Mapping to Reference: An Efficient Approach to Achieve Sufficient Consensus for Phylogenomic Study of Oryza Chloroplast Genome

Abstract

The chloroplast is one of the most important organelles in plants, it plays a significant role in following the heredity of the plant species over millions of years. To achieve chloroplast sequence there are many approaches, some of them easy like mapping, while others are time-consuming and need more computing resources. Here three approaches have been utilized Oryza sativa raw data as a model, to compare (multiple rounds of mapping to reference and Denovo) to find the fastest way to produce the most reliable consensus for phylogenomic studies, by comparing variations numbers and variation reduction percentages among all three pipelines (A, B, and C). It has been concluded that simple two rounds of mapping will be enough to construct trustworthy phylogeny.