Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex - PubMed (original) (raw)

Comparative Study

. 2002 Dec;130(4):1728-38.

doi: 10.1104/pp.014951.

Affiliations

Comparative Study

Comparative sequence analysis of the sorghum Rph region and the maize Rp1 resistance gene complex

Wusirika Ramakrishna et al. Plant Physiol. 2002 Dec.

Abstract

A 268-kb chromosomal segment containing sorghum (Sorghum bicolor) genes that are orthologous to the maize (Zea mays) Rp1 disease resistance (R) gene complex was sequenced. A region of approximately 27 kb in sorghum was found to contain five Rp1 homologs, but most have structures indicating that they are not functional. In contrast, maize inbred B73 has 15 Rp1 homologs in two nearby clusters of 250 and 300 kb. As at maize Rp1, the cluster of R gene homologs is interrupted by the presence of several genes that appear to have no resistance role, but these genes were different from the ones found within the maize Rp1 complex. More than 200 kb of DNA downstream from the sorghum Rp1-orthologous R gene cluster was sequenced and found to contain many duplicated and/or truncated genes. None of the duplications currently exist as simple tandem events, suggesting that numerous rearrangements were required to generate the current genomic structure. Four truncated genes were observed, including one gene that appears to have both 5' and 3' deletions. The maize Rp1 region is also unusually enriched in truncated genes. Hence, the orthologous maize and sorghum regions share numerous structural features, but all involve events that occurred independently in each species. The data suggest that complex R gene clusters are unusually prone to frequent internal and adjacent chromosomal rearrangements of several types.

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Figures

Figure 1

Figure 1

Physical map of the rph1 region from sorghum inbred BTx623. Each circle represents an Rp1 homolog (i.e. rph1 gene). Physical distances and names of BACs are represented by lines above and below the positions of the_rph1_ genes. The names of BACs in parentheses are from the naming convention used in fingerprint analysis (Klein et al., 2000; P.E. Klein, personal communication).

Figure 2

Figure 2

Sequence organization of the sorghum genomic segment as represented by overlapping BACs Sb95A23 and Sb98N08. The five Rp1 homologs were named rph1-1 to_rph1-5_. All other genes are given simplex numbers from 1 to 19. Arrows indicate genes or truncated genes, plus their size and proposed direction of transcription. A through C, Multiple copies of the same gene family. Asterisks, SSRs that contain tandem repeat numbers of eight or more. Retrotransposons are indicated by rectangles without arrows on top. Novel full-length LTR-retrotransposons were named as described by SanMiguel et al. (2002). MITEs are indicated by small triangles. Arrowheads with bars between genes 15C and 17 indicate direct repeat sequences of 468 and 470 bp that are 91% identical to each other and separated by 6,112 bp. Gene 19p is given its unique designation because the sequenced region only contains the 3′ portion (p) of the gene.

Figure 3

Figure 3

Comparison of Rp1 and rph1_gene structures. N-term is the N-terminal region that contains the NBS, LRR1 is LRR region 1 and LRR2 is LRR region 2. The region between LRR1 region and LRR2 region is domain C. The region from the end of LRR2 region to the position of the stop codon predicted for the maize_Rp1_-D gene is domain E. Asterisks, Stop codons. Genes_rph1-3 and rph1-5 are missing their N termini and most of their LRR1 regions.

Figure 4

Figure 4

A neighbor-joining tree of barley, maize, and sorghum Rp1 homologs. A neighbor-joining tree was constructed based on synonymous substitutions in the N-terminal region of all the barley, maize, and sorghum Rp1 gene family members from the present study and those present in the GenBank database. Bootstrap values based on 1,000 replicates are indicated at the nodes.

Figure 5

Figure 5

A model for the origin of the current state of the sequenced rph1 complex from a single region with only one_rph_ gene. Horizontal arrows designate the positions, orientations, and approximate transcript sizes for the indicated genes.

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