Correlated evolution of LTR retrotransposons and genome size in the genus eleocharis

<p>Abstract</p> <p>Background</p> <p>Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus <it>Eleocharis </it>(<it>Cyperaceae</it>), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-<it>copia </it>and Ty3-<it>gypsy </it>in relation to changes in both genome size and karyotype in <it>Eleocharis</it>. We also examined how this relationship is reflected in the phylogeny of <it>Eleocharis</it>.</p> <p>Results</p> <p>Using flow cytometry, we measured the genome sizes of members of the genus <it>Eleocharis </it>(Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in <it>Eleocharis</it>. We analyzed PCR-amplified sequences of various <it>reverse transcriptases </it>of the LTR retrotransposons Ty1-<it>copia </it>and Ty3-<it>gypsy </it>(762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-<it>copia </it>and Ty3-<it>gypsy </it>within the genomes of the analyzed species. We detected an increasing density of Ty1-<it>copia </it>elements in evolutionarily younger <it>Eleocharis </it>species and found a positive correlation between Ty1-<it>copia </it>densities and C_/n-values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-<it>copia </it>sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-<it>copia</it>. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later-diverging <it>Eleocharis </it>species.</p> <p>Conclusions</p> <p>Using several different approaches, we were able to distinguish between the roles of LTR retrotransposons, polyploidy and agmatoploidy/symploidy in shaping <it>Eleocharis </it>genomes and karyotypes. Our results confirm the occurrence of both polyploidy and agmatoploidy/symploidy in <it>Eleocharis</it>. Additionally, we introduce a new player in the process of genome evolution in holokinetic plants: LTR retrotransposons.</p

Evidence for Centromere Drive in the Holocentric Chromosomes of Caenorhabditis

In monocentric organisms with asymmetric meiosis, the kinetochore proteins, such as CENH3 and CENP-C, evolve adaptively to counterbalance the deleterious effects of centromere drive, which is caused by the expansion of centromeric satellite repeats. The selection regimes that act on CENH3 and CENP-C genes have not been analyzed in organisms with holocentric chromosomes, although holocentrism is speculated to have evolved to suppress centromere drive. We tested both CENH3 and CENP-C for positive selection in several species of the holocentric genus Caenorhabditis using the maximum likelihood approach and sliding-window analysis. Although CENP-C did not show any signs of positive selection, positive selection has been detected in the case of CENH3. These results support the hypothesis that centromere drive occurs in Nematoda, at least in the telokinetic meiosis of Caenorhabditis

Data from: Holokinetic drive: centromere drive in chromosomes without centromeres

Similar to how the model of centromere drive explains the size and complexity of centromeres in monocentrics (organisms with localized centromeres), our model of holokinetic drive is consistent with the divergent evolution of chromosomal size and number in holocentrics (organisms with non-localized centromeres) exhibiting holokinetic meiosis (holokinetics). Holokinetic drive is proposed to facilitate chromosomal fission and/or repetitive DNA removal (or any segmental deletion) when smaller homologous chromosomes are preferentially inherited or chromosomal fusion and/or repetitive DNA proliferation (or any segmental duplication) when larger homologs are preferred. The hypothesis of holokinetic drive is supported primarily by the negative correlation between chromosome number and genome size that is documented in holokinetic lineages. The supporting value of two older cross-experiments on holokinetic structural heterozygotes (the rush Luzula elegans and butterflies of the genus Antheraea) that indicate the presence of size-preferential homolog transmission via female meiosis for holokinetic drive is discussed, along with the potential negative consequences of holokinetic drive in comparison with centromere drive

Correction: Evidence for Centromere Drive in the Holocentric Chromosomes of <i>Caenorhabditis</i>

<p>Correction: Evidence for Centromere Drive in the Holocentric Chromosomes of <i>Caenorhabditis</i></p

Data to Figure 1

Fig. 1A: Chromosome numbers reported in selected holokinetic genera. Fig. 1B: Chromosome size divergence in monocentric and holocentric plant genera

Neighbor-joinning tree of Caenorhabditis CENH3^HCP-3 gene.

<p>Bold branches indicate the lineages under positive selection. Numbers above branches are the ω values. The value of ω = 999 indicates the branch for which dS = 0.</p