Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes - PubMed (original) (raw)

Comparative Study

doi: 10.1038/ng0197-47.

Affiliations

• PMID: 8988168
• DOI: 10.1038/ng0197-47

Comparative Study

Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes

L A Lyons et al. Nat Genet. 1997 Jan.

Abstract

Precise comparisons of mammalian gene maps require common anchor loci as landmarks for conserved chromosomal segments. Using a computer script that automates DNA sequence database alignments, we designed 410 evolutionarily conserved primer pair sequences which are specific for anchor locus gene amplification from any mammalian species' DNA. Primer pairs were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequence (25-400 bp) to allow for gene identification. A total of 318 primer pairs were optimized for domestic cats, and 86% of the sequenced feline PCR products showed homology to the gene of primer origin. A screen of 20 mammals from 11 orders revealed that 35-52% of the 318 primers yielded a single PCR product without further optimization suggesting that nearly 75% can be optimized for any eutherian mammal.

PubMed Disclaimer

Comment in

• Landmarks in the Rosetta Stone of mammalian comparative maps.
  Nadeau JH, Sankoff D. Nadeau JH, et al. Nat Genet. 1997 Jan;15(1):6-7. doi: 10.1038/ng0197-6. Nat Genet. 1997. PMID: 8988158 No abstract available.

Similar articles

• Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference.
  Murphy WJ, O'Brien SJ. Murphy WJ, et al. Nat Protoc. 2007;2(11):3022-30. doi: 10.1038/nprot.2007.429. Nat Protoc. 2007. PMID: 18007639
• Utility of comparative anchor-tagged sequences as physical anchors for comparative genome analysis among the Culicidae.
  Chambers EW, Lovin DD, Severson DW. Chambers EW, et al. Am J Trop Med Hyg. 2003 Jul;69(1):98-104. Am J Trop Med Hyg. 2003. PMID: 12932106
• Anchored reference loci for comparative genome mapping in mammals.
  O'Brien SJ, Womack JE, Lyons LA, Moore KJ, Jenkins NA, Copeland NG. O'Brien SJ, et al. Nat Genet. 1993 Feb;3(2):103-12. doi: 10.1038/ng0293-103. Nat Genet. 1993. PMID: 8499943 Review.
• Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.
  Housley DJ, Zalewski ZA, Beckett SE, Venta PJ. Housley DJ, et al. BMC Genomics. 2006 Oct 9;7:253. doi: 10.1186/1471-2164-7-253. BMC Genomics. 2006. PMID: 17029642 Free PMC article.
• Comparative genomics: lessons from cats.
  O'Brien SJ, Wienberg J, Lyons LA. O'Brien SJ, et al. Trends Genet. 1997 Oct;13(10):393-9. doi: 10.1016/s0168-9525(97)01297-3. Trends Genet. 1997. PMID: 9351340 Review.

Cited by

• Cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) mutations associated with the domestic cat AB blood group.
  Bighignoli B, Niini T, Grahn RA, Pedersen NC, Millon LV, Polli M, Longeri M, Lyons LA. Bighignoli B, et al. BMC Genet. 2007 Jun 6;8:27. doi: 10.1186/1471-2156-8-27. BMC Genet. 2007. PMID: 17553163 Free PMC article.
• The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes.
  Chowdhary BP, Raudsepp T, Kata SR, Goh G, Millon LV, Allan V, Piumi F, Guérin G, Swinburne J, Binns M, Lear TL, Mickelson J, Murray J, Antczak DF, Womack JE, Skow LC. Chowdhary BP, et al. Genome Res. 2003 Apr;13(4):742-51. doi: 10.1101/gr.917503. Genome Res. 2003. PMID: 12671008 Free PMC article.
• Synteny and regional marker order assignment of 26 type I and microsatellite markers to the horse X- and Y-chromosomes.
  Shiue Y-L, Millon LV, Skow LC, Honeycutt D, Murray JD, Bowling AT. Shiue Y-L, et al. Chromosome Res. 2000;8(1):45-55. doi: 10.1023/a:1009275102977. Chromosome Res. 2000. PMID: 10730588
• A radiation hybrid map of the cat genome: implications for comparative mapping.
  Murphy WJ, Sun S, Chen Z, Yuhki N, Hirschmann D, Menotti-Raymond M, O'Brien SJ. Murphy WJ, et al. Genome Res. 2000 May;10(5):691-702. doi: 10.1101/gr.10.5.691. Genome Res. 2000. PMID: 10810092 Free PMC article.
• Direct selection of conserved cDNAs from the DiGeorge critical region: isolation of a novel CDC45-like gene.
  McKie JM, Wadey RB, Sutherland HF, Taylor CL, Scambler PJ. McKie JM, et al. Genome Res. 1998 Aug;8(8):834-41. doi: 10.1101/gr.8.8.834. Genome Res. 1998. PMID: 9724329 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Other Literature Sources

  • The Lens - Patent Citations Database

• Molecular Biology Databases

  • Mouse Genome Informatics (MGI)

• Miscellaneous

  • NCI CPTAC Assay Portal