Rice genome organization: the centromere and genome interactions

Abstract

Over the last decade, many varied resources have become available for genome studies in rice. These resources include over 4000 DNA markers, several bacterial artificial chromosome (BAC) libraries, P-1 derived artificial chromosome (PAC) libraries and yeast artificial chromosome (YAC) libraries (genomic DNA clones, filters and end-sequences), retrotransposon tagged lines, and many chemical and irradiated mutant lines. Based on these, high-density genetic maps, cereal comparative maps, YAC and BAC physical maps, and quantitative trait loci (QTL) maps have been constructed, and 93 % of the genome has also been sequenced. These data have revealed key features of the genetic and physical structure of the rice genome and of the evolution of cereal chromosomes. This Botanical Briefing examines aspects of how the rice genome is organized structurally, functionally and evolutionarily. Emphasis is placed on the rice centromere, which is composed of long arrays of centromere-specific repetitive sequences. Differences and similarities amongst various cereal centromeres are detailed. These indicate essential features of centromere function. Another view of various kinds of interactive relationships within and between genomes, which could play crucial roles in genome organization and evolution, is also introduced. Constructed genetic and physical maps indicate duplication of chromosomal segments and spatial association between specific chromosome regions. A genome-wide survey of interactive genetic loci has identified various reproductive barriers that may drive speciation of the rice genome. The significance of these findings in genome organization and evolution is discussed.

Fig. 1. Schematic illustration of centromere structure for animal and plant species. All centromeres have short tandem repeats (approx. 170 bp unit length) of different, but extensive, length, and transposon‐like moderately repeated sequences surrounding the tandem repeat sequences. Orange and green blocks represent short tandem repeat arrays and other colour blocks are moderately repetitive sequences. Diagrams are for Schizosaccharomyces pombe, Drosophila melanogaster, Homo sapiens, Arabidopsis thaliana and Zea mays.

Fig. 2. Distribution of centromere‐specific repetitive sequences of rice on one of the three YAC/BAC contigs of CEN5 that spans more than 630 kb. Numbers of copies were calculated from both strands and expressed in arbitrary units. RCS2 short tandem repeat blocks were observed only on this contig. Other retrotransposon‐related sequences of RIRE3, RIRE8 and RIRE7 included the RCE1 sequence clustered around the RCS2 blocks but were scattered on two other contigs (modified from Nonomura and Kurata, 2001).