Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

Abstract

Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.

Figure 1. Gene map of O. glaberrima chloroplast genome.

The different types of genes are colour coded. Genes shown inside are transcribed clockwise while those on the outside are transcribed anticlockwise. The inner circle represents the two inverted repeats (IRA and IRB) which are separated by the short single copy (SSC) and the long single copy (LSC).

Figure 2. Bootstrapping consensus and maximum parsimony tree showing phylogenetic relationships among Oryza AA genome species conducted using whole chloroplast sequences.

O. officinalis acted as the out-group. The same topology was obtained from Neighbour joining and maximum likelihood criteria. Indicated accession numbers are GenBank unique identifiers. The same topology was obtained when one of the inverted repeat regions was excluded. Deleting the indels resulted in a poorly resolved and inconsistent phylogeny.

Figure 3. Phylogenetic tree showing relationships among Oryza AA genome species based on whole chloroplast sequences.

The divergence dates for the various labelled nodes were calculated using strict and relaxed clocks and are shown in Table 2. Divergence between Triticum aestivum and Zea mays was used as the calibration point while O. officinalis acted as the out-group. The tree is not drawn to scale.