Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)

Abstract

A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5-16.5%. The sum of expansions and contractions observed in regions >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged approximately 2 million years ago.

Figure 1.—

Detailed alignment view of the comparative physical map of O. punctata (BB genome type) and O. sativa (AA genome type) using SyMap (Soderlund et al. 2006). Alternating light and dark pink boxes on the left indicate O. punctata contigs. Beige bars on the right indicate O. sativa genome sequence (International Rice Genome Sequencing Project 2005). A red “X” on beige bars indicates a CentO position of O. sativa (International Rice Genome Sequencing Project 2005). Each purple line denotes the best alignment between an O. punctata BES onto the O. sativa genome sequence. The small black boxes on the beige bars indicate a physical gap in the O. sativa genome sequence (International Rice Genome Sequencing Project 2005). Black arrows indicate a position of a punctata expansion (details in Figure 2); red arrows indicate a position of a punctata contraction (details in Figure 2).

Figure 2.—

Alignment views with expansions/contractions of segments of the O. punctata genome against the collinear segment in O. sativa. The sizes of loci on O. punctata contigs were calculated using [1.27 kb/CB].

Figure 3.—

Inversion between two species on chromosome 8. (A) O. punctata contigs 111 and 112 contain an inversion with respect to the O. sativa genome sequence. The inversion was detected by 79 BES alignments and two clones containing the breakpoints of the inversion were selected (red highlighted). (B) The confirmation of the inversion by FISH analysis. (Left) The clones selected for FISH analysis. (Right) FISH pattern of the clones on pachytene chromosome of O. punctata.

Figure 4.—

Detailed view of an intrachromosomal transposition on chromosome 6. The 15 BESs from 744 CB of contig 75 to 41 CB of contig 76 were aligned to 18.3–18.7 Mb of O. sativa chromosome 6. The integrity of the contig assembly of the locus was confirmed by the overgo hybridization method described by Chen et al. (2002; data not shown).