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Insights from 295 diverse origin rice to elucidate chloroplast variation and evolution based on whole genome re-sequencing
Chloroplast (cp) DNA sequence data are a versatile tool for plant identification, barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized to infer evolutionary relationship of plant species. Although the overall structure of the chloroplast genome is generally well conserved, a number of mutations have been observed. Thus, documentation of chloroplast sequence variation has also been an valuable asset in plant population and evolutionary studies for over two decades. Recently, advance in chloroplast genome assembly from whole genome NGS data has become available. In the present study, chloroplast variations among 295 diverse origin accessions were detected based on Oryza rufipogon, which thought to be the progenitor of cultivated rice.. Variation calling was carried out using the whole genome re-sequencing data of those accessions along with the five rice reference cp genomes. Phylogenetic and evolution analysis of the six references and 295 accessions were performed using the whole reference genome sequence and the variation data, respectively. Also, nucleotide polymorphisms of 295 rice accessions were validated by using previously characterized 50 ecotypes. Differential SNP frequency across the rice cp genome suggests a regional dependent preferential high variation occurrence during the evolution of chloroplast
