title: The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowering plants: a genome-wide investigation of indica rice.
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.
authors.affiliation: Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China.
authors.forename: Xiangjun
authors.initials: X
authors.lastname: Tian
authors.forename: Jing
authors.initials: J
authors.lastname: Zheng
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D002467:Cell Nucleus / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics* / Q000378:metabolism; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D011995:Recombination, Genetic
chemical_list: D012343:RNA, Transfer