Singlecopy genes define a conserved order between

Authors: Nagendra K Singh Vivek Dalal Kamlesh Batra Binay K Singh G Chitra Archana Singh Irfan A Ghazi Mahavir Yadav Awadhesh Pandit Rekha Dixit Pradeep K Singh Harvinder Singh Kirpa R Koundal Kishor Gaikwad Trilochan Mohapatra Tilak R Sharma

Publish Date: 2006/07/25

Volume: 7, Issue: 1, Pages: 17-35

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Abstract

The highquality rice genome sequence is serving as a reference for comparative genome analysis in crop plants especially cereals However early comparisons with bread wheat showed complex patterns of conserved synteny gene content and colinearity gene order Here we show the presence of ancient duplicated segments in the progenitor of wheat which were first identified in the rice genome We also show that singlecopy SC rice genes those representing unique matches with wheat expressed sequence tag EST unigene contigs in the whole rice genome show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy MC or duplicated rice genes While 587 of the 1244 mapped SC rice genes were located in single syntenic wheat chromosome groups the remaining 413 were distributed randomly to the other six nonsyntenic wheat groups This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism The breakdown of rice–wheat synteny due to such transpositions was much greater near the wheat centromeres Furthermore the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy aneuploidy centromeric fusions and translocations Apart from the binmapped wheat EST contigs we also compared 56298 predicted rice genes with 39813 wheat EST contigs assembled from 409765 EST sequences and identified 7241 SC rice gene homologs of wheat Based on the conserved colinearity of 1063 mapped SC rice genes across the bins of individual wheat chromosomes we predicted the wheat bin location of 6178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 354 initial success This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat Overall only 464 of these SC genes code for proteins with known functional domains the remaining 536 have unknown function and hence represent an important but yet under explored category of genesThis work was supported by the Indian Council of Agricultural Research and the Department of Biotechnology Government of India We are thankful to NCBI Softberrycom USDA and RGP for making their databases and genome analysis tools publicly available We are grateful to Dr Dave Matthews for his help with wheat EST data sets and Drs Bikram Gill and Li Qi for providing kindly the DNA samples of wheat deletion lines A summary of this work was presented at the 5th International Rice Genetics Symposium in Manila

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