Skip to main content
SpringerLink
Log in

Examination of sequence homology between human chromosome 20 and the mouse genome: intense conservation of many genomic elements

  • Original Investigation
  • Published:
Human Genetics Aims and scope Submit manuscript

Abstract

The conservation of genomic organization of mammalian species has been of interest for its usefulness in characterizing the genetics of traits and diseases and as one tool for examining evolution. The recent rough draft sequencing of the mouse and human genomes provides the opportunity for more detailed analyses. The current study examines the extent of homology between human chromosome 20 and the mouse genome by comparing putative coding and non-coding sequence to provide insight into organizational and sequence similarities between the species. The relative position of each of 460 putative coding orthologues was the same in both species, except for a single genomic segment rearrangement. The similarity extended to exon/intron structure, the size of introns, as well as strong evidence for the conservation of position of ancient LINE-1, LINE-2 and LTR repetitive sequence and the subtelomeric region of the long arm of human chromosome 20 and that of mouse chromosome 2. There was also evidence for conservation of a limited amount of non-coding single-copy sequence. Together these data provide additional insight into the extent of conservation of mammalian genomic organization and sequence.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    PubMed  Google Scholar 

  • Boissinot S, Entezam A, Furano AV (2001) Selection against deleterious LINE-1-containing loci in the human lineage. Mol Biol Evol 18: 926–35

    CAS  PubMed  Google Scholar 

  • Burge C, Karlin S (1977) Prediction of complete gene structures in human genomic. DNA J Mol Biol 268:78–94

    Google Scholar 

  • DeBry RW, Seldin MF (1996) Human/mouse homology relationships. (1996) Genomics 33:337–351

    Article  CAS  PubMed  Google Scholar 

  • Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S, Land M, Terry A, Zhou CLE, Rash S, Zhang Q, Gordon L, Kim J, Elkin C, Pollard MJ, Richardson P, Rokhsar D, Uberbacher E, Hawkins T, Branscomb E, Stubbs L (2001) Human chromosome 19 and related regions in mouse: conservative and LINEage-specific evolution. Science 293:104–111

    Article  CAS  PubMed  Google Scholar 

  • International Human Genome Sequencing Consortium (2001) Initial Sequencing and analysis of the human genome Nature 409:860–921

    Google Scholar 

  • Lundin, LG (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1–19

    Article  CAS  PubMed  Google Scholar 

  • Makalowski W, Boguski, MS (1998) Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci USA 95:9407–9412

    Article  CAS  PubMed  Google Scholar 

  • Makalowski W, Zhang J, Boguski MS (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res 6:846–57

    CAS  PubMed  Google Scholar 

  • Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520–562

    Google Scholar 

  • Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, Deng Z, Evangelista CC, Gan W, Heiman TJ, Li J, Li Z, Merkulov GV, Milshina NV, Naik AK, Qi R, Shue BC, Wang A, Wang J, Wang X, Yan X, Ye J, Yooseph S, Zhao Q, Zheng L, Zhu SC, Biddick K, Bolanos R, Delcher AL, Dew IM, Fasulo D, Flanigan MJ, Huson DH, Kravitz SA, Miller JR, Mobarry CM, Reinert K, Remington KA, Zhang Q, Zheng XH, Nusskern DR, Lai Z, Lei Y, Zhong W, Yao A, Guan P, Ji RR, Gu Z, Wang ZY, Zhong F, Xiao C, Chiang CC, Yandell M, Wortman JR, Amanatides PG, Hladun SL, Pratts EC, Johnson JE, Dodson KL, Woodford KJ, Evans CA, Gropman B, Rusch DB, Venter E, Wang M, Smith TJ, Houck JT, Tompkins DE, Haynes C, Jacob D, Chin SH, Allen DR, Dahlke CE, Sanders R, Li K, Liu X, Levitsky AA, Majoros WH, Chen Q, Xia AC, Lopez JR, Donnelly MT, Newman MH, Glodek A, Kraft CL, Nodell M, Ali F, An HJ, Baldwin-Pitts D, Beeson KY, Cai S, Carnes M, Carver A, Caulk PM, Center A, Chen YH, Cheng ML, Coyne MD, Crowder M, Danaher S, Davenport LB, Desilets R, Dietz SM, Doup L, Dullaghan P, Ferriera S, Fosler CR, Gire HC, Gluecksmann A, Gocayne JD, Gray J, Hart B, Haynes J, Hoover J, Howland T, Ibegwam C, Jalali M, Johns D, Kline L, Ma DS, MacCawley S, Magoon A, Mann F, May D, McIntosh TC, Mehta S, Moy L, Moy MC, Murphy BJ, Murphy SD, Nelson KA, Nuri Z, Parker KA, Prudhomme AC, Puri VN, Qureshi H, Raley JC, Reardon MS, Regier MA, Rogers YH, Romblad DL, Schutz J, Scott JL, Scott R, Sitter CD, Smallwood M, Sprague AC, Stewart E, Strong RV, Suh E, Sylvester K, Thomas R, Tint NN, Tsonis C, Wang G, Wang G, Williams MS, Williams SM, Windsor SM, Wolfe K, Wu MM, Zaveri J, Chaturvedi K, Gabrielian AE, Ke Z, Sun J, Subramanian G, Pfannkoch CM, Barnstead M, Stephenson LD, Venter JC (2002) A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 31:296:1661–1671

