Physical Maps of Chromosomes


Physical maps of chromosomes are a way of visualizing the entire chromosome in a single figure. Physical maps can come in a variety of formats, including actual photographs of chromosomes, genetic maps where the relative locations of genes are mapped, restriction maps showing the location of restriction enzyme cutting sites along the deoxyribonucleic acid (DNA), and finally maps based on the known DNA sequence along the entire chromosome.

Keywords: genetic map; restriction map; chromosome sequence map; DNA atlases

Figure 1.

Picture of the four chromosomes from a wild type Drosophila female (top left), and XXY female (top right). Shown below is a mechanism for ‘crossing‐over’, which explains the origins of the extra chromosome found in the XXY female. The drawings are based on Bridges .

Figure 2.

Genome atlas for phiX174. The outer three lanes correspond to DNA structural properties (curvature, stacking energy and nucleosomal ‘position preference’). All the genes go in the same direction (clockwise), and hence are annotated as blue. Two different types of inverted repeats are indicated in the next two lanes, followed by GC skew and the inner‐most circle is the relative AT content (red being more AT rich, and blue represents GC rich). Hansen Permissions.

Figure 3.

Restriction map (left), and gene map (right) for the bacteriophage phiX174. Note that the genes are all in the same orientation, as indicated by the green arrows. The red lines represent different mapped transcripts. These figures were kindly provided by Flemming Hansen.

Figure 4.

Genome atlas for the bacterial genome of Bradyrhizobium japonicum, strain USDA 110. The lanes are similar to those in the atlas in Figure , except the repeats are now global direct and inverted repeats, which represent regions of at least 100 bp with homology either on the same strand (direct repeats), or on the opposite strand (inverted repeats). As is characteristic for many bacterial genomes, the overall level of repeats is quite low, with less than 5% of the genome containing repeats with more than 80% homology.



Bridges CB (1916) Non‐disjunction as proof of the chromosome theory of heredity (concluded). Genetics 1: 107–163 PMID: 17245853 [PubMed].

Gerstein MB, Bruce C, Rozowsky JS et al. (2007) What is a gene, post‐ENCODE? History and updated definition. Genome Research 17: 669–681 PMID: 17567988 [PubMed – in process].

Hoskins RA, Carlson JW, Kennedy C et al. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316: 1625–1628.

Kaneko T, Nakamura Y, Sato S et al. (2002) Complete genomic sequence of nitrogen‐fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Research 9: 189–197 PMID: 12597275 [PubMed – indexed for MEDLINE].

Kotewicz ML, Jackson SA, LeClerc JE and Cebula TA (2007) Optical maps distinguish individual strains of Escherichia coli O157: H7. Microbiology 153: 1720–1733 PMID: 17526830 [PubMed – in process].

Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH and Ussery DW (2000) A DNA structural atlas for E. coli. Journal of Molecular Biology 299: 907–930 PMID: 10843847 [PubMed – indexed for MEDLINE].

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Ussery DW, Borini S and Wassenaar TM (2008) Computing for comparative genomics: Bioinformatics for microbiologists. London: Springer‐Verlag.

Further Reading

Gregory TR (ed.) (2005) The Evolution of the Genome. London, UK: Elsevier Academic Press.

Morgon TH (1919) The Physical Basis of Heredity, Monographs on Experimental Biology. Philadelphia: J.B. Lippincott.

Morton NE (2005) Linkage disequilibrium maps and association mapping. Journal of Clinical Investigation 115: 1425–1430 PMID: 15931377 [PubMed – indexed for MEDLINE].

O'Brian S, Menninger JC and Nash G (eds) (2006) Atlas of Mammalian Chromosomes. Hoboken, NJ: Wiley.

Valouev A, Schwartz DC, Zhou S and Waterman MS (2006) An algorithm for assembly of ordered restriction maps from single DNA molecules. Proceedings of the National Academy of Sciences of the USA 103: 15770–15775 PMID: 17043225 [PubMed – indexed for MEDLINE].

Yim YS, Moak P, Sanchez‐Villeda H et al. (2007) A BAC pooling strategy combined with PCR‐based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8: 47 PMID: 17291341 [PubMed – indexed for MEDLINE].

Zhao S and Stodolsky M (2004) Bacterial Artificial Chromosomes: Volume 1: Library Construction, Physical Mapping, and Sequencing (Methods in Molecular Biology). Totowa, NJ: Humana Press.

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How to Cite close
Ussery, David W(Mar 2009) Physical Maps of Chromosomes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001425]