogaster. Science. 2000;287:2185–2195.

    Article  PubMed  Google Scholar 

  • Allsop, A.E. Bacterial genome sequencing and drug discovery. Curr. Opin. Biotech. 1998; 9:637–642.

    Article  PubMed  CAS  Google Scholar 

  • Amaya, E., Offield, M.F. and R.M. Grainger. Frog genetics: Xenopus tropicalis jumps into the future. T.I.G. 1998; 14:253–255.

    CAS  Google Scholar 

  • Andersson, L. et al. Comparative genome organisation of vertebrates. Mamm. Genome. 1996; 7:717–734.

    Article  PubMed  CAS  Google Scholar 

  • Bassett Jr, D.E., Boguski, M.S., Spencer, F., Reeves, R., Kim, S-h., Weaver, T. and P. Hieter. Genome cross-referencing and XREFdb: Implications for the identification and analysis of genes mutated in human disease. Nat. Genet. 1997; 15:339–344.

    Article  PubMed  CAS  Google Scholar 

  • Bennetz, J.L. Plant genomics takes root, branches out. T.I.G. 1999;15:85–87.

    Google Scholar 

  • Bennetzen, J.L. and E.A. Kellogg. Do plants have a one-way ticket to genomic obesity? Plant. Cell. 1997; 9:1509–1513.

    PubMed  CAS  Google Scholar 

  • Bevan, M. et al Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999; 402:769–777.

    Article  PubMed  Google Scholar 

  • Bevan, M and G. Murphy, G. The small, the large and the wild: the value of comparison in plant genomics. T.I.G. 1999;15:211–214.

    CAS  Google Scholar 

  • Birchall, P.S., Fishpool, R.M. and D.G. Albertson. Expression patterns of predicted genes from the C. elegans genome sequence visualized by FISH in whole organisms. Nat. Genet. 1995; 11:314–320.

    Article  PubMed  CAS  Google Scholar 

  • Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science. 1997; 277, 1453–1461.

    Article  PubMed  CAS  Google Scholar 

  • Blaxter, M. Caenorhabditis elegans is a nematode. Science. 1998; 282:2041–2046.

    Article  PubMed  CAS  Google Scholar 

  • Botstein, D., Chervitz, S.A. and Cherry, J.M. Yeast as a model organism. Science. 1997;277, 1259–1260.

    Article  PubMed  CAS  Google Scholar 

  • Bork, P. Powers and pitfalls in sequence analysis: the 70% hurdle. Genome. Res. 2000; 10:398–400.

    CAS  Google Scholar 

  • Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F. Huynen, M. and Y. Yuan. Predicting function: from genes to genomes and back. J. Mol. Biol. 1998; 283:707–725.

    Article  PubMed  CAS  Google Scholar 

  • Burns, N., Grimwade, B., Ross-Macdonald, P.B., Choi, E-Y., Finberg, K., Roeder, G.S. and M. Snyder. Large-scale analysis of gene expression, protein localisation and gene disruption in Saccharomyces cerevisiae. Genes Dev. 1994; 8:1087–1105.

    Article  PubMed  CAS  Google Scholar 

  • Burset, M. And Guigo, R. Evaluation of gene structure prediction programs. Genomics. 1996;34, 353–367.

    Article  PubMed  CAS  Google Scholar 

  • Caskey, C.T., Pizzuti, A., Fu, Y.H., Fenwick, R.G. and D.L. Nelson. Triplet repeat mutations in human disease. Science. 1992; 256:784–789.

    Article  PubMed  CAS  Google Scholar 

  • Celegans Sequencing consortium. Genome sequence of the nematode C.elegans: A platform for investigating biology. Science. 1998; 282:2012–2018.

    Article  Google Scholar 

  • Chervitz, S.A. et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 1998; 282:2022–2028.

    Article  PubMed  CAS  Google Scholar 

  • Cho, R.J. et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. Biol. 1998; 2:65–73.

