Chloroplast Genome Assembly And Analysis Based On High-throughput Sequencing Of Mixed DNA Samples

Chloroplast DNA sequences provide a basic source of transformation and phylogenetic studies, however, there are only269complete chloroplast genome published among Viridiplantae till December25th,2012, which prevents chloroplast genomics from moving forward. Traditional methods obtaining complete genome sequences need to extract and purify chloroplast DNA firstly, which was troublesome, time consuming and difficult. As high-throughput sequencing technology advances, more and more complete genomes are sequenced.Based on early studies, this study had optimized a simple and rapid method for chloroplast genome extraction. For chloroplast genomes are highly conserved, we managed to obtain complete sequences using short reads among whole genome sequencing by Illumina HiSeq2000, through de novo assembly and gap closer based on pair-ends and site of sequences.The major results are as follows:1.Bases on the whole genome sequence of Oiyza rufipogon (Dongxiang), we assembled4scaffolds and the coverage to reference was100%;2.Bases on the whole genome sequence of Glycine soja (Lanxi1), Glycine gracilis (Yongkang1), we assembled5,9scaffolds and the coverage to reference was100%,97%respectively;3.Bases on the whole genome sequence of Echinochloa oryzicola (STB03) we assembled103scaffolds and the coverage to reference was76%;4.We chose the results of chloroplast type and the SSRs diversity of soybean to test and verified the accuracy of the results of Lanxi1, which showed the same as reported previously.Our experiments provided a new strategy for obtaining chloroplast genomes sequences, but had certain limitations.5.The domestication results of chloroplast genomes data represent:japonica rice was developed from ordinary rice in china; ordinary rice in Australia had close relatives to Oryza rufipogon in south Australia; Glycine gracilis was probably derived from Glycine soja and cultivation soybean; Although Echinochloa oryzicola and Oryza rufipogon were similar in morphology, Echinochloa oryzicola was more closer with maize in the aspect of evolution.