Building a Reference Genome for Indica Rice

Recent advances in PacBio sequencing technology have provided a cost efficient way to build reference quality genomes for plants. Rice has two subspecies, japonica and indica. Although there exists a high quality reference genome for japonica rice for many years, there is a need for a reference genome for indica rice, in various applications, such as SNP or gene discovery. We have sequenced a Chinese indica variety, R498, by PacBio technology to sequencing depth of 110x. The preliminary assembled contig length is about 1.1Mb, which is far shorter than that of several other genomes sequenced by PacBio. To connect these contigs, we sequenced a BAC library of 30k clones and used individually assembled BAC clone to connect those contigs. The connected contigs are further assembled onto 12 chromosomes using a genetic map derived from a RIL population of 400 lines.