Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization

Abstract

The genus Oryza to which cultivated rice belongs has 24 species (2n = 24 or 48), representing seven genomes (AA, BB, CC, EE, FF, BBCC and CCDD). The genomic constitution of five of these species is unknown. These five species have been grouped into two species complexes, the tetraploid ridleyi complex (O. ridleyi, O. longiglumis) and the diploid meyeriana complex (O. granulata, O. meyeriana, O. indandamanica). To evaluate the genomic structure of these species in terms of divergence at the molecular level vis-a-vis other known genomes of Oryza, we used the total genomic DNA hybridization approach. Total genomic DNA (after restriction digestion) of 79 accessions of 23 Oryza species, 6 related genera, 5 outgroup taxa (2 monocots, 3 dicots) and 6 F1s and BC1s derived from crosses of O. sativa with wild species were hybridized individually with 32P-labeled total genomic DNA from 12 Oryza species: O. ridleyi, O. longiglumis, O. granulata, O. meyeriana, O. brachyantha, O. punctata, O. officinalis, O. eichingeri, O. alta, O. latifolia, O. australiensis, and O. sativa. The labeled genomic DNAs representing the ridleyi and meyeriana complexes cross-hybridized best to all the accessions of their respective species, less to those representing other genomes of Oryza and related genera, and least to outgroup taxa. In general, the hybridization differential measured in terms of signal intensities was >50-fold under conditions that permit detection of 70-75% homologous sequences, both in the presence and in the absence of O. sativa DNA as competitor. In contrast, when total DNAs representing other Oryza genomes were used as probes, species of the O. ridleyi and O. meyeriana complexes did not show any significant cross-hybridization (<5%). These results demonstrate that the genome(s) of both of these complexes are highly diverged and distinct from all other known genomes of Oryza. We, therefore, propose new genomic designations for these two species complexes: GG for the diploid O. meyeriana complex and HHJJ for the allotetraploid O. ridleyi complex. The results also suggest that the uniqueness of these genomes is not restricted to species-specific highly repetitive DNA sequences, but also applies to dispersed sequences present in single or low to moderate copy numbers. Furthermore these appear to share relatively more genome-specific repeat sequences between themselves than with other genomes of rice. The study also demonstrates the potential of total genomic DNA hybridization as a simple but powerful tool, complementary to existing approaches, for ascertaining the genomic makeup of an organism.

Cytogenetic comparisons between A and G genomes in Oryza using genomic in situ hybridization

“…Obviously, the increase in genome size of O. meyeriana was mainly due to the amplification of repetitive sequences. This result is consistent with the conclusion reported by Aggarwal et al [2], who demonstrated that the uniqueness of the G genome is due to the species-specific highly repetitive DNA sequences by using total genomic hybridization. Furthermore, because the whole chromosomal regions of O. meyeriana were evenly enhanced with DAPI stain (Figure 1C), our results proved that the chromosomes of O. meyeriana had been extended and evenly enhanced with repetitive sequences during the genome evolution.…”

“…This result clearly showed considerable divergence of the middle to highly repetitive DNA sequences and confirmed the wide genetic differences between the two species. These observations are in agreement with the results that O. meyeriana is considered as the most distinct species from those with an A genome and occupies the most basal position in the phylogeny of the genus [2,3]. The quantity of repetitive sequence is the main factor that determines the genome size of similar ploidy [33,34].…”

“…The genus Oryza is composed of two cultivated and more than 20 wild species, and 10 genome sets have been identified including the diploids and tetraploids [1][2][3]. Wild rice species are extremely valuable gene resources for the genetic improvement of cultivated rice and for the study of genomics [4].…”

“…meyeriana is a diploid wild rice species with G genome [2] and distributes in the tropics and subtropics of South and Southeast Asian countries [18]. It is one of three native wild rice species in China growing in the southern Yunnan Province and the southwestern Hainan Province [19,20].…”

“…A variety of beneficial traits, such as disease and pest resistances, and tolerances to drought and shade stress, have been found in O. meyeriana [18,21]. Efforts have been devoted to understanding the genomic composition [2] and genetic variation [3,19,20] of O. meyeriana. However, the cytological features of O. meyeriana and the genomic relationship between A and G genomes have not been thoroughly investigated.…”