Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

Restrictions to photosynthesis can limit plant growth at high temperature in a variety of ways. In addition to increasing photorespiration, moderately high temperatures (35-42 ∞ ∞ ∞ ∞ C) can cause direct injury to the photosynthetic apparatus. Both carbon metabolism and thylakoid reactions have been suggested as the primary site of injury at these temperatures. In the present study this issue was addressed by first characterizing leaf temperature dynamics in Pima cotton ( Gossypium barbadense ) grown under irrigation in the US desert south-west. It was found that cotton leaves repeatedly reached temperatures above 40 ∞ ∞ ∞ ∞ C and could fluctuate as much as 8 or 10 ∞ ∞ ∞ ∞ C in a matter of seconds. Laboratory studies revealed a maximum photosynthetic rate at 30-33 ∞ ∞ ∞ ∞ C that declined by 22% at 45 ∞ ∞ ∞ ∞ C. The majority of the inhibition persisted upon return to 30 ∞ ∞ ∞ ∞ C. The mechanism of this limitation was assessed by measuring the response of photosynthesis to CO 2 in the laboratory. The first time a cotton leaf (grown at 30 ∞ ∞ ∞ ∞ C) was exposed to 45 ∞ ∞ ∞ ∞ C, photosynthetic electron transport was stimulated (at high CO 2 ) because of an increased flux through the photorespiratory pathway. However, upon cooling back to 30 ∞ ∞ ∞ ∞ C, photosynthetic electron transport was inhibited and fell substantially below the level measured before the heat treatment. In the field, the response of assimilation ( A ) to various internal levels of CO 2 ( C i ) revealed that photosynthesis was limited by ribulose-1,5-bisphosphate (RuBP) regeneration at normal levels of CO 2 (presumably because of limitations in thylakoid reactions needed to support RuBP regeneration). There was no evidence of a ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) limitation at air levels of CO 2 and at no point on any of 30 A -C i curves measured on leaves at temperatures from 28 to 39 ∞ ∞ ∞ ∞ C was RuBP regeneration capacity measured to be in substantial excess of the capacity of Rubisco to use RuBP. It is therefore concluded that photosynthesis in field-grown Pima cotton leaves is functionally limited by photosynthetic electron transport and RuBP regeneration capacity, not Rubisco activity.

SummaryIn northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mndependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N.In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples withand without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed.We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases -a number comparable to many white-rot wood decomposers.These results support the hypothesis that some ectomycorrhizal fungi -Cortinarius species in particular -may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.

Summary• Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato.• We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified.• A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production.• Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

1. Communities of litter saprotrophic and root-associated fungi are vertically separated within boreal forest soil profiles. It is unclear whether this depth partitioning is maintained exclusively by substrate-mediated niche partitioning (i.e. distinct fundamental niches), or by competition for space and resources (i.e. distinct realized niches). Improved understanding of the mechanisms driving spatial partitioning of these fungal guilds is critical, as they modulate carbon and nutrient cycling in different ways. 2.Under field settings, we tested the effects of substrate quality and the local fungal species pool at various depths in determining the potential of saprotrophic and mycorrhizal fungi to colonize and exploit organic matter. Natural substrates of three qualities -fresh or partly decomposed litter or humus -were incubated in the corresponding organic layers of a boreal forest soil profile in a fully factorial design. After one and two growing seasons, fungal community composition in the substrates was determined by 454-pyrosequencing and decomposition was analyzed. 3. Fungal community development during the course of the experiment was determined to similar degrees by vertical location of the substrates (24% of explained variation) and by substrate quality (20%), indicating that interference competition is a strong additional driver of the substrate-dependent depth partitioning of fungal guilds in the system. During the first growing season, litter substrates decomposed slower when colonized by root-associated communities than when colonized by communities of litter saprotrophs, whereas humus was only slightly decomposed by both fungal guilds. During the second season, certain basidiomycetes from both guilds were particularly efficient in localizing and exploiting their native organic substrates although displaced in the vertical profile. This validates that fungal community composition, rather than microclimatic factors, were responsible for observed depth-related differences in decomposer activities during the first season. 4. In conclusion, our results suggest that saprotrophic and root-associated fungal guilds have overlapping fundamental niches with respect to colonization of substrates of different qualities, and that their substrate-dependent depth partitioning in soils of ectomycorrhiza-dominated ecosystems is reinforced by interference competition. Through competitive interactions, mycorrhizal fungi can thus indirectly regulate litter decomposition rates by restraining activities of more efficient litter saprotrophs.