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Review
. 2000 Sep;12(9):1523-40.
doi: 10.1105/tpc.12.9.1523.

Comparative genomics of plant chromosomes

A H Paterson  1 , J E Bowers, M D Burow, X Draye, C G Elsik, C X Jiang, C S Katsar, T H Lan, Y R Lin, R Ming, R J Wright
Affiliations
Review

Comparative genomics of plant chromosomes

A H Paterson et al. Plant Cell. 2000 Sep.
No abstract available

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Figures

Figure 1.
Figure 1.
Composite Restriction Fragment Length Polymorphism Linkage Map of Brassica oleracea, and Its Alignment to the Map of Arabidopsis thaliana. The filled circles next to the loci indicate homoeologous Brassica loci (chromosomes 1 to 9, near right) or homologous Arabidopsis loci (chromosomes 1 to 5, far right) detected by the same probe. When all the circles are open, no polymorphism was detected for homoeologous (Brassica) or homologous (Arabidopsis) loci. An R next to the probe name indicates that the probe hybridizes to a repetitive DNA sequence in Arabidopsis. Specific colors were assigned to each homoeologous (Brassica) and homologous (Arabidopsis) chromosome. Markers that appear to represent duplication of Brassica chromatin or orthology between Brassica and Arabidopsis (based on criteria described in Lan et al., 2000a) were connected by colored columns. Open columns indicate possible triplicated (Brassica) or duplicated (Arabidopsis) regions. Vertical axis indicates centimorgans. (Modified from Lan et al. [2000a], with permission.)
Figure 1.
Figure 1.
Composite Restriction Fragment Length Polymorphism Linkage Map of Brassica oleracea, and Its Alignment to the Map of Arabidopsis thaliana. The filled circles next to the loci indicate homoeologous Brassica loci (chromosomes 1 to 9, near right) or homologous Arabidopsis loci (chromosomes 1 to 5, far right) detected by the same probe. When all the circles are open, no polymorphism was detected for homoeologous (Brassica) or homologous (Arabidopsis) loci. An R next to the probe name indicates that the probe hybridizes to a repetitive DNA sequence in Arabidopsis. Specific colors were assigned to each homoeologous (Brassica) and homologous (Arabidopsis) chromosome. Markers that appear to represent duplication of Brassica chromatin or orthology between Brassica and Arabidopsis (based on criteria described in Lan et al., 2000a) were connected by colored columns. Open columns indicate possible triplicated (Brassica) or duplicated (Arabidopsis) regions. Vertical axis indicates centimorgans. (Modified from Lan et al. [2000a], with permission.)
Figure 2.
Figure 2.
Comparative Mapping of Cereal Chromosomes. The genetic maps of relevant regions of the genomes of rice, wheat, barley, and maize are aligned to the map of sorghum. DNA marker loci indicated by a line (at left of the gene name) were directly mapped in the cited populations, whereas those indicated by an arrow were mapped in other populations and the appropriate locations were inferred on the basis of map positions of flanking markers. Approximate locations of centromeres (ovals within linkage groups), telomeres (circles at ends of linkage groups), and breakpoints of chromosomal rearrangements (double squiggles) distinguishing taxa have been indicated. For DNA marker loci that conflict with the most-parsimonious interpretation of chromosomal correspondence between taxa, alternative map positions have been indicated in parentheses, adjacent to the appropriate locus in sorghum. For cases in which the exact determination of marker order in local regions could not be inferred, the order most parsimonious with that in other species was assumed. Because the populations used to map “anchor loci” were small (56 to 90 individuals), local reversals in order of closely linked markers (>3 cM) do not provide conclusive evidence of chromosomal rearrangement between taxa. Dark lines connecting selected probes on sorghum linkage groups D and I represent evidence of segmental duplication of this chromosomal region, as previously described (Chittenden et al., 1994). (Excerpted with permission from Paterson et al. [1995]. Copyright 1995, American Association for the Advancement of Science.)
Figure 3.
Figure 3.
Examples of Colinearity of Monocot and Dicot Genes. Arabidopsis cDNAs that show DNA sequence conservation (BLASTx > 150) with genes from monocots or more distant taxa were used to detect RFLPs and were then added to existing genetic maps of Sorghum bicolor × S. propinquum, Arabidopsis thaliana, B. oleracea (T.-H. Lan et al., 2000a), and Gossypium trilobum × G. raimondii (C. Brubaker, A.H. Paterson, and J.F. Wendel, unpublished data). Lowercase letters indicate that additional loci were detected by the same DNA probe. Chromosomal locations of duplicate loci are shown either directly or in parentheses. AEST, Arabidopsis cDNAs; pSB, sorghum PstI genomic DNA clones. LG, linkage group. (Modified from Paterson et al. [1996], with permission.)
