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.
Highlights
The repetitive content of the genome, once considered to be “junk DNA”, is an essential component of genomic architecture and evolution
Characterizing repetitive content in genomes We determined that the repetitive content, characterized using Repeat Explorer (RE) [33]
Simple and low complexity repeats were found in high content. ribosomal DNA (rDNA) occupies approximately 1.7-2.5%, 0.9% and 0.1% in C. sativa, M. notabilis, and H. lupulus genomes respectively (Additional file 1: Table S2)
Summary
The repetitive content of the genome, once considered to be “junk DNA”, is an essential component of genomic architecture and evolution. Repetitive sequences occupy the majority of any typical eukaryotic genome, yet are poorly understood in many respects. The effect of this repetitive content has been under debate for decades [1]. Others think repetitive elements might play important roles in the host’s genome by altering a gene’s function [3], or by acting as raw material for new genes [4]. These ideas are not mutually exclusive, with repetitive sequences likely having both positive and negative effects in most genomes.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