    CAS  Google Scholar 

  • Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O. and I. Herskowitz. The transcriptional program of sporulation in the budding yeast. Science. 1998; 282:699–705.

    Article  PubMed  CAS  Google Scholar 

  • Clark, M.S. and Wall, W.J. Chromosomes: The complex code. London. Chapman and Hall. 1996.

    Google Scholar 

  • Claverie, J-M. Computational methods for the identification of genes in vertebrate genomic sequence. Hum. Mol. Genet. 1997; 6: 1735–1744.

    Article  PubMed  CAS  Google Scholar 

  • Clines, G.A., Ashley, J.A., Shah, S. and M. Lovett. The structure of the human multiple Exotoses 2 gene and characterization of homologs in mouse and Caenorhabditis elegans. Genome Res. 1997; 7:359–367.

    PubMed  CAS  Google Scholar 

  • Dawkins, R.L., C. Leelayuwat, S. Gaudieri, G. Tay, J. Hui, S. Cattley, P. Martinez and J. Kulski.. Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease. Immunol. Rev. 1999; 167:275–304.

    Article  PubMed  CAS  Google Scholar 

  • DeRisi, J.L., Iyer, V.R. and P.O. Brown. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997; 278:680–686.

    Article  PubMed  CAS  Google Scholar 

  • Dujon, B. The yeast genome project: what did we learn? T.I.G. 1996; 12:263–270.

    CAS  Google Scholar 

  • Dunham, I. et al. The DNA sequence of human chromosome 22. Nature. 1999; 402:489–495.

    Article  PubMed  CAS  Google Scholar 

  • Ferea, T.L. and P.O. Brown. Observing the living genome. Curr. Opin. Genet. Dev. 1999; 9:715–722.

    Article  PubMed  CAS  Google Scholar 

  • Fickett, J.W. and A.G. Hatzigeorgiou. Eukaryotic promoter recognition. Genome Res. 1997;7, 861–878.

    PubMed  CAS  Google Scholar 

  • Field, D., Hood, D. and R. Moxon. Contribution of genomics to bacterial pathogenesis. Curr. Opin. Genet. Dev. 1999; 9:700–703.

    Article  PubMed  CAS  Google Scholar 

  • Fleischmann, R.D. et al. Whole genome random sequencing and assembly of Haemophilus influenzae. Science. 1995;269:496–512.

    Article  PubMed  CAS  Google Scholar 

  • Fraser, C.M. et al. The minimal gene complement of Mycoplasma genitalium. Science. 1995;270:397–403.

    Article  PubMed  CAS  Google Scholar 

  • Hanke, J., Zastrow, I., Aydin, A., Lehmann, J., Luft, S., Reich, J.G. and P. Bork. Alternative splicing of human genes: more the rule than the exception? T. I. G. 1999; 15:389–390.

    CAS  Google Scholar 

  • Hastie, N. The genetics of Wilm’s tumour — a case of disrupted development. Ann. Rev. Genet. 1994;28:523–558.

    Article  PubMed  CAS  Google Scholar 

  • Galli, J., Li, L-S., Glaser, A., Östenson, C-G., Jiao, H., Fakhrai-Rad, H., Jacod, H.J., Lander, E.S. and H. Luthman. Genetic analysis of non-insulin dependent diabetes mellitus in the GK rat. Nat. Genet. 1996; 12:31–37.

    Article  PubMed  CAS  Google Scholar 

  • Georges, M. And L. Andersson. Livestock genomics comes of age. Genome. Res. 1996; 6:907–921.

    Article  PubMed  CAS  Google Scholar 

  • Gellin, J., Brown, S., Marshall Graves, J.A., Rothschild, M., Schook, L., Womack, J. and M. Yerle. Comparative gene mapping workshop: progress in agriculturally important animals. Mamm. Genome. 2000; 11:140–144

    Article  PubMed  CAS  Google Scholar 

  • Greenhouse, D.D., Festling, M.F.W., Hasan, S. and A.L. Cohen. Genetic monitoring of inbred strains of rats. A manual on colony management, basic monitoring techniques and genetic variants of the laboratory rat. (ed. H. Hedrich and M. Adams), pp. 411–480. Pub. Gustav Fischer Verlag. 1990.

