Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

Structure, stability and ecological significance of natural epigenetic variation: a large-scale survey in Plantago lanceolata.

Within-species diversity is an important driver of ecological and evolutionary processes. Recent research has found that plants can harbour significant epigenetic diversity, but its extent, stability and ecological significance in natural populations is largely unexplored. We analysed genetic, epigenetic and phenotypic variation in a large number of natural grassland populations of Plantago lanceolata, covering a broad geographical and environmental range. Within-population diversity and among-population differentiation were calculated from genetic and epigenetic marker data and from measurements of phenotypic traits, both for plants in the field and for the F1 generation grown in a common environment. We found weak but significant epigenetic population structure. A large part of the epigenetic population differences observed in the field was maintained in a common environment. Epigenetic differences were consistently related to genetic and environmental variation, and to a lesser degree to phenotypic variation and land use, with more grazed populations harbouring greater epigenetic diversity. Our study demonstrates that epigenetic diversity exists in natural populations of a common grassland species, and that at least part of this epigenetic diversity is stable, nonrandom and related to environmental variation. Experimental and more detailed molecular studies are needed to elucidate the mechanistic basis of these observed patterns.

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

Septoglomus fuscum and S. furcatum, two new species of arbuscular mycorrhizal fungi (Glomeromycota).

Two new arbuscular mycorrhizal fungal species, (Glomeromycota) Septoglomus fuscum and S. furcatum, are described and illustrated. Spores of S. fuscum usually occur in loose hypogeous clusters, rarely singly in soil or inside roots, and S. furcatum forms only single spores in soil. Spores of S. fuscum are brownish orange to dark brown, globose to subglobose, (20-)47(-90) µm diam, rarely ovoid, 21-50 × 23-60 µm. Their spore wall consists of a semi-persistent, semi-flexible, orange white to golden yellow, rarely hyaline, outer layer, easily separating from a laminate, smooth, brownish orange to dark brown inner layer. Spores of S. furcatum are reddish brown to dark brown, globose to subglobose, (106-) 138(-167) µm diam, rarely ovoid, 108-127 × 135-160 µm, usually with one subtending hypha that is frequently branched below the spore base, or occasionally with two subtending hyphae located close together. Spore walls consists of a semipermanent, hyaline to light orange outermost layer, a semipermanent, hyaline to golden yellow middle layer, and a laminate, smooth, reddish brown to dark brown innermost layer. None of the spore-wall layers of S. fuscum and S. furcatum stain in Melzer's reagent. In the field, S. fuscum was associated with roots of Arctotheca populifolia colonizing maritime dunes located near Strand in South Africa and S. furcatum was associated with Cordia oncocalyx growing in a dry forest in the Ceará State, Brazil. In single-species cultures with Plantago lanceolata as host plant, S. fuscum and S. furcatum formed arbuscular mycorrhizae. Phylogenetic analyses of the SSU, ITS and LSU nrDNA sequences placed the two new species in genus Septoglomus and both new taxa were separated from described Septoglomus species.

The arbuscular mycorrhizal Paraglomus majewskii sp. nov. represents a distinct basal lineage in Glomeromycota.

Paraglomus majewskii sp. nov. (Glomeromycota) is described and illustrated. It forms single spores, which are hyaline through their life cycle, globose to subglobose, (35-)63(-78) µm diam, sometimes egg-shaped, 50-70 × 65-90 µm, and have an unusually narrow, (3.2-)4.6(-5.9) µm, cylindrical to slightly flared subtending hypha. The spore wall of P. majewskii consists of an evanescent, short-lived outermost layer, a laminate middle layer, and a flexible innermost layer, which adheres tightly to the middle layer. None of the spore wall layers stain in Melzer's reagent. In single-species cultures with Plantago lanceolata as the host plant P. majewskii formed arbuscular mycorrhizae staining violet in trypan blue. P. majewskii has been isolated from several, distant geographic regions and from different habitats. In phylogenetic analyses of partial nrDNA SSU and LSU sequences the fungus formed mono-phyletic group with Paraglomus species; however it represents a well separated distinct lineage. Its nrDNA sequences are highly similar to in planta arbuscular mycorrhizal fungal sequences from different habitats in Spain and Ecuador.