Polyploidy and DNA methylation: new tools available

Most plant species are recent or ancient polyploids (displaying at least one round of genome duplication in their history). Cultivated species (e.g. wheat, cotton, canola, sugarcane, coffee) and invasive species are often relatively recent polyploids, and frequently of hybrid origin (i.e. allopolyploids). Despite the genetic bottleneck occurring during the allopolyploid speciation process, the formation of such species from two divergent lineages leads to fixed heterozygosity decisive to their success. New phenotypes and new niche occupation are usually associated with this mode of speciation, as a result of both genomic rearrangements and gene expression changes of different magnitudes depending on the different polyploid species investigated. These gene expression changes affecting newly formed polyploid species may result from various, interconnected mechanisms, including (i) functional interactions between the homoeologous copies and between their products, that are reunited in the same nucleus and cell; (ii) the fate of duplicated copies, selective pressure on one of the parental copy being released which could lead to gene loss, pseudogenization, or alternatively, to subfunctionalization or neofunctionalization; and (iii) epigenetic landscape changes that in turn affect gene expression. As one of the interrelated processes leading to epigenetic regulation of gene expression, the DNA methylation status of newly formed species appears to be consistently affected following both hybridization and genome doubling. In this issue, Verhoeven et al. have investigated the fate of DNA methylation patterns that could affect naturally occurring new asexual triploid lineages of dandelions. As a result of such a ploidy level change, the authors demonstrate stably transmitted DNA methylation changes leading to unique DNA methylation patterns in each newly formed lineage. Most studies published to date on plant DNA methylation polymorphism were performed using restriction enzymes sensitive to methylation. Recently, new high‐throughput methods were made available, thanks to the development of ‘next‐generation sequencing’ techniques. The combination of these methods offers powerful and promising tools to investigate epigenetic variation in both model and non‐model systems.     

Soil carbon balance in a clonal Eucalyptus plantation in Congo: effects of logging on carbon inputs and soil CO2 efflux

Soil CO₂ efflux was measured in clear‐cut and intact plots in order to quantify the impact of harvest on soil respiration in an intensively managed Eucalyptus plantation, and to evaluate the increase in heterotrophic component of soil respiration because of the decomposition of harvest residues. Soil CO₂ effluxes showed a pronounced seasonal trend, which was well related to the pattern of precipitation and soil water content and were always significantly lower in the clear‐cut plots than in the intact plots. On an annual basis, soil respiration represented 1.57 and 0.91 kg_C m^?2 yr^?1 in intact and clear‐cut plots, respectively. During the first year following harvest, residues have lost 0.79 kg_C m^?2 yr^?1. Our estimate of heterotrophic respiration was calculated assuming that it was similar to soil respiration in the clear‐cut area except that the decomposition of residues did not occur, and it was further corrected for differences in soil water content between intact and clear‐cut plots and for the cessation of leaf and fine root turnover in clear cut. Heterotrophic respiration in clear‐cut plots was estimated at 1.18 kg_C m^?2 yr^?1 whereas it was only 0.65 kg_C m^?2 yr^?1 in intact plots (41% of soil respiration). Assumptions and uncertainties with these calculations are discussed.     

Spartina anglica C. E. Hubbard: a natural model system for analysing early evolutionary changes that affect allopolyploid genomes

Spartina anglica arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced East American Spartina alterniflora and following genome duplication of the hybrid ( S.  ×  townsendii ). This system allows investigations of the early evolutionary changes that accompany stabilization of a new allopolyploid species in natural populations. Various molecular data indicate that S. anglica has resulted from a unique parental genotype. This young species contains two distinctly divergent homoeologous genomes that have not undergone extensive change since their reunion. No burst of retroelements has been encountered in the F₁ hybrid or in the allopolyploid, suggesting a 'structural genomic stasis' rather than 'rapid genomic changes'. However, modifications of the methylation patterns in the genomes of S.  ×  townsendii and S. anglica indicate that in this system, epigenetic changes have followed both hybridization and polyploidization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 475–484.