Whole genome sequence (WGS) analysis for exploring plant relationships

Shotgun sequencing plant genomic DNA preparations generates large quantities of sequence data in a single run. Using the Illumina GAII, whole genome shot-gun sequence (WGS) data was generated for Oryza sativa cv Nipponbarre, and the rice wild relatives Oryza meridionalis and Oryza australiensis. Two other grass species were also sequenced, Potamophila parviflora, from the Oryzeae tribe and Microlaena stipoides from the subfamily Ehartoideae. The Illumina Genome Analyser generates short sequence reads of 36 -75 bp. These short reads are usually converted to contiguous DNA sequence data by either de novo assembly or by assembling the data using an existing genome sequence as a scaffold. We used both approaches to retrieve the whole chloroplast sequence of cultivated rice and related species from whole genome sequence data. Assembly and phylogenetic analysis of the sequence data will be discussed with an emphasis on construction of novel chloroplast genomes with and without comparison to a reference genome as a strategy for application in simple, cost-effective phylogenetic analysis, identification and barcoding of plants.