Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses.Full Tex

Detecting flying insects using car nets and DNA metabarcoding

Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples were processed with a DNA metabarcoding protocol to estimate taxonomic composition, and the results were compared to known flying insect richness and occurrence data. Insect and hoverfly richness and diversity were assessed across biogeographic regions and dominant land cover types. We detected 15 out of 19 flying insect orders present in Denmark, with high proportions of especially Diptera compared to Danish estimates, and lower insect richness and diversity in urbanised areas. We found 319 species not known for Denmark and 174 species assessed in the Danish Red List. Our results indicate that the methodology can assess the flying insect fauna at large spatial scales to a wide extent, but may be, like other methods, biased towards certain insect orders.Statistical analyses were carried out in RStudio on the original samples (size sorted samples were merged prior to analysis). Scripts can be found here: https://github.com/CecSve/InsectMobile_CarNet. The data in this Dryad repository are the data used in script 02. Funding provided by: Aage V. Jensens FondeCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100002721Award Number:Flying insects were collected with car nets during June 2018 in Denmark. Citizen scientists drove back and forth on 5 km routes and the insects were shipped to the Natural History Museum of Denmark in 96% EtOH. The insects were size sorted in two size fractions prior to DNA extraction with a non-destructive DNA lysis buffer and further processing with a DNA metabarcoding protocol. The full laboratory protocol for the research project 'InsectMobile' can be accessed here: https://dx.doi.org/10.17504/protocols.io.bmunk6ve. Only the output of fwh primer pair is used in this study

FungalTraits : a user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.Supplementary Information: Fig. S1. Trait distributions of fungal genera in different fungal phyla.Fig. S2. Trait distributions of Stramenopila genera in different Stramenopila phyla.Fig. S3. Distribution of the ten most common fungal guilds among annotated sequences.Table S1. Traits of genera.Table S2. Traits of sequences.Table S3. Traits of species hypothesis.Table S4. Example dataset for genus-level annotation using the vlookup function in Excel.Table S5. Comparison of workflows and outputs conducted in FunTraits and FUNGuild.Supplementary item 1. List of trait states for genera and sequences.Supplementary item 2. Instructions for annotators of fungal ITS sequences.Estonian Science Foundation, the University of Tartu and the European Regional Development Fund.https://www.springer.com/journal/132252021-11-01hj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog