Evolution of Genome Size and Complexity in Pinus

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.

The first insight into the Taxus genome via fosmid library construction and end sequencing

“…Periods of retrotransposon expansion and not polyploidy may partially explain the genome size variation within conifer. These expansions may accompany genomic or environmental stress, potentially establishing the heritable variation on which selection can act to form new species (Morse et al 2009). Some Taxusspecific retrotransposon-like sequences were detected in the present study, such as LTR/caulimoviru, LTR/foamy, LINE/R1, and LINE/Tad1, which were not detected in BAC clones of Pinus and Picea.…”

The Norway spruce genome sequence and conifer genome evolution

“…Previous examinations of small genomic subsets indicated that conifer genomes contain numerous pseudogenes 5,6,22,23 . The gene-like fraction of the P.abies 1.0 assembly was identified by alignment of RNA-Seq reads and de novo assembled transcripts (Supplementary Information 2.10).…”

“…However, despite their abundance and importance, our understanding of conifer genomes is limited. Most conifers have 12 (2n 5 24) chromosomes, probably reflecting the ancestral karyotype 4 , which are typically of similar size, each being roughly comparable to the size of the human genome, and containing high proportions of repetitive elements 5,6 . The gene space of conifer genomes has not been well characterized, although several reports have suggested that gene families in conifers may be larger than their angiosperm counterparts 7 and that conifer genomes contain numerous pseudogenes 8 .…”

Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L

“…Unfortunately, the candidate gene sequences from González-Martínez et al (2008) were not included in this study, thus validation of previous associations was not possible. In both studies, the SNPs represent a small proportion of the total variation in the loblolly pine genome, which is B24,000 MB (Ahuja and Neale, 2005;Morse et al, 2009). Thus, there is future opportunity to identify additional genes that influence D 13 C and growth traits.…”