Figure 4.
Figure 4.
Evidence for Nearly Genome-wide Duplication of Arabidopsis Chromatin. (A) Dot plot showing locations of duplicated genes in Arabidopsis. The x and y axes each represent 1452 completely sequenced Arabidopsis BACs, arranged in their chromosomal order, according to the reference genetic markers in (B). Points on the graph represent the best two BLAST hits on the Arabidopsis BACs, for 15,199 Arabidopsis ESTs showing high similarity (<1 × 10−14 likelihood of occurring by chance) to two nonoverlapping BACs, selected from >30,000 Arabidopsis ESTs available in GenBank (accession numbers AV530001 to AV560000). The 15,199 ESTs that were duplicated hit 5084 different BAC pairs, shown as points in the figure. Regions in which five or more BAC pairs showed hits in a square 6 × 6 region of 36 BACs are shown in red, indicating regions of duplication. Because of the resolution of this figure, it is difficult visually to resolve the number of points in a region; a tight clustering of points may appear less significant than a more dispersed grouping. A total of 42 segments appear to be duplicated. The 880 points that are shown in red represent 5780 (19.2%) of the total number of ESTs and 38% of the ESTs that were duplicated. (B) Representation of duplications on Arabidopsis chromosomes. Duplicated regions from (A) are shown along the Arabidopsis genetic map, including commonly used reference markers. Colored blocks represent the chromosomal location of the duplicated copy for the indicated chromosomal region. Of the 1452 completely sequenced Arabidopsis BACs on which this comparison was based, 841 (58%) appear to have been duplicated. Because these BACs cover only ∼90% of the genome, this suggests that at least two-thirds of the Arabidopsis genome has been duplicated. Only 49 (3%) appear to be represented in more than one duplicated region, suggesting that relatively little of the genome is involved in higher order levels of duplication (such as triplication). Curiously, the regions surrounding the centromeres show little evidence of duplication, although the physical maps and sequences of these regions tend to be less complete. Centimorgans are shown to left of chromosomes.
Figure 4.
Figure 4.
Evidence for Nearly Genome-wide Duplication of Arabidopsis Chromatin. (A) Dot plot showing locations of duplicated genes in Arabidopsis. The x and y axes each represent 1452 completely sequenced Arabidopsis BACs, arranged in their chromosomal order, according to the reference genetic markers in (B). Points on the graph represent the best two BLAST hits on the Arabidopsis BACs, for 15,199 Arabidopsis ESTs showing high similarity (<1 × 10−14 likelihood of occurring by chance) to two nonoverlapping BACs, selected from >30,000 Arabidopsis ESTs available in GenBank (accession numbers AV530001 to AV560000). The 15,199 ESTs that were duplicated hit 5084 different BAC pairs, shown as points in the figure. Regions in which five or more BAC pairs showed hits in a square 6 × 6 region of 36 BACs are shown in red, indicating regions of duplication. Because of the resolution of this figure, it is difficult visually to resolve the number of points in a region; a tight clustering of points may appear less significant than a more dispersed grouping. A total of 42 segments appear to be duplicated. The 880 points that are shown in red represent 5780 (19.2%) of the total number of ESTs and 38% of the ESTs that were duplicated. (B) Representation of duplications on Arabidopsis chromosomes. Duplicated regions from (A) are shown along the Arabidopsis genetic map, including commonly used reference markers. Colored blocks represent the chromosomal location of the duplicated copy for the indicated chromosomal region. Of the 1452 completely sequenced Arabidopsis BACs on which this comparison was based, 841 (58%) appear to have been duplicated. Because these BACs cover only ∼90% of the genome, this suggests that at least two-thirds of the Arabidopsis genome has been duplicated. Only 49 (3%) appear to be represented in more than one duplicated region, suggesting that relatively little of the genome is involved in higher order levels of duplication (such as triplication). Curiously, the regions surrounding the centromeres show little evidence of duplication, although the physical maps and sequences of these regions tend to be less complete. Centimorgans are shown to left of chromosomes.
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