The Sequence of Rice Chromosomes 11 and 12, Rich in Disease Resistance Genes and Recent Gene Duplications

Overview

Journal BMC Biol

Publisher Biomed Central

Specialty Biology

Date 2005 Sep 29

PMID 16188032

Citations 95

Affiliations

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Abstract

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals.

Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes.

Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested.

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References

Johal G, Briggs S . Reductase activity encoded by the HM1 disease resistance gene in maize. Science. 1992; 258(5084):985-7. DOI: 10.1126/science.1359642. View

Swigonova Z, Bennetzen J, Messing J . Structure and evolution of the r/b chromosomal regions in rice, maize and sorghum. Genetics. 2004; 169(2):891-906. PMC: 1449108. DOI: 10.1534/genetics.104.034629. View

Guyot R, Keller B . Ancestral genome duplication in rice. Genome. 2004; 47(3):610-4. DOI: 10.1139/g04-016. View

Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R . Human-mouse alignments with BLASTZ. Genome Res. 2003; 13(1):103-7. PMC: 430961. DOI: 10.1101/gr.809403. View

Bryan G, Wu K, Farrall L, Jia Y, Hershey H, McAdams S . tA single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell. 2000; 12(11):2033-46. PMC: 150156. DOI: 10.1105/tpc.12.11.2033. View

Lai J, Ma J, Swigonova Z, Ramakrishna W, Linton E, Llaca V . Gene loss and movement in the maize genome. Genome Res. 2004; 14(10A):1924-31. PMC: 524416. DOI: 10.1101/gr.2701104. View

Goff S, Ricke D, Lan T, Presting G, Wang R, Dunn M . A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002; 296(5565):92-100. DOI: 10.1126/science.1068275. View

Zhang Z, Schwartz S, Wagner L, Miller W . A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000; 7(1-2):203-14. DOI: 10.1089/10665270050081478. View

Causse M, Fulton T, Cho Y, Ahn S, Chunwongse J, Wu K . Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics. 1994; 138(4):1251-74. PMC: 1206261. DOI: 10.1093/genetics/138.4.1251. View

10.

Song R, Llaca V, Linton E, Messing J . Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family. Genome Res. 2001; 11(11):1817-25. PMC: 311139. DOI: 10.1101/gr.197301. View

11.

Zhou T, Wang Y, Chen J, Araki H, Jing Z, Jiang K . Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics. 2004; 271(4):402-15. DOI: 10.1007/s00438-004-0990-z. View

12.

Messing J, Crea R, Seeburg P . A system for shotgun DNA sequencing. Nucleic Acids Res. 1981; 9(2):309-21. PMC: 326694. DOI: 10.1093/nar/9.2.309. View

13.

Sasaki T, Matsumoto T, Antonio B, Nagamura Y . From mapping to sequencing, post-sequencing and beyond. Plant Cell Physiol. 2005; 46(1):3-13. DOI: 10.1093/pcp/pci503. View

14.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

15.

Gale M, Devos K . Comparative genetics in the grasses. Proc Natl Acad Sci U S A. 1998; 95(5):1971-4. PMC: 33824. DOI: 10.1073/pnas.95.5.1971. View

16.

Yu J, Hu S, Wang J, Wong G, Li S, Liu B . A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002; 296(5565):79-92. DOI: 10.1126/science.1068037. View

17.

Monosi B, Wisser R, Pennill L, Hulbert S . Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet. 2004; 109(7):1434-47. DOI: 10.1007/s00122-004-1758-x. View

18.

Haas B, Delcher A, Mount S, Wortman J, Smith Jr R, Hannick L . Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003; 31(19):5654-66. PMC: 206470. DOI: 10.1093/nar/gkg770. View

19.

Palmer L, Rabinowicz P, OShaughnessy A, Balija V, Nascimento L, Dike S . Maize genome sequencing by methylation filtration. Science. 2003; 302(5653):2115-7. DOI: 10.1126/science.1091265. View

20.

Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N . Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science. 2003; 301(5631):376-9. DOI: 10.1126/science.1081288. View