Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats

Abstract

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

“…Interestingly, O. meridinolis did not group with any of the AA genome cluster. These results are consistent with the findings of evolutionary divergence study at PSTOL1 locus in wild, domesticated and weedy rice 63 but contradictory to the findings based on plastome analysis which shows O. longistaminata to be most diverged from AA-species 64 .…”

The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast

“…In addition to climatic conditions, some legumes prefer different light spectrums as shown by a study indicating that the red light significantly suppressed pod growth in soybean, but promoted the growth in cowpea [ 45 ]. A study with 22 chloroplast genomes from the genus Oryza that were grouped into shade-tolerant and sun-loving rice species showed a correlation between the positive selection of photosynthetic genes, e.g., rbcL , ndh , and psb , and the adaptation of rice species to different sunlight levels [ 13 ]. The positive selection of these genes was also observed in our Ka/Ks analysis, which included soybean and cowpea ( Table 2 ).…”

“…The chloroplast genome of Vigna radiata has been sequenced [ 7 , 10 ], where Lin et al, 2015 additionally used RNA-seq data to identify RNA editing events [ 10 ]. Many recent chloroplast genome studies focus their analysis on identifying positively selected genes, RNA editing events, and polycistronic transcription units [ 11 , 12 , 13 ]. The identification of the positively selected genes is important for evolutionary studies because these genes had a fixation of advantageous point mutations (positively selected sites) as an adaptation to the selective force (positive selection) from different ecological conditions [ 14 , 15 ].…”

“…The identification of the positively selected genes is important for evolutionary studies because these genes had a fixation of advantageous point mutations (positively selected sites) as an adaptation to the selective force (positive selection) from different ecological conditions [ 14 , 15 ]. The non-synonymous (Ka) and the synonymous (Ks) nucleotide substitution rates and the Ka/Ks ratio are commonly used to detect positive selection or adaptive evolution events [ 13 ]. For example, the adaptive evolution of chloroplast genes as identified by Ka/Ks ratios was reported to be responsible for the adaptation of rice species to diverse ecological habitats related to sunlight preferences [ 13 ].…”

“…The non-synonymous (Ka) and the synonymous (Ks) nucleotide substitution rates and the Ka/Ks ratio are commonly used to detect positive selection or adaptive evolution events [ 13 ]. For example, the adaptive evolution of chloroplast genes as identified by Ka/Ks ratios was reported to be responsible for the adaptation of rice species to diverse ecological habitats related to sunlight preferences [ 13 ]. Detailed sequences of genes and intergenic regions from the chloroplast genome are often used to study the phylogenetic relationship of plant species [ 16 , 17 ].…”