The distribution and copy number of copia -like retrotransposons in rice ( Oryza sativa L.) and their implications in the organization and evolution of the rice genome

Abstract

We used 22 fragments corresponding to the reverse transcriptase domain of copia-like retrotransposons as representatives to study the organization and distribution of these elements in the rice genome. The loci detected by these 22 fragments were assigned to 47 locations in the molecularlinkage map involving all 12 chromosomes. The distributional features of copia-like retrotransposons found in the rice genome indicated that (i) the loci detected were located mainly in one arm of each chromosome; (ii) one fragment usually detected several loci that were mapped to similar locations of different chromosomes; (iii) retrotransposons sharing high identity in nucleotide sequences were usually assigned to similar locations of the chromosomes; and (iv) concurrences of multiple loci, detected by different fragments, in similar locations or stretches of different chromosomes were common in the rice genome. We also determined that the copy number of copia-like retrotransposons in rice genome may be as low as Ϸ100 per haploid genome. The restricted distribution, along with low copy number, suggested that copia-like retrotransposons in rice were relatively inactive during evolution compared with those in other plants. The distributional features of the copia-like retrotransposons suggested the existence of possible lineages among the rice chromosomes, which in turn suggested that chromosome duplication and diversification may be a mechanism for the origin and evolution of the rice chromosomes. The information provided by fine mapping of the retroelements in the genetic linkage map may also be useful for gene tagging and molecular cloning.

Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential

“…In avian genomes, notable for their lack of SINEs, no association between SSRs and dispersed repeats is observed, and the overall frequency of SSRs is significantly lower than in the human genome, likely caused in part by the absence of the poly(A)-tailed SINEs whose middle and terminal sequences provide a source for SSR evolution in the human (Primmer et al 1997). Although the rice genome contains some putative SINEs (such as the pSINE-r family) (Mochizuki et al 1992) and numerous retrotransposons (Hirochika 1997;Wang et al 1999) these two classes of repetitive DNA were only rarely associated with SSRs in this study.…”

“…The avoidance of flanking sequences corresponding to known repetitive DNA has become a routine procedure during the development of microsatellite markers for mammalian genomes (Fondon et al 1998;Steen et al 1999) because positioning PCR primers in repetitive regions generates spurious or nonspecific products. In rice, little is known about the relationships, if any, between microsatellites and different classes of middle repetitive sequences, although several families of transposable elements as well as centromere-associated sequences have been identified in the rice genome (Bureau and Wessler 1994;Aragon-Alcaide et al 1996;Jiang et al 1996;Hirochika 1997;Wang et al 1999;Mao et al 2000).…”

Control of transposon activity by a histone H3K4 demethylase in rice

“…More than 40% of the rice genome consists of repetitive sequences or TEs (25)(26)(27), including 14% LTR retrotransposons and ∼1% non-LTR retrotransposons (28). Non-LTR retrotransposons are comprised of long interspersed elements (LINEs) and short interspersed elements (SINEs) (29)(30)(31).…”

SDG714, a Histone H3K9 Methyltransferase, Is Involved in Tos17 DNA Methylation and Transposition in Rice

“…The rice genome is 430 Mb in size, and >40% of the genome is composed of repetitive sequences or transposable elements (Hirochika et al, 1992;Wang et al, 1999;Goff et al, 2002). Based on the mechanism of transposition, the transposable elements are classified into two groups, DNA transposable elements (class II) and retrotransposons (class I).…”

“…Based on the mechanism of transposition, the transposable elements are classified into two groups, DNA transposable elements (class II) and retrotransposons (class I). The movement of a DNA transposon is primarily mediated through a cut-and-paste mechanism, whereas retrotransposons undergo mobilization through an RNA intermediate, resulting in an increase of copy number (Hirochika, 1997;Wang et al, 1999;Jiang et al, 2003). Tos17 is a copia-like retrotransposon, one of only a few retrotransposons that can mobilize under prolonged cell culture conditions (Hirochika et al, 1996).…”