Alexey Shipunov

Hidden diversity of endophytic fungi in an invasive plant

Fungal endophytes are important in plant ecology and common in plants. We attempted to test cointroduction and host-jumping hypotheses on a community basis by comparing endophytes isolated from invasive spotted knapweed (Centaurea stoebe, Asteraceae) in its native and invaded ranges. Of 92 combined, sequence-based haplotypes representing eight classes of Fungi, 78 occurred in only one of the two ranges. In the native range of C. stoebe, one haplotype of Alternaria alternata was clearly dominant, whereas in the invaded range, no haplotype was dominant. Many haplotypes were closely related to one another and novel. For example, six putative, new species of Botrytis were discovered as endophytes of C. stoebe, which has never been reported to have Botrytis spp.. Apparent differences between the two communities of endophytes were significant according to an analysis of similarity, but phylogenetic community structure did not differ significantly between the ranges. Both host-jumping and cointroduction of fungal endophytes likely took place during the spotted knapweed invasion.

Endophytes influence protection and growth of an invasive plant

We investigated the symbiotic activities of fungal endophytes isolated from spotted knapweed, Centaurea stoebe. Previously, an analysis of community similarity had demonstrated differences in the endophyte communities of C. stoebe in its native and invaded ranges. Here, we found that specific endophytes can exert positive effects on their host, whereas others exert negative effects. Endophytes produced metabolites that inhibited germination of a competitor of C. stoebe. Endophytes also repelled a specialist insect herbivore, perhaps by producing biologically active volatiles. Yet other endophytes acted as cryptic pathogens of C. stoebe, suppressing its germination, reducing its growth, increasing the abundance of a generalist insect herbivore, and delaying or suppressing its flowering. Since, as reported here, endophytes are not functionally interchangeable, previously reported community differences could be contributing to the invasiveness of C. stoebe.

Changes in the composition of the RNA virome mark evolutionary transitions in green plants

BackgroundThe known plant viruses mostly infect angiosperm hosts and have RNA or small DNA genomes. The only other lineage of green plants with a relatively well-studied virome, unicellular chlorophyte algae, is mostly infected by viruses with large DNA genomes. Thus RNA viruses and small DNA viruses seem to completely displace large DNA virus genomes in late branching angiosperms. To understand better the expansion of RNA viruses in the taxonomic span between algae and angiosperms, we analyzed the transcriptomes of 66 non-angiosperm plants characterized by the 1000 Plants Genomes Project.ResultsWe found homologs of virus RNA-dependent RNA polymerases in 28 non-angiosperm plant species, including algae, mosses, liverworts (Marchantiophyta), hornworts (Anthocerotophyta), lycophytes, a horsetail Equisetum, and gymnosperms. Polymerase genes in algae were most closely related to homologs from double-stranded RNA viruses leading latent or persistent lifestyles. Land plants, in addition, contained polymerases close to the homologs from single-stranded RNA viruses of angiosperms, capable of productive infection and systemic spread. For several polymerases, a cognate capsid protein was found in the same library. Another virus hallmark gene family, encoding the 30 K movement proteins, was found in lycophytes and monilophytes but not in mosses or algae.ConclusionsThe broadened repertoire of RNA viruses suggests that colonization of land and growth in anatomical complexity in land plants coincided with the acquisition of novel sets of viruses with different strategies of infection and reproduction.

All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality

More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about “old” samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the “fresh” specimens.

Phylogenomic analysis of Picramnia, Alvaradoa, and Leitneria supports the independent Picramniales

Picramniales is a recently established monotypic order that has not yet acquired a stable position on the phylogenetic tree of flowering plants. While Picramnia and Alvaradoa were transferred from Simaroubaceae (Sapindales) into Picramniaceae (Picramniales), Leitneria was transferred from the “hamamelids” into Simaroubaceae. Using next‐generation sequencing, we obtained plastome sequences of Picramnia and Alvaradoa (partial) and Leitneria (complete). Protein coding and rRNA genes common for flowering plant plastomes were used for phylogenetic analysis. The resulting phylogenetic trees demonstrate a robust placement of Picramniales among the rosids as a sister group to Sapindales + Brassicales + Malvales. Leitneria is placed as a sister to Citrus. We also found that the plastome of Leitneria carries ycf68 gene that is absent from most other rosids and infA pseudogene.

Islands in lakes and the sea: How do they differ?

We studied plants on several neighbouring small islands in an Arctic lake and the sea and despite a common source of colonizers and similar environmental characteristics there were striking differences in the compositions of their floras. The best explanation of the differences could be a combination of several factors, most likely salinity and tides.