Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses

Sugarcane is an important crop worldwide for sugar and biofuel production. Modern sugarcane cultivars have large, highly complex, polyploid genomes, and like other grasses, have a significant transposable element (TE) content. Four sugarcane TE superfamilies, hAT, Mutator, Gypsy and Copia, were first described from an EST database and, with the availability of genomic sequence, further characterised and compared with TEs from other grasses. Here we summarise previous work and extend the knowledge of the structure, diversity, evolutionary history, age, transcriptional activity and genomic distribution of sugarcane TEs. We also compare and contrast sugarcane TEs with homologous sequences in rice and sorghum, as well as analyse the age and genomic distribution of sugarcane TEs with related lineages from sorghum and rice. Finally, we discuss the importance of defining sugarcane TE lineages for understanding the contribution of ancestral genomes to modern cultivars, for genome sequencing and annotation and in applied genetics.