A Case Study from Reseq to Refseq-Two High-Quality Reference Genome Sequences for indica Rice

Over the past 30 years we have performed many fundamental studies on two indica (one of two Asian cultivated rice subspecies) varieties Zhenshan 97 (ZS97) and Minghui 63 (MH63) which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. However, lacking of their high-quality reference genome sequences became an obstruction to answer more biological questions, especially for better understanding of the biological basis of heterosis. We tried to use Illumina high-throughput technology to sequence ZS97 and MH63 genomes (ReSeq), but failed to assemble them accurately. Hence, we conducted map-based sequencing of ZS97 and MH63 using the most advanced PacBio sequencing technologies. We produced over 108 (ZS97) and 174 (MH63) Gb of PacBio raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of Illumina paired-end whole-genome shotgun sequence data. The genome sequences (RefSeqs) were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. The two reference-quality genomes for the indica subspecies of rice are public available (GenBank accession numbers LNNJ00000000 and LNNK00000000). We are keeping improving the two RefSeqs and the latest results will be discussed in detail.