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Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes

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Abstract

The high-quality 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 single-copy (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 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic 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 bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat. Overall, only 46.4% of these SC genes code for proteins with known functional domains; the remaining 53.6% have unknown function, and hence, represent an important, but yet, under explored category of genes.

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Acknowledgements

This work was supported by the Indian Council of Agricultural Research and the Department of Biotechnology, Government of India. We are thankful to NCBI, Softberry.com, 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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  1. Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India

    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

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  1. Nagendra K. Singh
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Correspondence to Nagendra K. Singh.

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Singh, N.K., Dalal, V., Batra, K. et al. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes. Funct Integr Genomics 7, 17–35 (2007). https://doi.org/10.1007/s10142-006-0033-4

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