Transposable elements: a key piece in the genomic evolution and adaptation of Myrtaceae species.

Abstract

BACKGROUND: Myrtaceae is a family of woody trees with over 5,800 species, representing the sixth most diverse plant family. It includes many economically important members distributed throughout East Asia, Oceania, and the Americas, including but not limited to Eucalyptus grandis and Syzygium aromaticum. Most available Myrtaceae genome assemblies are arranged in 11 chromosomes, and possess large variability in genome sizes, sometimes over triple the size. Although coding sequences add to this disparity, transposable elements (TEs) are the main contributors to genome size variation. RESULTS: In our research, we have characterized the landscape of TEs in 18 species of Myrtaceae. Our results showed that LTR Class I elements are the main contributors to genome size variations in Myrtaceae. Furthermore, specific lineages among the Gypsy and Copia superfamilies are linked to historical events of transposon activity amongst Myrtaceae tribes. Extracted climatic and distribution data were in correlation with TE profiles, indicating possible lineages more sensitive to climatic conditions. A gene ontology over-representation analysis revealed shared biological processes influenced by TEs, and exclusive ones linked to different environmental responses. Lastly, we identified high-identity sequences among many species, and performed phylogenies for horizontal transposable element transfer (HTT) events analysis. A positive HTT of a Copia/Ivana TE among Syzygieae and Myrteae tribes could affect the regulation of proximal microorganism defense response genes. CONCLUSIONS: Our findings suggest that TEs may influence the genetic diversity present in Myrtaceae, where TE lineages contribute asymmetrically to their genomic profiles. More importantly, specific lineages are correlated with climatic variables possibly by their influence on proximal genes, a balance between genetic variation and fitness influence. Lastly, the impact of TEs on microorganism defense response genes appears to be a key element in the adaptation process of Myrtaceae species.