Abstract
The transfer and integration of tRNA genes from organellar genomes to the nuclear genome and between organellar genomes occur extensively in flowering plants. The routes of the genetic materials flowing from one genome to another are biased, limited largely by compatibility of DNA replication and repair systems differing among the organelles and nucleus. After thoroughly surveying the tRNA gene transfer among organellar genomes and the nuclear genome of a domesticated rice (Oryza sativa L. ssp. indica), we found that (i) 15 mitochondrial tRNA genes originate from the plastid; (ii) 43 and 80 nuclear tRNA genes are mitochondrion-like and plastid-like, respectively; and (iii) 32 nuclear tRNA genes have both mitochondrial and plastid counterparts. Besides the native (or genuine) tRNA gene sets, the nuclear genome contains organelle-like tRNA genes that make up a complete set of tRNA species capable of transferring all amino acids. More than 97% of these organelle-like nuclear tRNA genes flank organelle-like sequences over 20 bp. Nearly 40% of them colocalize with two or more other organelle-like tRNA genes. Twelve of the 15 plastid-like mitochondrial tRNA genes possess 5′- and 3′-flanking sequences over 20 bp, and they are highly similar to their plastid counterparts. Phylogenetic analyses of the migrated tRNA genes and their original copies suggest that intergenomic tRNA gene transfer is an ongoing process with noticeable discriminatory routes among genomes in flowering plants.
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Acknowledgments
This work was supported by grants from the Chinese Academy of Sciences (CAS; KSCX1-SW-03), the Ministry of Science and Technology (2004AA231050 and 2005AA235110), and the CAS Hundred Talents Program (to Jun Yu). We thank Dr. Xiyin Wang (Center of Bioinformatics, Peking University, China) for providing information on tRNA genes of the rice 93-11 nuclear genome, and we are grateful to Dr. Chunyuan Huang (School of Molecular and Biomedical Science, The University of Adelaide, Australia) and Dr. Jingui Zhu (Beijing Institute of Genomics, Chinese Academy of Sciences, China) for critical reading of the manuscript.
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Tian, X., Zheng, J., Hu, S. et al. The Discriminatory Transfer Routes of tRNA Genes Among Organellar and Nuclear Genomes in Flowering Plants: A Genome-Wide Investigation of indica Rice. J Mol Evol 64, 299–307 (2007). https://doi.org/10.1007/s00239-005-0200-6
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DOI: https://doi.org/10.1007/s00239-005-0200-6