    Google Scholar 

  • Hartzog, G.A., Basrai, M.A., Ricupero-Hovasse, S.L., Hieter, P. and F. Winston. Identification and analysis of a functional human homolog of the SPT4 gene of Saccharomyces cerevisiae. Mol. Cell. Biol. 1996; 16:2848–2856.

    PubMed  CAS  Google Scholar 

  • James, M.R. and K. Lindpaintner. Why map the rat? Trends Genet. 1997; 13:171–173.

    Article  PubMed  CAS  Google Scholar 

  • Kelly, P.D. et al. Genetic linkage mapping of zebrafish genes and ESTs. Genome. Res. 2000; 10:558–567.

    Article  PubMed  CAS  Google Scholar 

  • Kulski, J.K., S. Gaudieri, M. Bellgard, L. Balmer, K. Giles, H. Inoko and R.L. Dawkins. The evolution of MHC diversity by segmental duplication and transposition of retroelements. J. Mol. Evol. 1997; 45:599–609.

    Article  PubMed  CAS  Google Scholar 

  • Kyrpides, N.C. Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects worldwide. Bioinformatics. 1999; 15:773–774.

    Article  PubMed  CAS  Google Scholar 

  • Lin, L. The sleep disorder canine narcolepsy is caused by a mutation in the hypocretin (orexin) receptor 2 gene. Cell. 1999; 98:365–376.

    Article  PubMed  CAS  Google Scholar 

  • Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittman, M., Wang, C., Kobayashi, M., Horton, H. and E.L. Brown. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotech. 1996;14, 1675–1680.

    Article  CAS  Google Scholar 

  • Lynch, A.S., Briggs, D. and I.A. Hope. Developmental expression pattern screen for genes predicted in the C. elegans genome sequencing project. Nat. Genet. 1995; 11:309–313.

    Article  PubMed  CAS  Google Scholar 

  • Mangin M, Ikeda K, Broadus AE. Structure of the mouse gene encoding parathyroid hormone-related peptide. Gene. 1990; 95:195–202.

    Article  PubMed  CAS  Google Scholar 

  • Mangin M, Ikeda K, Dreyer BE, Broadus AE. Isolation and characterisation of the human parathyroid hormone-like peptide gene. Proc. Natl. Acad. Sci. USA 1989; 86:2408–2412.

    Article  PubMed  CAS  Google Scholar 

  • Marshal, E. Drug firms to create public database of genetic mutations. Science. 1999; 284:406–407.

    Article  Google Scholar 

  • Mironov, A.A., Fickett, J.W. and M.S. Gelfand. Frequent alternative splicing of human genes. Genome. Res. 1999; 15:755–771.

    Google Scholar 

  • Morrow, D.M., Tagle, D.A., Shiloh, Y., Collins, F.S. and P. Hieter. TEL1, an S. cerevisiae homologue of the human gene mutated in ataxia telangiectasia, is functionally related to the yeast checkpoint gene MECI. Cell. 1995;82, 831–840.

    Article  PubMed  CAS  Google Scholar 

  • Mushegian, A.R., Bassett Jr, D.E., Boguski, M.S., Bork, P. and E.V. Koonin. Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs. Proc. Natl. Acad. Sci. USA 1997;94:5831–5836.

    Article  PubMed  CAS  Google Scholar 

  • Nüsslein-Volhard, C. Of flies and fish. Science. 1994; 266:572–574.

    Article  PubMed  Google Scholar 

  • Oliver, S.G. From DNA sequence to biological function.. Nature. 1996; 379:597–600.

    Article  PubMed  CAS  Google Scholar 

  • Ostrander, E.A., Galibert, F. and D.F. Patterson. Canine genomics comes of age. T.I.G. 2000; 16:117–124.

