Structural Genomics of Angiosperm Trees: Genome Duplications, Ploidy, and Repeat Sequences

Abstract

Angiosperm genomes frequently undergo polyploidy, which results in a genome doubling event, followed by genome rearrangement and organisation. Such whole genome duplication events often result in immediate speciation, contributing to the spectacular radiation of the angiosperm lineage, while also creating two cop-ies of each gene, which subsequently diverge, further fuelling species evolution. In addition to the pronounced role that polyploidy plays in shaping plant genomes, repetitive elements also serve to drive smaller scale patterns of duplication, rear-rangement and novel variation. The action of repetitive elements is a pivotal source of evolutionary novelty, creating novel structural rearrangements, modulating gene expression and driving epigenetic variation. Recent advances in sequencing technologies are revolutionising our ability to explore ever more genomes, enabling new insight into the pronounced role that whole genome and local patterns of duplication have played in shaping tree genomes, including the prevalent signature of genome duplication in the Populus trichocarpa genome and the striking prevalence of gene duplication in Eucalyptus grandis. Keywords Polyploidy • whole genome duplication • repeat • transposable element • genome assembly • evolution The availability of an ever-increasing number of sequenced plant genomes (Michael and Jackson 2013) has shown that the genomes of plants are far more dynamic than those of their animal counterparts (Hettiarachchi et al. 2014). Indeed, vertebrate genomes separated by hundreds of millions of years of evolution and divergence can be relatively well aligned, with conserved large-scale synteny (Smith et al. 2002; Hillier et al. 2004; Dehal and Boore 2005). Additionally, conserved non-coding DNA sequences (CNS, also referred to as conserved non-coding elements, CNE) can be identified across the entire vertebrate lineage (Woolfe et al. 2005; Lee et al.