Cannabis Virome Reconstruction and Antiviral RNAi Characterization through Small RNA Sequencing.

Viral infections pose an emerging threat to hemp (Cannabis sativa) cultivation. We used Illumina small (s)RNA sequencing for virome reconstruction and characterization of antiviral RNA interference (RNAi) in monoecious and dioecious hemp varieties, which exhibited different virus-like symptoms. Through de novo and reference-based sRNA assembly, we identified and reconstructed Cannabis cryptic virus (family Partitiviridae), Cannabis sativa mitovirus 1 (Mitoviridae) and Grapevine line pattern virus (Bromoviridae) as well as a novel virus tentatively classified into Partitiviridae. Members of both Partitiviridae and Bromoviridae were targeted by antiviral RNAi, generating 21 nt and, less abundant, 22 nt sRNAs from both strands of the entire virus genome, suggesting the involvement of Dicer-like (DCL) 4 and DCL2 in viral sRNA biogenesis, respectively. Mitovirus sRNAs represented predominantly the positive-sense strand and had a wider size range, with the 21 nt class being most abundant on both strands. For all viruses, 21 and 22 nt sRNAs had predominantly 5'-terminal uridine or cytosine, suggesting their binding to antiviral Argonaute (AGO) 1 and AGO5, respectively. As no clear association of any virus with symptoms was observed, further studies should clarify if these viruses individually or in combination can cause hemp diseases.

Ust-Luga Seaport of Russia: Biological Invasions and Resting Stages Accumulation.

This article describes the results of a three-year study of invasive species of aquatic ecosystems in the vicinity of Ust-Luga, the largest Russian seaport in the Baltic. Taking into account the great importance of the participation of marine vessels in the dispersal of invasive species, an experimental study of the seasonality of accumulation of resting stages of aquatic invertebrates in the ballast compartments of a vessel located in the Baltic Sea of the Gulf of Finland was carried out. Experiments show that the time of filling the ballast compartments in late summer and autumn poses the greatest risk for the spread of aquatic invertebrates with ship ballast water. In the Baltic Russian port, 11 invasive species of zooplankton and zoobenthos were found, which comprises 15% of the biodiversity in the samples. Copepoda demonstrated the highest presence of invasive species in class among zooplankton groups (14%) and Malacostraca among benthos groups (80%). Alien species findings correspond to the main vectors of invasive species dispersal for the Baltic Sea: North America, Indochina, and the Ponto-Caspian region.

Extrachromosomal viral DNA produced by transcriptionally active endogenous viral elements in non-infected banana hybrids impedes quantitative PCR diagnostics of banana streak virus infections in banana hybrids.

The main edible and cultivated banana varieties are intra- and interspecific hybrids of the two main Musa species, Musa acuminata and Musa balbisiana, having diploid genomes denoted A and B, respectively. The B genome naturally hosts sequences of banana streak virus (BSV) named endogenous BSV (eBSV). Upon stress, eBSVs are identified as the origin of BSV infection for at least three BSV species, causing banana streak disease. For each of the three species, BSV and eBSV share >99.9 % sequence identity, complicating PCR-based diagnosis of viral infection in the B genome-containing bananas. Here, we designed a quantitative PCR-based method to only quantify episomal BSV particles produced, overcoming the limitation of eBSV also being detected by qPCR by using it as a 'calibrator'. However, our results revealed unexpected variation of eBSV amplification in calibrator plants composed of a clonal population of 53 replicating virus-free banana hybrids with the same AAB genotype. Our in-depth molecular analyses suggest that this calibrator variation is due to the variable abundance of non-encapsidated extrachromosomal viral DNA, likely produced via the transcription of eBSVs, followed by occasional reverse transcription. We also present evidence that accumulation of viral transcripts in AAB plants is downregulated both at post-transcriptional and transcriptional levels by an RNA interference mechanism that keeps the plants free of virus infection. Finally, we recommend that such eBSV amplification variation be taken into account to establish a quantitative viral diagnostic for banana plants with the B genome.

Genetic and morphological heterogeneity among populations of Eurytemora affinis (Crustacea: Copepoda: Temoridae) in European waters.

Our understanding of the systematics of the Eurytemora affinis complex developed at a fast pace over the last decades. Formerly considered as a complex of cryptic species, it is now believed to include three valid species: E. affinis, Eurytemora carolleeae, and Eurytemora caspica. American and European representatives have been studied in detail with respect to fine-scale geographic distribution, levels of genetic subdivision, evolutionary and demographic histories. Morphological components have been less explored. In this study, an analysis of the phylogeny and morphology of E. affinis was done, with a special focus on European populations. A total of 447 individuals of E. affinis from Europe were analyzed with genetic tools and 170 individuals according to morphological criteria. Common and new morphological and genetic features were analyzed. For this, we used ML and Bayesian methods to analyze the bar coding mt-DNA gene cytochrome c oxidase I subunit. Both genetic and morphological analyses showed high heterogeneities among the E. affinis populations from Europe. As a result, three local populations of E. affinis in Western Europe, including the European part of Russia, were established. Their genetic and morphological heterogeneity corresponded to the subspecies level.

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex.

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the "cryptic or pseudocryptic" dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in-depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy.