Background Information About Chromosomes
The genome of most eukaryotes is packaged into structures called chromosomes (many organisms also contain additional DNA present in mitochondria and chloroplasts). In most organisms, chromosomes are best viewed at metaphase where they adopt the classic 'X' shape due to the presence of sister chromatids held together at their centromeres.
The ratio of length between short and long arms of a particular chromosome remains constant for a particular organism and can be used to identify the chromosome. When referring to the physical position of a gene within an organism's genome both the chromosome number and the arm on which it resides is often given. For example: gene X may lie on the short arm of chromosome 1.
Another way of describing the relative positions of genes with respect to each other is to refer to a measure of the probability that genes will remain together through meiosis. If a gene co-segregates with another gene in 1 out of 100 meiotic events then they are said to be 1cM (centimorgan) apart. In the case where the entire chromosomal sequence is know then it becomes possible to measure distances in megabases (millions of bases).
The highest gene densities occur within the central regions of the long and short arms. Regions with low gene density, containing stretches of repeated sequences, are found at the centromere (centromeric repeats) and at the ends of chromosomes (telomeres containing telomeric repeats). Regions containing repeated sequences are often difficult to sequence and reassemble, and it is not uncommon for such regions to remain only partly sequenced following a genome sequencing project.
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