Evolution of genome size and complexity in Pinus

Abstract

Background: Genome 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/significance: Most 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.

Figure 1. Organization of the RLG_Gymny_EU912388-1 retrotransposon.

Percent G+C is shown above the Gymny schematic. Numbered ORFs are in gray with vertical lines indicating stop codons, putative 5′LTR as hatched box, PR protease, RT reverse transcriptase, INT integrase. ESTs, GSSs, and 454 reads are indicated as are the B8_650 marker, and the Southern probes Fr1075 and Fr1035.

Figure 2. RLG_Gymny_EU912388-1 is related to Arabidopsis Athila-like retrotransposons.

Relatedness tree generated from alignment of RT sequences in Figure S1 and the RT domain from the Arabidopsis Ta1-3 Copia-like retrotransposon (Accession number X13291; [38]). Bootstrap percent values based on 10,000 replications.

Figure 3. FISH showing the physical distribution of Gymny in somatic chromosome spread of Pinus taeda.

RLG_Gymny_EU912388-1 probes Fr1035 and Fr1075 were detected with Cy3 streptavidin (red) and 18S–28S rDNA was detected with FITC (green). Inset shows FISH to interphase nucleus.

Figure 4. The same region of three identical BAC macroarrays hybridized with (A) probe P1; (B) probe P2; and (C) probe P3.

Clones are spotted in duplicate so positive signal is a closely situated pair of spots. BACs within circles, squares, diamonds and ovals show differential hybridization among probes. While most symbols highlight a single BAC (i.e. a pair of spots), the oval highlights two BACs that hybridized to all three overgo probes.

Figure 5. Southern blot analyses of selected Pinus species.

The location of probes Fr1035 and Fr1075 in RLG_Gymny_EU912388-1 are indicated in Figure 1. (A, B) filters hybridized with Fr1075 probe; (C, D) filters hybridized with Fr1035 probe; (A, C) digested with HindIII; (B, D) digested with HaeIII; (E) representative HindIII digested DNA stained with ethidium bromide. Lanes (1) Pinus glabra, (2) P. taeda, (3) P. elliottii, (4) P. radiata, (5) P. echinata, (6) P. palustris, (7) P. virginiana, (8) P. pinea, (9) P. strobus.

Figure 6. Monophyletic lineages within the genus Pinus, with hypothesized time frame for amplification or introduction of Gymny elements into the subgenus Pinus lineage relative to IFG7 and TPE1.

The tree shown is derived from the analyses performed by Willyard et al. where the dates for the nodes were selected to show the maximum possible range of values using either wood or leaf fossil calibrations, and either nuclear DNA or chloroplast DNA markers.