Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses

Abstract

Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice sequence and two sorghum physical maps that integrate genetic markers, bacterial artificial chromosome (BAC) fingerprints, and BAC hybridization data. The sorghum maps largely tile a genomic component containing 41% of BACs but 80% of single-copy genes that shows conserved microsynteny with rice and partially tile a nonsyntenic component containing 46% of BACs but only 13% of single-copy genes. The remaining BACs are centromeric (4%) or unassigned (8%). The two genomic components correspond to cytologically discernible "euchromatin" and "heterochromatin." Gene and repetitive DNA distributions support this classification. Greater microcolinearity in recombinogenic (euchromatic) than nonrecombinogenic (heterochromatic) regions is consistent with the hypothesis that genomic rearrangements are usually deleterious, thus more likely to persist in nonrecombinogenic regions by virtue of Muller's ratchet. Interchromosomal centromeric rearrangements may have fostered diploidization of a polyploid cereal progenitor. Model plant sequences better guide studies of related genomes in recombinogenic than nonrecombinogenic regions. Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond.

Fig. 1.

Comparative physical maps. A segment of the rice chromosome 4 pseudomolecule is compared with BAC contigs from SP, SB, and Zea mays based on hybridization anchors (Table 1). The scales (MBP) of the rice pseudomolecule and sorghum contigs are equal, whereas maize contigs are shown at a 1:5 scale. Sorghum and maize contig lengths were estimated by multiplying the average fpc band size (4,740 bp, the observed average for rice) by the length of the contig in fpc consensus band (CB) units. Red lines represent cases for which loci were inferred in one genome (where no dot is shown) due to missing data. Maize contigs were from a recent release (www.genome.arizona.edu/fpc/maize, release 10/25/04), incorporating hybridization anchors from Table 1. Current sorghum contig assemblies are on-line (www.plantgenome.uga.edu/projects.htm).

Fig. 2.

Coverage of the rice genome by syntenic sorghum BAC contigs. Only hybridization markers that hit two or more BACs in the same contig were considered for microsynteny comparisons. Sorghum contigs were aligned to the rice sequence based on the criteria that two or more low copy probe loci (detecting five contigs or fewer) showed best matches between 5 and 500 kb apart in rice (anchoring 456 SP and 303 SB contigs). Sorghum chromosome (32) and linkage group designations (16) are as cited. Cytologically identified heterochromatic regions were approximated from refs. and based on relative distance from the centromere, assigning approximate base-pair locations without accounting for sequence gaps.

Fig. 3.

Comparison of rice genetic map, rice sequence, and sorghum genetic map. blast similarity between sorghum probes and the rice sequence required hits with E ≤10^-8 based on DNA blast. All other chromosomes are available (Figs. 15-26, which are published as supporting information on the PNAS web site). The rice genetic map is based on RGP restriction fragment length polymorphism 2000 (www.gramene.org).

Fig. 4.

Restructuring of rice pericentromeric regions over time. The genomic distributions of best-matching copies at differing degrees of synonymous divergence (K_s, in parentheses, upper right) are plotted. The numbers of K_s 0.2-0.6 pairs were counted in 100-gene sliding windows and compared with the random expectation using a χ² test. All significant regions are plotted in Fig. 2, and a sampling is shown in Fig. 4 in purple (chr. 2) or red (chr. 3) boxes. Duplicated regions (blue boxes) were described elsewhere (1). The bars to the left of the axis show the number of data points in each of the three indicated regions (two restructured, one duplicated) for each window of K_s values. Additional windows (making the set consecutive) for the whole genome are available (Figs. 5-14), with centromere locations indicated by red dots.