The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species.
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 ofO. minutawith otherOryzaspecies 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 theO.minutacp genome. Comparison of the completeO. minutacp genome with another elevenOryzaspecies 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 andmatKgene showed same topologies and O.minutaforms a single clade with parentalO. punctata. Thus, the completeO.minutacp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Sajjad
S
Asaf
School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea; Department of Agriculture, Abdul Wali Khan University MardanMardan, Pakistan.
Muhammad
M
Waqas
Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa Nizwa, Oman.
Abdul L
AL
Khan
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Muhammad A
MA
Khan
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Sang-Mo
SM
Kang
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Qari M
QM
Imran
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Raheem
R
Shahzad
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Saqib
S
Bilal
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
Byung-Wook
BW
Yun
School of Applied Biosciences, Kyungpook National University Daegu, South Korea.
In-Jung
IJ
Lee
SSRs; codon usage; cp genome; phylogeny; repeat analysis; sequence divergence; wild rice (Oryza minuta)