High-quality assembly of sweet basil genome

Abstract

Sweet basil, sometimes called the King of Herbs, is well known for its culinary uses, especially in the Italian sauce 'Pesto'. It is also used in traditional medicine, as a source for essential oils and as an ornamental plant. So far, basil was bred by classical and traditional methods due to lack of a reference genome that will allow optimized application of the most up-to-date sequencing techniques. Here, we report on the first completion of the sweet basil genome of the cultivar 'Perrie', a fresh-cut Genovese-type basil, using several next generation sequencing platforms followed by genome assembly with NRGENE's DeNovoMAGIC assembly tool. We determined that the genome size of sweet basil is 2.13 Gbp and assembled it into 12,212 scaffolds. The highquality of the assembly is reflected in that more than 90% of the assembly size is composed of only 107 scaffolds. An independent analysis of single copy orthologues genes showed a 93% completeness which reveal also that 74% of them were duplicated, indicating that the sweet basil is a tetraploid organism. A reference genome of sweet basil will enable to develop precise molecular markers for various agricultural important traits such as disease resistance and tolerance to various environmental conditions. We will gain a better understanding of the underlying mechanisms of various metabolic processes such as aroma production and pigment accumulation. Finally, it will save time and money for basil breeders and scientists and ensure higher throughput and robustness in future studies.

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

“… 8 as well as the level of heterozygosity in the sequenced genomes. Dudai et al 23 report ‘Perrie’ as highly homozygous while our ‘Genovese’ sample was heterozygous. The ‘Genovese’ N50 contig length was slightly larger than the Dudai et al ‘Perrie’ assembly (48.30 − 45.71 kb, respectively), although the N50 scaffold size was substantially smaller (1.51 − 19.30 Mb) ( Supplementary Table S5 ).…”

“…Of the species assembled in this study, a previous assembly was reported for O. basilicum cultivar, ‘Perrie’ 23 while the present study assembled the cultivar ‘Genovese’. Both cultivars are tetraploid (2 n = 4 x = 48) yet flow cytometry estimates of haploid genome size differ; ‘Perrie’ was estimated at 1.59 Gb, 59 while our flow cytometry estimate of ‘Genovese’ was 2.34 Gb is in agreement with previous estimations 8 , 9 and estimated size using k -mer frequency as well as from the Supernova programme.…”

“… 3 In addition, for O. basilicum , transcriptomes were generated for cultivars ‘Tiguillo’ and ‘Red Rubin’ 21 as well as ‘CIM Saumya’, 22 and a genome assembly of the O. basilicum cultivar ‘Perrie’ has recently been reported although the actual sequence is not currently available. 23 There is a growing number of Lamiaceae species with assembled genomes (see Supplementary Dataset S1 ) that have enabled identification of genes involved in specialized metabolism and a broader understanding of genome organization with respect to specialized metabolism. 24 However, the genetic repertoire encoding chemical diversity within the culinary herbs remain largely unexplored.…”

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

“…Indeed, the analysis of the BUSCO gene-set in our genome was more complete, with less fragmented and missing genes. 15 , 16 We also found higher percentage of duplicated genes in the set (74% vs. 56%), suggesting a better capture of homeologous genes. Finally, of the annotated genes, 55,484 proteins were assigned to at least one GO process, function or cellular component ( Supplementary Fig.…”

“…This lag also hinders the development of advanced genome editing tools for basil, since it is challenging to overcome off-targeting and redundancy without a reference genome. In the project reported here, we followed-up on our previous effort 16 to close the-above described research and breeding gaps. To this end, the genome of the cultivar ‘Perrie’ was sequenced on Illumina platforms and assembled using NRGENE’s DeNovoMagic TM assembler.…”