Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice

Abstract

This paper describes a fluorescence in situ hybridization (FISH) analysis of three different repetitive sequence families, which were mapped to mitotic metaphase chromosomes and extended DNA fibers (EDFs) of the two subspecies of rice (OrYza sativa), indica and japonica (2n = 2x = 24). The repeat families studied were (1) the tandem repeat sequence A (TrsA), a functionally non-significant repeat; (2) the [TTTA-GGG]n telomere sequence, a non-transcribed, tandemly repeated but functionally significant repeat; and (3) the 5S ribosomal RNA (5S rDNA). FISH of the TrsA repeat to metaphase chromosomes of indica and japonica cultivars revealed clear signals at the distal ends of twelve and four chromosomes, respectively. As shown in a previous report, the 17S ribosomal RNA genes (17S rDNA) are located at the nucleolus organizers (NORs) on chromosomes 9 and 10 of the indica cultivar. However, the japonica rice lacked the rDNA signals on chromosome 10. The size of the 5S rDNA repeat block, which was mapped on the chromosome 11 of both cultivars, was 1.22 times larger in the indica than in the japonica genome. The telomeric repeat arrays at the distal ends of all chromosome arms were on average three times longer in the indica genome than in the japonica genome. Flow cytometric measurements revealed that the nuclear DNA content of indica rice is 9.7% higher than that of japonica rice. Our data suggest that different repetitive sequence families contribute significantly to the variation in genome size between indica and japonica rice, though to different extents. The increase or decrease in the copy number of several repetitive sequences examined here may indicate the existence of a directed change in genome size in rice. Possible reasons for this phenomenon of concurrent evolution of various repeat families are discussed.

Variation of the genome size estimate with environmental conditions in Drosophila melanogaster

“…It is becoming more and more evident, however, that genome size varies according to the population and even the individual concerned, and depends on various exogenous factors, the main effects of which seem to be the mobilization and increase in the copy number of transposable elements (2,7,32). Various correlations between genome size and latitude, altitude, temperature, light (9,12,13,33), developmental rate (5), etc., are well documented, especially across species.…”

Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions

“…D1453; Ohtsubo et al 1994) was positioned by FISH on the ends of the long arms of chromosomes 11L and 12L in japonica rice and on eight chromosomal ends in indica rice (Ohmido and Fukui 1997;Ohmido et al 2000Ohmido et al , 2001. Three telomereassociated sequences, GenBank accession nos.…”

“…In the human genome, subtelomeres vary in size from 8 kb up to 300 kb Der-Sarkissian et al 2002), whereas in plant genomes, such as tomato (Broun et al 1992;Zhong et al 1998), rice (Ohmido and Fukui 1997;Ohmido et al 2000Ohmido et al , 2001, and tomato (+) potato hybrids , such regions can measure up to 1,000 kb. The highly variable distribution of large duplicated subtelomeric segments are caused by homology-based, non-allelic (ectopic) recombination events between nonhomologous chromosomes Scherf et al 2001;Der-Sarkissian et al 2002).…”

“…Rice centromeres and flanking pericentromeric heterochromatin (Singh et al 1996a, b;Cheng et al 2001Cheng et al , 2002Feng et al 2002) and telomeres (Ohmido and Fukui 1997) have been well studied at the cytogenetic level. Fluorescence in situ hybridization (FISH) revealed that the Arabidopsis type (CCCTAAA) n telomere repeat sequence hybridized to all 24 chromosomal ends (Ohmido et al 2000(Ohmido et al , 2001. In that same study, the average size of a rice telomere was measured at 3.5 kb.…”

“…japonica) (Ohtsubo et al 1994;Ohmido and Fukui 1997;Cheng et al 2001). FISH analysis of extended DNA fibers of japonica rice revealed that TrsA was organized in two arrays of 82 kb and 241 kb each that were located adjacent to the telomere tandem arrays, on 6L and 12L, respectively (Ohmido et al 2000(Ohmido et al , 2001.…”