An intact, but dormant LTR retrotransposon defines a moderately-sized family in white spruce (Picea glauca)

Within seed plants, the genomes of the conifer lineage are extraordinarily large and complex. While the evolutionary mechanisms driving this expansion are poorly understood, increasing evidence implicates retrotransposon activity as the driving force. We have isolated in targeted fashion and sequenced two independent white spruce genomic BAC clones for CYP701A24, involved in the biosynthesis of the phytohormone gibberellic acid. Sequence comparison showed little similarity between the two clones, one carrying the bona fide target CYP701A24 and the other an intronless fragment of a CYP701A24 pseudogene. In proximity of both CYP701A24 loci, we detected several signatures of the long terminal repeat (LTR) retrotransposon class. Sequence characterization identified one outstanding Ty3-gypsy class element, which was termed Picnicker1 for its size and degree of sequence conservation in the LTR. Representation of its homologous sequence in genomic amplicons and within the white spruce draft genome revealed that Picnicker1 is the founding member of a moderately sized family. Dating of the insertion event with the synonymous substitution rate applied to the nucleotide polymorphisms of the LTR suggested an age postdating major speciation in spruce. Independent support for an evolutionary recent incident was provided by an investigation of the genomic locus in a range of spruce species with increasing relatedness to white spruce, and in white spruce for a range of geographical origins. Transcript evidence revealed that related members of the family, but not Picnicker1 still flourish as part of the dynamic content in modern spruce genomes