    CAS  Google Scholar 

  • Patterson, D.F. Canine genetic disease information system: A computerised knowledge base of genetic diseases in dogs. Mosby-Harcourt (in press) 2000.

    Google Scholar 

  • Patthy, L. Genome evolution and the evolution of exon-shuffling — a review. Gene. 1999; 238:103–114.

    Article  PubMed  CAS  Google Scholar 

  • Perrière, G., Duret, L. and M. Gouy. HOBACGEN: database system for comparative genomics in bacteria. Genome. Res. 2000; 10:379–385.

    Article  PubMed  Google Scholar 

  • Pickeral, O.K., Makalowski, W., Boguski, M.S. and J.D. Boeke. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome. Res. 2000; 10:411–415.

    Article  PubMed  CAS  Google Scholar 

  • Power DM, Ingleton PM, Flanagan J, Canario AVM, Danks J, Elgar G, Clark MS. Genomic structure and expression of Parathyroid Hormone-related Protein Gene (PTHrP) in a teleost, Fugu rubripes. Gene. 2000 (in press).

    Google Scholar 

  • Ross-Macdonald, P., Sheehan, A., Roeder, S.G. and M. Snyder. A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 1997; 94:190–195.

    Article  PubMed  CAS  Google Scholar 

  • Sanger, F. et al. J.The nucleotide sequence of bacteriophage ФX174. Mol. Biol. 1978;125:225–246.

    Article  CAS  Google Scholar 

  • Sasaki, T., Yano, M., Kurata, N. and K. Yamamoto. The Japanese rice genome research program. Genome. Res. 1996; 6:661–666.

    Article  PubMed  CAS  Google Scholar 

  • Saunders, N.J. and E.R. Moxon. Implications of sequencing bacterial genomes for pathogenesis and vaccine development. Curr. Opin. Biotech. 1998; 9:618–623.

    Article  PubMed  CAS  Google Scholar 

  • Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and B. Futcher. Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell. 1998; 9:3273–3297.

    PubMed  CAS  Google Scholar 

  • Steen, R.G. et al. A high density integrated genetic linkage and radiation hybrid map of the laboratory rat. Genome. Res. 2000; 9:1–8

    Google Scholar 

  • Stoll, M. et al. New target regions for human hypertension via comparative genomics. Genome. Res. 2000; 10:473–482.

    Article  PubMed  CAS  Google Scholar 

  • Thiede MA, Rutledge GA. Nucleotide sequence of a parathyroid hormone-related peptide expressed by the 10 day chicken embryo. Nucleic Acids Res. 1990; 18:3062.

    Article  PubMed  CAS  Google Scholar 

  • Wang, D.G. et al. Large-scale identification, mapping and genotyping of single nucleotide polymorphisms in the human genome. Science. 1998; 280:1077–1081.

    Article  PubMed  CAS  Google Scholar 

  • Wright, F.A., O’Connor, D.T., Roberts, E., Kutey, G., Barry, C.C., Yoneda, L.U., Timberlake, D. and G. Schlager. Genome scan for blood pressure loci in mice. Hypertension. 1999; 34:625–630.

    Article  PubMed  CAS  Google Scholar 

  • Yasuda T, Banville D, Rabbani SA, Hendy GN, Goltzman D. Characterisation of the human parathyroid hormone-like peptide gene: Functional and evolutionary aspects. J. Biol. Chem. 1989a; 264: 7720–7725.

    PubMed  CAS  Google Scholar 

  • Yasuda T, Banville D, Rabbani SA, Hendy GN, Goltzman D. Rat parathyroid hormone-like peptide: Comparison with the human homologue and expression in malignant and normal tissue. Mol. Endocrinol. 1989b; 3:518–525.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Springer Science+Business Media New York

About this chapter

Cite this chapter

Clark, M.S. (2000). Comparative Genomics: An Introduction: Sequencing Projects and Model Organisms. In: Clark, M.S. (eds) Comparative Genomics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-4657-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-4657-3_1

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-7107-6

  • Online ISBN: 978-1-4615-4657-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics