Identification of helitron sequences in the coral genome and implications for host defense.

Abstract

Abstract Helitrons are mobile elements found in the genomes of numerous plant and animal species. Helitrons can mobilize flanking sequences when they transpose, and so have the potential to duplicate genes and remodel genomes. The stony coral Acropora has an expanded immune gene repertoire in comparison to the closely-related anemone species Nematostella, especially in the number of TLR and IL-1R genes. Mechanisms behind the expansion are not currently known. Although helitron sequences have been identified in Nematostella, no helitrons have been identified in Acropora. BLAST searches against the Acropora genome using Nematostella amino acid sequences as queries revealed seven candidate Acropora helitrons. Six of the seven Acropora candidates had large open reading frames in the forward direction. One candidate element was split between two adjacent reading frames. Conserved domain searches were performed within the open reading frames using the databases at NCBI. As expected, Helitron N-like and replicative protein A (RPA) domains were shared between Acropora and Nematostella elements. UPGMA trees were constructed using highly conserved regions, and one candidate Acropora element clustered more closely with the Nematostella reference helitron than with other Acropora sequences. Interestingly, P-loop domains were common to cnidarian helitrons and a subset of plant helitron reference sequences containing plant disease resistance gene motifs in regions overlapping with a nucleotide-binding domain critical for resistance gene function. Together, these studies will help to determine if helitrons played a role in the expansion of the Acropora immune gene repertoire.