The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species

Abstract

Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O. minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete O. minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

Keywords: SSRs; codon usage; cp genome; phylogeny; repeat analysis; sequence divergence; wild rice (Oryza minuta).

Figure 1

Gene map of the O. minuta chloroplast genome. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Genes belonging to different functional groups are color coded. The darker gray color in the inner circle corresponds to the GC content, and the lighter gray color corresponds to the AT content.

Figure 2

Analysis of repeated sequences in twelve Oryza chloroplast genomes. (A) Total of three repeat types; (B) frequency of the palindromic repeat by length; (C) frequency of the tandem repeat by length; (D) frequency of forward repeat by length.

Figure 3

Analysis of simple sequence repeats (SSRs) in twelve Oryza chloroplast genomes. (A) Number of different SSR types detected in twelve genomes; (B) frequency of identified SSR motifs in different repeat class types; (C) frequency of identified SSRs in coding regions; (D) frequency of identified SSRs in LSC, SSC and IR regions.

Figure 4

Alignment of twelve chloroplast genome sequences. VISTA-based identity plot showing sequence identity among twelve Oryza species using O. minuta as a reference. The thick black line shows the inverted repeats (IRs) in the chloroplast genomes.

Figure 5

Pairwise sequence distances of Oryza minuta genes with O. australiensis, O. nivara, O. rufipogon, O. sativa L. ssp. indica, O. sativa L. ssp. japonica, O. barthii, O. glumipatula, O. longistaminata, O. meridionalis, O. officinalis, and O. punctata.

Figure 6

Comparison of border distances between adjacent genes and junctions of LSC, SSC, and two IR regions among chloroplast genomes of twelve Oryza species. Boxes above or below the main line indicate the adjacent border genes. The figure is not to scale with regard to sequence length and only shows relative changes at or near IR/SC borders.

Figure 7

Phylogenetic trees were constructed for 14 species from the rice tribe using different methods, and two Bayesian trees are shown for data sets of the entire genome sequence and 65 shared genes. (A) The entire genome sequence data set (B). The data set of 65 shared genes. Each data set was used with four different methods, Bayesian inference (BI), maximum parsimony (MP), maximum likelihood (ML) and neighbor-joining (NJ). Numbers above the branches are the posterior probabilities of BI and bootstrap values of MP, ML, and NJ, respectively. Stars represent positions for O. minuta (KU179220) in the two trees.