Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement - PubMed (original) (raw)

Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement

Wusirika Ramakrishna et al. Plant Cell. 2002 Dec.

Abstract

Rp1 is a complex disease resistance locus in maize that is exceptional in both allelic variability and meiotic instability. Genomic sequence analysis of three maize BACs from the Rp1 region of the B73 inbred line revealed 4 Rp1 homologs and 18 other gene-homologous sequences, of which at least 16 are truncated. Thirteen of the truncated genes are found in three clusters, suggesting that they arose from multiple illegitimate break repairs at the same sites or from complex repairs of each of these sites with multiple unlinked DNA templates. A 43-kb region that contains an Rp1 homolog, six truncated genes, and three Opie retrotransposons was found to be duplicated in this region. This duplication is relatively recent, occurring after the insertion of the three Opie elements. The breakpoints of the duplication are outside of any genes or identified repeat sequence, suggesting a duplication mechanism that did not involve unequal recombination. A physical map and partial sequencing of the Rp1 complex indicate the presence of 15 Rp1 homologs in regions of approximately 250 and 300 kb in the B73 inbred line. Comparison of fully sequenced Rp1-homologous sequences in the region demonstrates a history of unequal recombination and diversifying selection within the Leu-rich repeat 2 region, resulting in chimeric gene structures.

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Figures

Figure 1.

Figure 1.

Sequence Organization on Two BACs from the rp1 Complex. The four Rp1 homologs were named rp1-1 through rp1-4. Arrows indicate genes and arrowheads indicate truncated genes, plus their size and proposed direction of transcription. Asterisks indicate simple sequence repeats (SSRs) that contain eight or more tandem repeats. Lines connecting the two BACs indicate the 43-kb duplicated region. Grande, Ji, Opie, and PREM-1 are maize retrotransposons. Miniature inverted repeat transposable elements (MITEs) are indicated by small triangles. The two large arrowheads indicate inverted repeat sequences of 2283 and 2284 bp that are 96% identical to each other (ignoring indels) and separated by 199 bp.

Figure 2.

Figure 2.

Physical Map of the Rp1 Region in Maize Inbred Line B73. Each circle represents an Rp1 homolog. Open circles represent the four Rp1 homologs in BACs sequenced in the present study, and those with vertical arrows are part of the 43-kb duplicated region. The truncated Suc phosphate synthase–like and ATPase-like genes are designated by closed and open rectangles, respectively. Physical distances and BACs harboring Rp1 homologs are represented by lines above and below the rp1 complex map.

Figure 3.

Figure 3.

Mosaic Gene Structure of the Rp1 Homologs. N-term indicates the N-terminal nucleotide binding site region (domain A), LRR1 indicates Leu-rich repeat region 1 (domain B), and LRR2 indicates Leu-rich repeat region 2 (domain D). Domain C is the region between LRR1 and LRR2. Domain E is the region between LRR2 and the end of the gene (stop codon). Recombination breakpoints are located in the LRR regions, creating chimeric gene structures. Gray and black boxes represent the highest similarity to Rp1-D and rp1-2/rp1-4, respectively. Hatched boxes represent regions that are unique to the specific Rp1 homologs.

Figure 4.

Figure 4.

Sliding-Window Analysis Showing Diversifying and Purifying Selection across the Rp1 Homologs. Each data point represents a window size of 150 bp. Nonsynonymous substitution/synonymous substitution (Ka/Ks) values >1, ∼1, and <1 indicate diversifying, neutral, and purifying selection, respectively. Abbreviations are as in Figure 3.

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