Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimenbased collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized.

BackgroundGenetic influences on gene expression in the human fetal brain plausibly impact upon a variety of postnatal brain-related traits, including susceptibility to neuropsychiatric disorders. However, to date, there have been no studies that have mapped genome-wide expression quantitative trait loci (eQTL) specifically in the human prenatal brain.ResultsWe performed deep RNA sequencing and genome-wide genotyping on a unique collection of 120 human brains from the second trimester of gestation to provide the first eQTL dataset derived exclusively from the human fetal brain. We identify high confidence cis-acting eQTL at the individual transcript as well as whole gene level, including many mapping to a common inversion polymorphism on chromosome 17q21. Fetal brain eQTL are enriched among risk variants for postnatal conditions including attention deficit hyperactivity disorder, schizophrenia, and bipolar disorder. We further identify changes in gene expression within the prenatal brain that potentially mediate risk for neuropsychiatric traits, including increased expression of C4A in association with genetic risk for schizophrenia, increased expression of LRRC57 in association with genetic risk for bipolar disorder, and altered expression of multiple genes within the chromosome 17q21 inversion in association with variants influencing the personality trait of neuroticism.ConclusionsWe have mapped eQTL operating in the human fetal brain, providing evidence that these confer risk to certain neuropsychiatric disorders, and identifying gene expression changes that potentially mediate susceptibility to these conditions.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1567-1) contains supplementary material, which is available to authorized users.

We use multiple photosynthetic, chlororespiratory, and plastid translation apparatus loci and their associated noncoding regions (ca. 16 kb per taxon, prior to alignment) to make strongly supported inferences of the deep internal branches of monocot phylogeny. Most monocot relationships are robust (an average of ca. 91 % bootstrap support per branch examined), including those poorly supported or unresolved in other studies. Our data strongly support a sister-group relationship between Asparagales and the commelinid monocots, the inclusion of the orchids in Asparagales, and the status of Petrosaviaceae as the sister group of all monocots except Acarus and Alismatales. The latter finding supports recognition of the order Petrosaviales. Also strongly supported is a placement of Petermannia disjunct from Colchicaceae (Liliales) and a sister-group relationship between Commelinales and Zingiberales. We highlight the remaining weak areas of monocot phylogeny, including the positions of Dioscoreales, Liliales, and Pandanales. Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions. Ceratophyllum and Chloranthaceae appear to have a destabilizing effect on the position of the monocots among other angiosperms; the issue of monocot placement in broader angiosperm phylogeny remains problematic.

The Verrucariaceae (Ascomycota) is a family of mostly lichenized fungi with a unique diversity of algal symbionts, including some algae that are rarely or never associated with other lichens. The phylogenetic position of most of these algae has not yet been studied and, because morphology-based identifications can often be misleading, molecular data is necessary to revisit their identity and to explore patterns of association between fungal and algal partners. For this reason, the diversity of photobionts in this lichen family was investigated using molecular markers (rbcL and nuSSU) amplified from DNA extracts of lichen thalli and cultured isolates. Although a single algal genus, Diplosphaera (Trebouxiophyceae), was associated with 12 out of the 17 sampled genera of Verrucariaceae, representatives of eight other genera in five orders of the Chlorophyta and one genus in the Xanthophyceae also form lichen associations with members of the family. Fungal genera with simple crustose thalli (e.g. Hydropunctaria, Wahlenbergiella, Bagliettoa) use a high diversity and unusual selection of photobionts. In contrast, fungal genera with more complex thalli (e.g. Placidium, Dermatocarpon) tend to have lower photobiont diversity. Habitat requirements and phylogenetic histories are both partly reflected in the observed patterns of associations between lichenized fungi from the family Verrucariaceae and their photobionts.

Heterocystous cyanobacteria form symbiotic associations with a wide range of plant and fungal hosts. We used a molecular phylogenetic approach to investigate the degree of host specialization of cyanobacteria associated with four closely related species of the lichenized fungus Peltigera, and to compare these strains with other symbiotic cyanobacteria. We conducted phylogenetic analyses on 16S, rbcLX, and trnL sequences from cyanobacteria associated with multiple specimens of each lichen species and from symbionts of other fungi and plants, as well as from free-living strains of Nostoc and related genera of cyanobacteria. The genus Nostoc comprises two divergent lineages, but symbiotic strains occur primarily within a single monophyletic lineage that also includes free-living representatives. Cyanobacteria from the same lichen species were often more closely related to strains from other species or to plant symbionts or free-living strains than to each other. These results indicate that host specialization is low for the genus Nostoc, and suggest that opportunities for coevolution with its partners may be rare.