Annotation Pipeline for the Wheat Chromosome 6B Sequencing Project

We present an annotation pipeline for the Japanese Wheat Chromosome 6B Sequencing Project. As a part of the International Wheat Genome Sequencing Consortium (IWGSC, http://www.wheatgenome.org/), the Japanese team is responsible for sequencing bread wheat chromosome 6B (cv. Chinese Spring). Our pipeline was developed to annotate all the assembled sequences generated by next-generation sequencing technologies. The primary gene structures are determined by mapping wheat full-length cDNAs as well as other cDNA sequences derived from monocot species. Since gene structures inferred from EST mapping are generally truncated, an ab initio gene prediction program, AUGUSTUS, is used so that the complete structures can be determined. About 80 % of the wheat genome is composed of repetitive elements. Therefore, to construct a repeat library of newly-detected consensus sequences, we adopted a de novo repeat family identification program, RepeatModeler, for our assembled sequences. With this new repeat library and a public library, TREP, we mask the repetitive elements using CENSOR. Candidates of functional non-coding RNA genes, such as miRNA, tRNA and rRNA, are also predicted. For miRNAs prediction, a homology-based analysis pipeline, which uses blastn and mFold with the miRBase data as query sequences, was created. Here we report application of our pipeline to 192 BAC clone sequence datasets generated by 454 GS-FLX Titanium.