Plant Synteny, Colinearity and Genome Evolution


Plant genomes exhibit a tremendous range of chromosome size and number, however, gene numbers and types do not appear to vary a great deal between different plant species. Genomic colinearity provides some insight into genome evolution and a tool for gene isolation and characterization.

Keywords: chromosome structure; DNA markers; genetic mapping; genome rearrangement; inversion; translocation

Figure 1.

Comparative genetic maps of five grass species: rice, foxtail millet, sorghum, maize and barley. Individual bars indicate chromosomes, and the chromosomes of any given grass species are all drawn in the same colour. The 12 chromosomes of the rice genetic map are shown central to the figure, with each chromosome numbered. Chromosomes of all other species are numbered or lettered, with ‘pt’ used as a designation to show that only part of a chromosome is represented by a comparison to a particular rice segment. The designation ‘C’ indicates the approximate locations of centromeres, when known, while red arrowheads indicate the positions of telomeres. Black arrows with two arrowheads indicate the size and location of inversions, whereas the arrows with only one arrowhead indicate the size and locations of translocations. Three translocations that are found only in the Panicoid species (maize, sorghum and foxtail millet) are shown in red. A dotted arrow in the centre of the figure shows a duplicated segment of the rice genome that is found on chromosomes 11 and 12. Chequerboard areas of the figure indicate regions where the mapping data are currently ambiguous. Black dots (connected by a black line) show the positions of three deoxyribonucleic acid (DNA) markers (rz474, the phytochrome A gene, and α‐tubulin genes) and one morphological marker (plant height). These markers have not been mapped in all of the species shown, but those that have been mapped are found in colinear locations on rice chromosome 3, foxtail millet chromosome IX, sorghum chromosome C, maize chromosomes 1 and 5, and barley chromosome 4.

Figure 2.

Comparative sequence analysis of orthologous regions of the maize and sorghum genomes carrying pollen‐specific adh genes. The size and orientation of genes are represented by arrows, while three genes that are present in the sorghum region but missing from the maize region are indicated by red arrows. Shaded areas between the two line drawings indicate conserved regions. The maize sequence has several blocks of repetitive deoxyribonucleic acid (DNA) (exclusively composed of retrotransposons) that are found between the genes, and are numbered 1 to 6.



Blanc G, Barakat A, Guyot R et al. (2000) Extensive duplication and reshuffling in the Arabidopsis thaliana genome. Plant Cell 12: 1093–1101.

Bonierbale MW, Plaisted RL and Tanksley SD (1988) RFLP maps based on a common set of clones reveals modes of evolution in potato and tomato. Genetics 120: 1095–1103.

Gale MD and Devos KM (1998) Plant comparative genetics after ten years. Science 282: 656–659.

Ku H‐M, Vision T, Liu J and Tanksley SD (2000) Comparing sequenced segment of the tomato and Arabidopsis genomes: large scale duplication followed by selective gene loss creates a network of synteny. Proceedings of the National Academy of Sciences of the USA 97: 9121–9126.

Moore G, Devos KM, Wang Z and Gale MD (1995) Grasses, line up and form a circle. Current Biology 5: 737–739.

Paterson AH, Lan T‐H, Reischmann KP et al. (1996) Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence. Nature Genetics 14: 380–382.

SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y and Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nature Genetics 20: 43–45.

Tikhonov AP, SanMiguel PJ, Nakajima Y et al. (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proceedings of the National Academy of Sciences of the USA 96: 7409–7414.

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How to Cite close
Bennetzen, Jeffrey L, and Devos, Katrien(Jul 2001) Plant Synteny, Colinearity and Genome Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0002015]