    Google Scholar 

  • Murphy WJ, Sun S, Chen Z, Yuhki N, Hirschmann D, Menotti-Raymond M, O'Brien SJ (2000) A radiation hybrid map of the cat genome: implications for comparative mapping. Genome Res 10:691–702

    CAS  PubMed  Google Scholar 

  • Murphy WJ, Stanyon R, O'Brien SJ (2001) Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol 2:5

    Article  Google Scholar 

  • Nadeau JH, Sankoff D (1998) The lengths of undiscovered conserved segments in comparative maps. Mamm Genome 9:491–5

    Article  CAS  PubMed  Google Scholar 

  • Nadeau JH, Davisson MT, Doolittle DP, Grant P, Hillyard AL, Kosowsky M, Roderick TH (1991) Comparative map for mice and humans. Mamm Genome 1:S461-S515

    PubMed  Google Scholar 

  • Needleman S, Wunsch C (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 48:443–453

    CAS  PubMed  Google Scholar 

  • O'Brien SJ, Womack JE, Lyons LA, Moore KJ, Jenkins NA, Copeland NG (1993) Anchored reference loci for comparative genome mapping in mammals Nat Genet 3:103–112

    Google Scholar 

  • Ovchinnikov I, Troxel AB, Swergold GD (2001) Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. Genome Res 11:2050–2058

    Article  CAS  PubMed  Google Scholar 

  • Schibler L, Vaiman D, Oustry A, Giraud-Delville C, Cribiu, EP (1998) Comparative gene mapping: a fine-scale survey of chromosome rearrangements between ruminants and humans. Genome Res 8:901–915

    CAS  PubMed  Google Scholar 

  • Schughart K, Kappen C, Ruddle FH (1989) Duplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc Natl Acad Sci USA 86:7067–7071

    CAS  PubMed  Google Scholar 

  • Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker — a web server for aligning two genomic DNA sequences. Genome Res 10:577–86

    CAS  PubMed  Google Scholar 

  • Seldin MF, Saunders AM, Rochelle JM, Howard TA (1991) A proximal mouse chromosome 9 linkage map that further defines linkage groups homologous with segments of human chromosomes 11, 15, and 19. Genomics 9:678–685

    CAS  PubMed  Google Scholar 

  • Smit AFA (1993) Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res 21:1863–1872

    CAS  PubMed  Google Scholar 

  • Smit AFA (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Devel 9:657–663

    Article  CAS  Google Scholar 

  • Smit AFA, Toth G, Riggs AD, Jurka J (1995) Ancestral, mammalian wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 246:401–417

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Rowe Program in Genetics, Department of Biological Chemistry and Department of Medicine, University of California at Davis, Davis, CA 95616, USA

    Lingxiang Zhu & Michael F. Seldin

  2. Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY 10032, USA

    Gary D. Swergold

Authors
  1. Lingxiang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gary D. Swergold
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael F. Seldin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael F. Seldin.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhu, L., Swergold, G.D. & Seldin, M.F. Examination of sequence homology between human chromosome 20 and the mouse genome: intense conservation of many genomic elements. Hum Genet 113, 60–70 (2003). https://doi.org/10.1007/s00439-003-0920-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00439-003-0920-x

Keywords

Search

Navigation