Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

Abstract

Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the four species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all four species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.

The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding

“…Then, the contigs were assembled by the DeNovoMagic assembler, and the final assembly consisted of 12,212 scaffolds with a total genome size of ∼2.13 Gbp, and less than 1.3% gaps ( Table 1 ). The genome size is in good agreement with that of Bornowski et al 15 who found a genome size of 2.07 Gbp. The N50 scaffold size was approximately 19 Mbp, and the N90 scaffold size was approximately 5.8 Mbp.…”

“…Long-terminal repeats (LTRs) were the most commonly found types (48% of the genome), and of those, copia-like and gypsy were the most prevalent ( Table 2 ). These values are higher than those reported by Bornowski et al 15 who found 67% repetitive elements and 37% LTR elements.…”

“…Since 2 n = 48 for O. basilicum , 6 the N90 #scaffold value suggests that the size of some of the scaffolds is almost that of a complete chromosome, thereby indicating the high quality of the assembly. Bornowski et al 15 reported an N50 of ∼ 1.5 Mbp with > 17,000 scaffolds greater than 10 Kbp. The apparent differences may be attributed to all/any of the three following reasons: (i) in this study, we used the highly homozygous cultivar, ‘Perrie’; (ii) the coverage of 121× used in this study is almost twice the 65× used by Bornowski et al 15 ; and (iii) the assembler used by us has previously been shown to produce highly contiguous genomes of multiple polyploid organisms.…”

“…Bornowski et al 15 reported an N50 of ∼ 1.5 Mbp with > 17,000 scaffolds greater than 10 Kbp. The apparent differences may be attributed to all/any of the three following reasons: (i) in this study, we used the highly homozygous cultivar, ‘Perrie’; (ii) the coverage of 121× used in this study is almost twice the 65× used by Bornowski et al 15 ; and (iii) the assembler used by us has previously been shown to produce highly contiguous genomes of multiple polyploid organisms. 20 , 37 , 38 Overall, the draft genome presented here provides a more contiguous version of the sweet basil genome for the use of the scientific community at large.…”

“…For O. sanctum , 2 n has been reported to be 16, 32, 36 and 72. 11 , 13 , 14 A major advance was recently achieved with the publication of a draft genome for the home garden basil cultivar ‘Genovese’ by Bornowski et al 15 They assembled 2.07 Gbp in > 17 thousand scaffolds (greater than 10 Kbp) with an N50 of ∼ 1.6 Mbp.…”