Sequence variation in the gene encoding the 10-kDa prolamin in Oryza (Poaceae). I. Phylogenetic Implications

Abstract

Oryza L. (Poaceae) contains approximately 20 wild and two domesticated species and nine genomes. Major disagreements exist on its systematics and genome evolution. Sequence polymorphism in the gene that encodes the 10-kDa prolamin polypeptide (a seed storage protein) was used to determine phylogenetic relationships and evaluate current systematics for 19 Oryza species. This gene in Oryza is approximately 402-bp long, and includes a 72-bp signal peptide region. A strict consensus tree shows Oryza brachyantha (FF) as the most basal species, followed by a polytomy of three clades that can be delineated based on genome composition: (1) the GG clade: Oryza granulata and Oryza meyeriana, (2) the EE clade: Oryza australiensis, and (3) the ABCD clade: the remaining Oryza species. Two subclades within the ABCD clade emerge, one containing species with the AA genome, the other with components of the BC and D genomes. Members of the AA subclade form a polytomy and were delineated by a single 3-base deletion. The African species Oryza punctata (BB) and the South American-endemic CCDD genome species form a strong lineage, pointing to a close genetic affinity of O. punctata to the missing DD genome donor. The strong association between the CC and BBCC species implies convergence at the gene level. The study supports the following sectional units of Oryza: Section Oryza (Series sativae and officinaliae), Section australiensis, Section Granulata, Section Brachyantha.

Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA

“…There is inconsistency of topology in previous reports, monophyletic or paraphyletic (Wang et al, 1992;Aggarwal et al, 1999;Ge et al, 1999;Joshi et al, 2000;Nishikawa et al, 2005). The position of the FF genome varies greatly among studies, ranging from the most basal site of the genus to inside newly diverged species clusters (Wang et al, 1992;Ge et al, 1999;Joshi et al, 2000;Mullins and Hilu, 2002;Nishikawa et al, 2005). Wang et al (1992) reported EE genome species to be clustered with other O. officinalis complex species, but later studies reported that the EE genome branched before the diversification of AA, BB, CC and CCDD genome species (Ge et al, 1999;Zou et al, 2008).…”

“…Wang et al (1992) reported EE genome species to be clustered with other O. officinalis complex species, but later studies reported that the EE genome branched before the diversification of AA, BB, CC and CCDD genome species (Ge et al, 1999;Zou et al, 2008). Other studies could not resolve the evolutionary pattern of EE and its close species with statistical significance (Joshi et al, 2000;Mullins and Hilu, 2002;Nishikawa et al, 2005).…”

“…Recently, Zou et al (2008) reconstructed the phylogeny of diploid Oryza species using a large number of genes. But studies employing almost all members of the genus including allotetraploid species have given inconsistent results in terms of tree topology, and insufficient resolution (Wang et al, 1992;Aggarwal et al, 1999;Ge et al, 1999;Joshi et al, 2000;Mullins and Hilu, 2002;Nishikawa et al, 2005). These problems would be caused by differences in molecular markers and/or strains used, and limitations of the methods.…”

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification

“…Rice has all major TE types found in other plants, including retrotransposons, MITEs and other DNA elements (Bureau et al 1996;Mao et al 2000;Tarchini et al 2000;Mullins and Hilu 2002;Feschotte et al 2003;IRGSP 2005). Each type can be identified by its terminal sequences, its transposase and its target site duplication.…”

“…Oryza brachyantha, an FF genome-type grown mainly in dry regions of Central Africa, is evolutionarily distant to AA genome species (Mullins and Hilu 2002;Nishikawa et al 2005). O. brachyantha has the smallest genome within the Oryza genus, based on the c-value of nuclear DNA; it is~346-362 Mbp/1C compared to the~438 Mb/ 1C of cultivated rice -although actual genome size (~389 Mb) based on O. sativa sequence is smaller (Uozu et al 1997;IRGSP 2005;Ammiraju et al 2006).…”