Orthology between genomes of Brachypodium, wheat and rice

被引：42

作者：

Kumar S. ^{[1
]}

Mohan A. ^{[1
]}

Balyan H.S. ^{[1
]}

Gupta P.K. ^{[1
]}

机构：

[1] Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University

来源：

BMC Research Notes | / 2卷 / 1期

关键词：

Rice Genome; Wheat Chromosome; Wheat Genome; Orthologous Sequence; Homoeologous Group;

D O I：

10.1186/1756-0500-2-93

中图分类号：

学科分类号：

摘要：

Background. In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, Brachypodium distachyon genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, Brachypodium EST contigs were utilized to resolve orthologous relationships among the genomes of Brachypodium, wheat and rice. Findings. Comparative sequence analysis of 3,818 Brachypodium EST (bEST) contigs and 3,792 physically mapped wheat EST (wEST) contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of Brachypodium, wheat and rice. Conclusion. The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals. © 2009 Gupta et al; licensee BioMed Central Ltd.

引用

共 28 条

[11]

Rice Pseudomolecules Information

[12]

Bolot S., Abrouk M., Masood-Quraishi U., Stein N., Messing J., Feuillet C., Salse J., The 'inner circle' of the cereal genome, Curr Opin Plant Biol, 12, pp. 1-7, (2008)

[13]

Sorrells M.E., La Rota M., Bermudez-Kandianis C.E., Greene R.A., Kantety R., Munkvold J.D., Mahmoud A., Ma X., Gustafson P.J., Qi L.L., Echalier B., Gill B.S., Matthews D.E., Lazo G.R., Chao S., Anderson O.D., Edwards H., Linkiewicz A.M., Dubcovsky J., Akhunov E.D., Dvorak J., Zhang D., Nguyen H.T., Peng J., Lapitan N.L.V., Gonzalez-Hernandez J.L., Anderson J.A., Hossain K., Kalavacharla V., Kianian S.F., Choi D.-W., Close T.J., Dilbirligi M., Gill K.S., Steber C., Walker-Simmons M.K., McGuire

[14]

Huo N., Gu Y.Q., Lazo G.R., Vogel J.P., Coleman-Derr D., Luo M.-C., Thilmony R., Garvin D.F., Anderson O.D., Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics, Genome, 49, pp. 1099-1108, (2006)

[15]

Faris J.D., Zhang Z., Fellers J.P., Gill B.S., Micro-colinearity between rice, Brachypodium and T. monococcum at the wheat domestication locus Q, Funct Integr Genomics, 8, pp. 149-164, (2008)

[16]

Bossolini E., Wicker T., Knobel P.A., Keller B., Comparison of orthologous loci from small grass genomes Brachypodium and rice: Implications for wheat genomics and grass genome annotation, Plant J, 49, pp. 704-717, (2007)

[17]

Akhunov E.D., Goodyear A.W., Geng S., Qi L.-L., Echalier B., Gill B.S., Miftahudin A., Gustafson J.P., Lazo G., Chao S., Anderson O.D., Linkiewicz A.M., Dubcovsky J., La Rota M., Sorrells M.E., Zhang D., Nguyen H.T., Kalavacharla V., Hossain K., Kianian S.F., Peng J., Lapitan N.L.V., Gonzalez-Hernandez J.L., Anderson J.A., Choi D.-W., Close T.J., Dilbirligi M., Gill K.S., Walker-Simmons M.K., Steber C., McGuire P.E., Qualset C.O., Dvorak J., The organization and rate of evolution of wheat genom

[18]

See D.R., Brooks S., Nelson J.C., Brown-Guedira G., Friebe B., Gill B.S., Gene evolution at the ends of wheat chromosomes, Proc Natl Acad Sci USA, 103, pp. 4162-4167, (2006)

[19]

Genomics and Gene Discovery BEST Resource

[20]

Brachypodium BLAST Server

← 1 2 3 →