Diversity and evolution of the repetitive genomic content in Cannabis sativa

Abstract

BackgroundThe repetitive content of the genome, once considered to be “junk DNA”, is in fact an essential component of genomic architecture and evolution. In this study, we used the genomes of three varieties of Cannabis sativa, three varieties of Humulus lupulus and one genotype of Morus notabilis to explore their repetitive content using a graph-based clustering method, designed to explore and compare repeat content in genomes that have not been fully assembled.ResultsThe repetitive content in the C. sativa genome is mainly composed of the retrotransposons LTR/Copia and LTR/Gypsy (14% and 14.8%, respectively), ribosomal DNA (2%), and low-complexity sequences (29%). We observed a recent copy number expansion in some transposable element families. Simple repeats and low complexity regions of the genome show higher intra and inter species variation.ConclusionsAs with other sequenced genomes, the repetitive content of C. sativa’s genome exhibits a wide range of evolutionary patterns. Some repeat types have patterns of diversity consistent with expansions followed by losses in copy number, while others may have expanded more slowly and reached a steady state. Still, other repetitive sequences, particularly ribosomal DNA (rDNA), show signs of concerted evolution playing a major role in homogenizing sequence variation.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4494-3) contains supplementary material, which is available to authorized users.

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

“…The genome of Humulus Jupulus is twice as large as Humulus japonicas, although minimal information is known about H. japonicus. Our finding suggests that hop and C. sativa contain a similar percentage of repeat content, as C. sativa is ∼73% repetitive [42]. The similar repeat percentage between hop and C. sativa supports the hypothesis that hop genome expansion is a consequence of WGD followed by a return to a diploid state through rearrangement and gene loss [57, 58], rather than LTR-driven expansion observed in other plants [59].…”

“…Lupulus and var. cordifolius [42]. Our long-read assembly has allowed for a more-accurate estimation of repeat content, suggesting that hop is 78% repetitive, comparable to maize (Figure 2a,b).…”

“…An expanded assembly capturing regions beyond gene space will also enable future work on enhancers and regulatory DNA that were obscured due to fragmentation. Going forward, a chromosome-level assembly will provide a foundation for investigating the occurrence of WGD in hop [42], and to understand how duplication, repeat-expansion, and conserved synteny have driven biosynthesis and disease resistance in hop.…”

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

“…Copy number variation (CNV) in cannabinoid synthase genes has been reported previously (van Bakel et al 2011; McKernan 2015; Weiblen et al 2015; Pisupati et al 2018; Vergara 2019). These studies were conducted with fragmented references or assays targeting specific genes.…”

“…We further classified these variants to identify highly damaging mutations in protein coding regions of the genome. Additionally, these whole genome sequence data were utilized to assess copy number variation (CNV) in critical genes in the terpene synthase pathway, cannabinoid synthase pathway and the pathogen response pathway (Pisupati et al 2018). This refined map of protein coding variants and copy number variants can facilitate directed breeding efforts for desired chemotypes, pathogen resistance and a better understanding of rare cannabinoid synthesis (Citti 2019).…”