Abstract
Since rapid sequencing of bacterial genomes is currently feasible, it has been suggested that sequences for entire genomes of complex organisms will be commonplace in the future. We do not anticipate this happening within the near future, although the technology advances rapidly: A systematics thesis from the late 1980s would commonly be based on 5,000 base pairs of sequence, a thesis of a student of the early 1990s was commonly based on about 50,000 bases of sequence and students currently doing systematics PhDs are commonly basing their theses on 500,000 base pairs of data. Comparative genomics with just ten higher eukaryotic taxa might require a thesis to hold over 50,000,000,000 bases of sequence if entire genomes are utilized. This jump in information content would require the technology to implement a 10,000-fold increase in efficiency.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Thornton JW and DeSalle R (2000) Gene 5 family evolution and homology: Genomics meets phylogenetics. Annu. Rev. Hum. Genom. 1: 41–73
Nelson M, McClelland M (1992) Use of DNA methyltransferase/endonuclease enzyme combinations for maegabase mapping of chromosomes. Meth. Enz. 216: 279–303
Birren B, Lai E (1993) Pulse field gel electrophoresis: a practical approach (San Diego: Academic Press)
Adams MD, CS, Holt RA, Evans CA et al. (2000) The genome sequence of Drosophila melanogaster. Science 87, 2204–15
Myers EW, SG, Delcher AL, Dew, IM, Fasulo, DP (2000) A whole-genome as-sembly of Drosophila. Science 287, 2196–204
BurtDW, B.C., Dunn, I.C, Jones, C.T et al (1999) The dynamics of chromosome evolution in birds and manmmals Nature 402: 411–13
Schofield JP, Elgar G, Greystrong J et al(1997) Regions of human chromosome 2 (2q32-q35) and mouse chromosome 1 show synteny with the pufferfish gen-ome (Fugu rubripes). Genomics 45, 158–67
Trower MK, Purvis IJ, Sanseau P et al. (1996) Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease. Proc Natl Acad Sci US A 93, 1366–9
Chamberlain JS, Gibbs RA, Ranier JE et al. (1988) Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nuclei Acids Res. Dec 9;16(23):11141–56
Sorokin A, Lapidus A, Capuano V, Galleron N et al. (1996) A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing. Genome Methods 6, 448–453
Cheng S, Fockler C, Barnes WM et al. (1994) Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci USA 19: 5695–5699
Nag DK, Huang HV, Berg DE (1988) Bidirectional chain-termination nucleotide sequencing: transposon Tn5seql as a mobile source of primer sites. Gene 64: 135–45
Goryshin IY and Reznikoff WS (1998) Tn5 in vitro transposition. J. Biol. Chem. 273: 7363–74
Zangenberg G, Saiki RK and Reynolds R (1999) Multiplex PCR: Optimization and guidelines. In: M Innis, GDH and JJ Sninsky, (eds): PCR applications. Academic Press, San Diego, 566
DeSalle R and Bonwich E (1996) DNA isolation, manipulation and characterization from old tissues. Genet Eng (N Y) 18: 13–32
Chase MW, Soltis DE, Olmsted RG et al (1993) Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missuri Botanical Garden 80: 528–80
Kallersjo M, Farris JS, Chase MW et al. (1998) Simultaneous parsemony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Plant Syst Evol 213: 259–287
Rokas A and Holland PWH (2000) Rare genomic changes as a tool for phylogenetics. TREE 15: 454–459
Breen M, Thomas R, Binns MM et al. (1999) Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human. Genomics Oct 15;61(2):145–55
Scalzi JM and Hozier JC (1998) Comparative genome mapping: mouse and rat homologies revealed by fluorescence in situ hybridization. Genomics Jan 1;47(1):44–51
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer Basel AG
About this chapter
Cite this chapter
Phillips, A.J. (2002). Comparative Phylogenomics: A Strategy for High-throughput Large-scale Sub-genomic Sequencing Projects for Phylogenetic Analysis. In: DeSalle, R., Giribet, G., Wheeler, W. (eds) Techniques in Molecular Systematics and Evolution. Methods and Tools in Biosciences and Medicine. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8125-8_8
Download citation
DOI: https://doi.org/10.1007/978-3-0348-8125-8_8
Publisher Name: Birkhäuser, Basel
Print ISBN: 978-3-7643-6257-7
Online ISBN: 978-3-0348-8125-8
eBook Packages: Springer Book Archive