A genome analysis for closely-related rice species using an automatic read annotation pipeline for the Next Generation Sequencing data

Abstract

The DNA Data Bank of Japan has been developing a high-throughput read annotation pipeline for the next generation sequencing data. As an example of the annotation pipeline, we report preliminary analysis of genomic variation about two accessions of Oryza longistaminata by a next generation sequencing technology, sequencing by synthesis (illumina Solexa, illumina Inc., San Diego, CA). At the sequencing, approximately 12 mega reads were generated with the paired-end design, where the read length was 75 bp. The generated reads were aligned to O. sativa (Nipponbare) reference genome by using the MAQ program (Li et al., Genome Res, 2008). The results showed that genome coverage for O.longistaminata against Nipponbare was around 40% and the maximum error rate by read position was 2%. Further, we attempted de novo assembly and SNP detection in the preliminary analysis.