Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny

Singh, N. K., Raghuvanshi, S., Srivastava, S. K., Gaur, A., Pal, A. K., Dalal, V., Singh, A., Ghazi, I. A., Bhargav, A., Yadav, M., Dixit, A., Batra, K., Gaikwad, K., Sharma, T. R., Mohanty, A., Bharti, A. K., Kapur, A., Gupta, V., Kumar, D., Vij, S., Vydianathan, R., Khurana, P., Sharma, S., McCombie, W. R., Messing, J., Wing, R., Sasaki, T., Mohapatra, T., Khurana, J. P., Tyagi, A. K. (2004) Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Functional and Integrative Genomics, 4 (2). pp. 102-117. ISSN 1438793X (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/15085449
DOI: 10.1007/s10142-004-0109-y

Abstract

The DNA sequence of 106 BAC/PAC clones in the minimum tiling path (MTP) of the long arm of rice chromosome 11, between map positions 57.3 and 116.2× cM, has been assembled to phase 2 or PLN level. This region has been sequenced to 10× redundancy by the Indian Initiative for Rice Genome Sequencing (IIRGS) and is now publicly available in GenBank. The region, excluding overlaps, has been predicted to contain 2,932 genes using different software. A gene-by-gene BLASTN search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 1,143 of the predicted rice genes (38.9%) have significant homology to wheat ESTs (bit score ≥ 100). Further BLASTN search of these 1,143 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 113 of the genes to be placed in bins located on wheat chromosomes of different homoeologous groups. The largest number of genes, about one-third, mapped to the homoeologous group 4 chromosomes of wheat, suggesting a common evolutionary origin. The remaining genes were located on wheat chromosomes of different groups with significantly higher numbers for groups 3 and 5. Location of bin-mapped wheat contigs to chromosomes of all the seven homoeologous groups can be ascribed to movement of genes (transpositions) or chromosome segments (translocations) within rice or the hexaploid wheat genomes. Alternatively, it could be due to ancient duplications in the common ancestral genome of wheat and rice followed by selective elimination of genes in the wheat and rice genomes. While there exists definite conservation of gene sequences and the ancestral chromosomal identity between rice and wheat, there is no obvious conservation of the gene order at this level of resolution. Lack of extensive colinearity between rice and wheat genomes suggests that there have been many insertions, deletions, duplications and translocations that make the synteny comparisons much more complicated than earlier thought. However, enhanced resolution of comparative sequence analysis may reveal smaller conserved regions of colinearity, which will facilitate selection of markers for saturation mapping and sequencing of the gene-rich regions of the wheat genome. © Springer-Verlag 2004.

Item Type: Paper
Uncontrolled Keywords: Plant genome Rice Synteny Wheat complementary DNA contig article bacterial artificial chromosome chromosome 11q chromosome aberration chromosome analysis chromosome translocation computer program DNA sequence DNA transposition expressed sequence tag gene duplication gene location gene mapping gene sequence genetic analysis genetic conservation hexaploidy molecular cloning nonhuman plant genetics priority journal sequence analysis sequence homology chromosome map genetic marker genetics nucleotide sequence Triticum aestivum Base Sequence Chromosome Mapping Conserved Sequence Genetic Markers Oryza sativa Sequence Analysis, DNA Triticum
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
organism description > plant > rice
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > synteny
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 23 Apr 2013 19:11
Last Modified: 23 Apr 2013 19:11
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28241

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