The Cannabis Multi-Omics Draft Map Project

Abstract

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which "next generation" DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that posttranslational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources we have developed from proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. All data for this project is available to view or download at www.CannabisDraftMap.Org Proteomics is a science dedicated to the creation of comprehensive quantitative snapshots of all the proteins produced by an individual organism, tissue or cell. 1 The term was coined in the 1990s during the efforts to sequence the first complete human genomes. 2 While the technology was in place to complete the human genome draft in 2003, the first two drafts of the human proteome were not completed by teams led by Johns Hopkins and CIPSM researchers until 2014. These two separate and ambitious projects were the composite of thousands of hours of instrument run time utilizing the most sophisticated hardware available at that time. 3,4 Recent advances in mass spectrometry technology now permit the completion of proteome profiles in more practical time. Single celled organisms have been "fully" sequenced in less than an hour, and by use of multi-dimensional chromatography, relatively high coverage human proteomes have been completed in only a few days. 5-7 While much can be learned by sequencing DNA and RNA in a cell, quantifying and sequencing the proteome has distinct advantages as proteins perform physical and enzymatic activities in the cell and ar...

The First Publicly Available Annotated Genome for Cannabis plants

“…The generation of the EggNOG annotated protein FASTA and shotgun proteomics data was described in detail in our recent investigation. 1 The resources generated by the NCBI follow a well-established pipeline that has been extensively described in these publicly available resources. [2][3][4] Table 1 provides the web addresses for all data that will be described in this text.…”

A Single Nucleotide Polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated North American Cannabis

“…The Cannabis (2n = 2x = 20) draft genome has a haploid genomic sequence of over 876Mb – 1000Mb (Laverty et al, 2019; McKernan et al, 2020) and transcriptome of at least 30,000 genes (van Bakel et al, 2011, Jenkins and Orsburn, 2019a,b,c). The genome displays large amount of polymorphism with a single nucleotide polymorphism (SNP) present every one in a hundred to one in fifty base pairs (McKernan et al, 2020).…”

“…Given the recent release of the 10 chromosome map of the cannabis genome (Grassa, 2018; Laverty et al, 2019), metabolomic and proteomic insight (Jenkins and Orsburn, 2019a,b) as well as a fully annotated version of the cannabis genome resulting from the completion of the NCBI Cannabis sativa Annotation Release 100 (Jenkins and Orsburn, 2019c), we set out to characterise the functional basis of the SNPs used in the study. The previously designed targets developed using Cansat 3 (von Bakel et al, 2011) were subjected to a BLASTn search (Altschul et al, 1990) constrained to the taxa Cannabis using the NCBI online interface (https://blast.ncbi.nlm.nih.gov) accessed October 31, 2019.…”

Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

“…It also provides comprehensive genetic information [22], as studies showed that differences between fiber-and drug-type cannabis are at a genome-wide level and not necessarily limited to genes involved in THC production [5]. The recent release of the 10-chromosome map of the cannabis genome [23][24][25][26][27] may improve the understanding of the genetic architecture, identify a superior set of SNPs associated with interesting traits, and reduce future targeted genotyping costs by using fewer but more accurate SNPs [28].…”