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

Abstract

Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with > 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers.

Two independent loss-of-function mutations in anthocyanidin synthase homeologous genes make sweet basil all green

“…About 65% of the expressed ObANS RNA encoded mutant alleles. We have also observed an expression of mutated genes in the phenylpropenes biosynthesis pathway (Gonda et al, 2020). Phenotypically, polyploids can “allow” themselves to express mutated genes more than diploids since they have gene redundancy, as in the case of the flower color of ‘Cardinal’.…”

“…LGs were set, and map distances were calculated based on the grouping tree with the regression mapping function. Homeologous LGs were determined considering the BUSCO analysis of Gonda et al . (2020) that defined homeologous scaffolds.…”

Dual transcriptional analysis of Peronospora belbahrii and Ocimum basilicum in susceptible interactions

“…Raw RNA-seq reads were filtered and cleaned using Trimmomatic (BOLGER et al 2014) to remove adapters and low-quality reads. Clean reads were mapped with STAR (DOBIN et al 2013) to the sweet basil genome (GONDA et al 2020). Transcript quantification and differential gene expression analysis were performed using Cufflinks (v2.2.1) software (ROBERTS et al 2011) combined with gene annotations.…”

“…Analysis of the genomic locations of these genes found that two pairs of the five genes are located in homeologous scaffolds based on common BUSCO (Benchmarking Universal Single-Copy Orthologs) genes (Supplementary File 6) analyzed by (GONDA et al 2020). However, XLOC_035244 possibly contains a point mutation, which results in a protein that is 79 amino acids shorter than XLOC_006768 at the C-terminus (Table 2).…”

“…Bioinformatic analysis predicted 413 genes in P. belbahrii that encode for secreted proteins (THINES et al 2020), which may be critical for pathogenesis. The genome of sweet basil 'Perrie', a Genovese-type cultivar, was recently sequenced and annotated (GONDA et al 2020). The genome size of this tetraploid is 2.13 Gbp.…”