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Genome-wide analysis of intronless genes in rice and Arabidopsis

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Abstract

Intronless genes, a characteristic feature of prokaryotes, constitute a significant portion of the eukaryotic genomes. Our analysis revealed the presence of 11,109 (19.9%) and 5,846 (21.7%) intronless genes in rice and Arabidopsis genomes, respectively, belonging to different cellular role and gene ontology categories. The distribution and conservation of rice and Arabidopsis intronless genes among different taxonomic groups have been analyzed. A total of 301 and 296 intronless genes from rice and Arabidopsis, respectively, are conserved among organisms representing the three major domains of life, i.e., archaea, bacteria, and eukaryotes. These evolutionarily conserved proteins are predicted to be involved in housekeeping cellular functions. Interestingly, among the 68% of rice and 77% of Arabidopsis intronless genes present only in eukaryotic genomes, approximately 51% and 57% genes have orthologs only in plants, and thus may represent the plant-specific genes. Furthermore, 831 and 144 intronless genes of rice and Arabidopsis, respectively, referred to as ORFans, do not exhibit homology to any of the genes in the database and may perform species-specific functions. These data can serve as a resource for further comparative, evolutionary, and functional analysis of intronless genes in plants and other organisms.

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Acknowledgments

We are thankful to Rashmi Jain for technical assistance. This work was supported financially by the Department of Biotechnology, Government of India, and the University Grants Commission, New Delhi. MJ acknowledges the Council of Scientific and Industrial Research, New Delhi, for the award of Senior Research Fellowship.

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Authors and Affiliations

  1. Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India

    Mukesh Jain, Paramjit Khurana, Akhilesh K. Tyagi & Jitendra P. Khurana

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  1. Mukesh Jain
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  2. Paramjit Khurana
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  3. Akhilesh K. Tyagi
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Correspondence to Jitendra P. Khurana.

Electronic supplementary material

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Supplemental data file 1

Predicted intronless genes in rice. (PDF 263 kb)

Supplemental data file 2

Predicted intronless genes in Arabidopsis. (PDF 184 kb)

Supplemental data file 3

Cellular role and GO category of rice intronless genes predicted by ProtFun. (PDF 277 kb)

Supplemental data file 4

Cellular role and GO category of Arabidopsis intronless genes predicted by ProtFun. (PDF 174 kb)

Supplemental data file 5

Locus IDs of rice intronless genes present in archaea, bacteria, and/or eukaryotes (PDF 169 kb)

Supplemental data file 6

Locus IDs of Arabidopsis intronless genes present in archaea, bacteria, and/or eukaryotes. (PDF 147 kb)

Supplemental data file 7

Locus IDs of rice intronless genes present specifically in different taxonomic groups. (XLS 419 kb)

Supplemental data file 8

Locus IDs of Arabidopsis intronless genes present specifically in different taxonomic groups. (XLS 306 kb)

Supplemental data file 9

Locus IDs of rice and Arabidopsis intronless ORFans. (PDF 59 kb)

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Jain, M., Khurana, P., Tyagi, A.K. et al. Genome-wide analysis of intronless genes in rice and Arabidopsis . Funct Integr Genomics 8, 69–78 (2008). https://doi.org/10.1007/s10142-007-0052-9

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  • DOI: https://doi.org/10.1007/s10142-007-0052-9

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