# Multi-Omics Approaches to Study Molecular Mechanisms in _Camanabis sativa_
## 3 Genomic and Transcriptomic Cannabis Profiles  
Initial attempts to assemble the complex cannabis genome relied on the use of short-read sequencing technologies, but only recently have third-generation long-read sequencing technologies, such as Single-Molecule Real-Time (SMRT) sequencing (PacBio) and Oxford Nanopore Technologies (MinION) [25], led to an improved contiguity of reference sequences and correctly assembled ambiguous, highly repeated regions [25; 62]. These advances resulted in the creation of four assemblies related to different cultivars: 'Purple Kush' ('PK', a drug type Cannabis), 'Finola' ('FN', a fiber type Cannabis), 'Jamaican Lion' ('JL'; a wild accession) and 'CBDRx' ('cs10'; with high CBD content) [27; 63]. Comparisons of the transcriptome of 'PK' with that of the hemp cultivar 'FN' revealed that many genes encoding proteins involved in cannabinoid pathways are more highly expressed in 'PK' than in 'FN'. Subsequently, these reference assemblies were annotated with full-length male and female mRNA sequencing to provide better information about isoforms complexity, genes and Y chromosome identification [25]. To date, the 'cs10' genome sequence assembly is considered to be the most complete and contiguous genome and is broadly used as the reference genome for cannabis [64]. The presence of copy number variations (CNVs) in cannabinoid synthases have been demonstrated in several cannabis genome studies [25; 63] while the relation between cannabinoid synthase CNVs and cannabinoid content is still not clear [19]. Furthermore, highly similar loci are not adequately differentiated in short read sequencing approaches [19; 65]. The availability of a sufficiently complete genome is crucial for the understanding of the cannabinoid pathways through a better knowledge of the underlying genes. Cannabi-noid biosynthesis was investigated at molecular level, and several genes involved in this pathway were identified [48]. Furthermore, it was found that each gene consists of a single exon, with THCA synthase (THCAS) and CBCA synthase (CBCAS) sharing over 90% homology at amino acid level and over 80% homology to CBDAS [62; 66]. The availability of these more complete genomic resources allowed the identification of sex chromosomes and of approximately 3500 gender-specific genes in the cannabis genome [25; 67]. THCA and CBDA were found to be mainly produced in the infloresances of female cannabis crops [24; 25]. Thus, detecting male and female plants at early growth stages can increase yield and help design more specific cannabis breeding programs. The association between THCA and CBDA synthase sequences and Quantitative Trait Loci (QTL) has been also reported [8; 38]. An early study, using bi-parental mapping populations coming from a cross between hemp and drug cannabis, identified QTL regulating biochemical traits. Results suggested that THCA and CBDA synthase sequences are associated to a single multiple linked QTL [38]. Another study used a set of over 20 highly informative single nucleotide polymorphisms (SNP) markers related to cannabinoid and terpenoid expression to assess phylogenetic relationship, population genetics, and correlation with cannabis metabolites, demonstrating the utility of this method for efficient genotyping activities [8]. Other quite recent studies have been carried out, based on Genome Wide Association Studies (GWAS) in order to investigate novel cannabis genetic variants responsible for cannabis complex traits. For instance, candidate cannabinoid pathway genes have been identified, focusing on the alkyl side chain group whose genetic basis are mostly unknown although is a critical feature behind health properties [68]. These findings confirmed a previously known locus involved in cannabinoid synthesis pathway and other loci associated to chemotype variability [62], revealing 22 variants in a \(\beta\)-keto acyl carrier protein (ACP) reductase (BKR).