title: Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny.
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 10x 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.
authors.affiliation: Indian Initiative for Rice Genome Sequencing, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110012, New Delhi, India.
authors.forename: Nagendra K
authors.initials: NK
authors.lastname: Singh
authors.forename: Saurabh
authors.initials: S
authors.lastname: Raghuvanshi
authors.forename: Subodh K
authors.initials: SK
authors.lastname: Srivastava
authors.forename: Anupama
authors.initials: A
authors.lastname: Gaur
authors.forename: Ajit K
authors.initials: AK
authors.lastname: Pal
authors.forename: Vivek
authors.initials: V
authors.lastname: Dalal
authors.forename: Archana
authors.initials: A
authors.lastname: Singh
authors.forename: Irfan A
authors.initials: IA
authors.lastname: Ghazi
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Bhargav
authors.forename: Mahavir
authors.initials: M
authors.lastname: Yadav
authors.forename: Anupam
authors.initials: A
authors.lastname: Dixit
authors.forename: Kamlesh
authors.initials: K
authors.lastname: Batra
authors.forename: Kishor
authors.initials: K
authors.lastname: Gaikwad
authors.forename: Tilak R
authors.initials: TR
authors.lastname: Sharma
authors.forename: Amitabh
authors.initials: A
authors.lastname: Mohanty
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Anita
authors.initials: A
authors.lastname: Kapur
authors.forename: Vikrant
authors.initials: V
authors.lastname: Gupta
authors.forename: Dibyendu
authors.initials: D
authors.lastname: Kumar
authors.forename: Shubha
authors.initials: S
authors.lastname: Vij
authors.forename: Ravi
authors.initials: R
authors.lastname: Vydianathan
authors.forename: Parul
authors.initials: P
authors.lastname: Khurana
authors.forename: Sulabha
authors.initials: S
authors.lastname: Sharma
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
authors.forename: Rod
authors.initials: R
authors.lastname: Wing
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
authors.forename: Paramjit
authors.initials: P
authors.lastname: Khurana
authors.forename: Trilochan
authors.initials: T
authors.lastname: Mohapatra
authors.forename: Jitendra P
authors.initials: JP
authors.lastname: Khurana
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D005819:Genetic Markers; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA; D026801:Synteny; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers