Abstract
BackgroundGenome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.Methodology/Principal Findings Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA.Conclusions/SignificanceMost of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.
Highlights
IntroductionGymnosperms (conifers, cycads, gnetophytes and ginkgo) have among the most complex and largest genomes of any living organisms
Gymnosperms have among the most complex and largest genomes of any living organisms
Gymny is related to Athila but dispersed in the genome Retrotransposon integration and divergence can introduce genetic polymorphisms that can be detected as randomly amplified polymorphic DNAs (RAPDs) [35]
Summary
Gymnosperms (conifers, cycads, gnetophytes and ginkgo) have among the most complex and largest genomes of any living organisms. Conifers belonging to the genus Pinus, are excellent subjects for dissecting processes involved in genome evolution for several reasons. In contrast to large angiosperm genomes (most prominently maize) where gene duplications, diverse chromosome numbers and genome size variation among related species indicate historical polyploidization complemented by periods of retrotransposon expansion [8,9], all extant members of the genus Pinus are diploid with 2n = 24 chromosomes. Periods of retrotransposon expansion and not polyploidy may be of primary importance in explaining genome size variation within Pinus. Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, the elements involved are poorly understood
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