Genome Sequencing of Micro-Tom, a Model Cultivar of Tomato (Solanum lycopersicum)

Micro-Tom is one of cultivar of tomato (Solanum lycopersicum), which is known as a major crop and model plant in Solanaceae. Micro-Tom has phenotypic traits such as dwarf, and substantial EMS-mutagenized lines have been reported. There are two Micro-Tom varieties, which are Micro-Tom S9 and Micro-Tom MM, that have been maintained independently in Japan and France. Among the close varieties or cultivars such as Micro-Tom S9, MM and Heinz 1706, a cultivar whose whole genome sequence has been determined (The Tomato Genome Consortium, 2012), polymorphisms such as SNPs, indels and structural variations have been reported (Kobayashi et al., 2014; Hirakawa et al., 2013; Asamizu et al., 2012). Although whole genome sequencing of Micro-Tom S9 had been reported in 2014 (Kobayashi et al.), the sequences were built based on mapping of Micro-Tom reads against Heinz genome sequences. Therefore, to reveal detailed genome structure of Micro-Tom, we have conducted de novo assembly of Micro-Tom S9 by adding Illumina MiSeq reads. We obtained the 69M paired-end reads and 269M mate-pair reads, which were estimated as 63-fold of the Micro-Tom genome. The reads were assembled by MaSuRCA-2.3.2, and BAC end sequences of Micro-Tom S9 were used for scaffolding by SSPACE v2.0, and finally 2,925 scaffolds were constructed. Total length of the scaffolds was 79.8 Mb, and N50 length was 4.57 Mb. Gene prediction onto the scaffolds was performed by BRAKER1 v1.9, and the genes were filtered based on the search results of BLAST against NCBI nr database and InterProScan. The number of the genes predicted on the draft genome sequence was estimated approximately 32,000, which was close to those of Heinz 1706 (34,700 genes). Here we present the progress of the genome comparisons among Micro-Tom S9, MM, and Heinz 1706.