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Comparative Study
. 2003 May;13(5):999-1010.
doi: 10.1101/gr.814403. Epub 2003 Apr 14.

LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics

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Free PMC article
Comparative Study

LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics

Steve Hampson et al. Genome Res. .
Free PMC article

Abstract

The identification of homologous regions between chromosomes forms the basis for studies of genome organization, comparative genomics, and evolutionary genomics. Identification of these regions can be based on either synteny or colinearity, but there are few methods to test statistically for significant evidence of homology. In the present study, we improve a preexisting method that used colinearity as the basis for statistical tests. Improvements include computational efficiency and a relaxation of the colinearity assumption. Two algorithms perform the method: FullPermutation, which searches exhaustively for runs of markers, and FastRuns, which trades faster run times for exhaustive searches. The algorithms described here are available in the LineUp package (http://www.igb.uci.edu/ approximately baldig/lineup). We explore the performance of both algorithms on simulated data and also on genetic map data from maize (Zea mays ssp. mays). The method has reasonable power to detect a homologous region; for example, in >90% of simulations, both algorithms detect a homologous region of 10 markers buried in a random background, even when the homologous regions have diverged by numerous inversion events. The methods were applied to four maize molecular maps. All maps indicate that the maize genome contains extensive regions of genomic duplication and multiplication. Nonetheless, maps differ substantially in the location of homologous regions, probably reflecting the incomplete nature of genetic map data. The variation among maps has important implications for evolutionary inference from genetic map data.

Figures

Figure 1.
Figure 1.
The power to detect simulated regions of chromosomal homology with the FastRuns and FullPermutation algorithms. (Top) The proportion of data sets in which some portion of the homologous region was detected. (Middle) The average proportion of the homologous region detected. (Bottom) The average proportion of the nonhomologous region detected. For all graphs, black lines represents results based on simulations in which 20 markers define the homologous region; dark gray, 10 markers; and light gray, five markers. The symbols represent analyses with different values of D: D =  2 (triangles); D =  1 (circles); and D =  0 (squares). Horizontal lines represent approximate standard deviations when available. The apparent dip in ability to identify a portion of the conserved region after 40 inversions (but not 80 or 10,000) disappears as the size of the simulated data set increases (data not shown).
Figure 2.
Figure 2.
Regions of maize chromosome 4 detected as colinear with other maize chromosomes in BNL96, IBM2002, Pio99, and UMC98 genetic maps. Chromosome 4 is shown on the left of the figure, with map units scaled between zero and one to allow comparisons between the genetic maps. A map position of one represents the end of the chromosome in each of the maps.

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