Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice (<i>Oryza</i> spp.)
Xiyu Tan,
Guixiang Peng,
Sajid Muhammad,
Sidra Kaleem,
Mehmood Jan,
Raheel Munir,
Xiaoyuan Chen,
Arif Ali Khattak,
Abid Ali Abbas,
Yihang Chen,
Xiaolin Wang,
Muhammad Afzal,
Zhiyuan Tan
Affiliations
Xiyu Tan
College of Life Science, South China Agricultural University, Guangzhou 510642, China
Guixiang Peng
College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
Sajid Muhammad
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310023, China
Sidra Kaleem
Riphah Institute of Pharmaceutical Sciences, Islamabad 44600, Pakistan
Mehmood Jan
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Raheel Munir
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310023, China
Xiaoyuan Chen
Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
Arif Ali Khattak
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Abid Ali Abbas
College of Natural Resources and Environment, Zhejiang University, Hangzhou 310023, China
Yihang Chen
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Xiaolin Wang
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Muhammad Afzal
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Zhiyuan Tan
College of Agriculture, South China Agricultural University, Guangzhou 510642, China
Tandemly organized rRNA genes are a typical example of a multigene family, where individual members evolve co-ordinately within—but independently between—species due to gene conversion and unequal crossing over. More frequently, in eukaryotic species with an interspecies hybrid origin, expression of unhomogenized rRNA genes from one progenitor is epigenetically silenced because of nucleolus dominance, and distinct rRNA genes may lose functionality and evolve faster. Interestingly, we obtained unusual ribosomal gene sequences from Oryza species that showed great diversity and did not appear in the present rice genomic sequence. The diversity of rDNA sequences indicated that the homogenization in rice is incomplete and explains the introgression of distinct rRNA gene families into ancestral rice genomes before speciation and continent separation. The divergent large subunit (LSU) ribosomal genes are expressed, some of them differentially, depending on the N fertilization of plants. Detection of differential transcripts of the rRNA genes suggested that rRNA gene families are not functionally equivalent. Phylogenetic analysis assigned Oryza species branching order to monocots, and monocot lineages probably have the same ecological origin by molecular clock calculation. Therefore, our results suggested that the geographical distances of continent-separation cause barriers to the gene flow and homogenization among Oryza species which requires further explanation.
