Rice Mitochondrial Genomes

Rice (Oryza sativa) is the most important cereal crop for worldwide human consumption and it is one of the good models for genomics study of higher plants. Based on finishing the whole genome shot-gun sequencing of rice 12 chromosomes, here we focus on the mitochondrial genome assemblies of different rice varieties, their sequence polymorphisms, as well as the gene transfer among organellar and nuclear genomes.Based on highly redundant and high-quality sequences, we assembled rice mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite super-hybrid rice LYP9, respectively. Following up with a previous analysis on rice chloroplast genomes, we define mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms account for variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms refer to variations between subspecies among their major genotypes. In this study, we identified 96 SNPs (single nucleotide polymorphisms), 25 InDels (insertions and deletions), and three SSVs (segmental sequence variations) as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties were confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes are 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts, 21 and 38 times lower than its corresponding rates of the rice nuclear genome, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago.The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs, 1.13% and 1.09% for indels, respectively. Detecting the frequency of each neighboring nucleotide (A, C, G and T) of the sites with SNP, we found the neighboring-nucleotide effection (NNE) on SNP is very distinct, with significant bias of each nucleotide.The transfer and integration of tRNA genes from organellar genomes to the nuclear genome and between organellar genomes extensively exist in flowering plants. The routes of the genetic materials flowing from one genome to another are biased, which are 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 93-11, we found (i) 15 mitochondrial tRNA genes originate from the plastid;(ii) 43 and 80 nuclear tRNA genes are mitochondrion-like and plastid-like, respectively;(iii) 32 nuclear tRNA genes have both mitochondrial and plastid counterparts;(iv) 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 with organelle-like sequences over 20 bp. Nearly 40% of them co-localize with two or more other organelle-like tRNA genes. Twelve out 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 analysis on the migrated tRNA genes and their original copies suggests that the inter-genomic tRNA gene transfer is an ongoing process with noticeable discriminatory routes among the genomes in flowering plants.