Ecdysteroids and juvenile hormones of whiteflies, important insect vectors for plant viruses

Ecdysteroids and juvenile hormones (JHs) regulate many physiological events throughout the insect life cycle, including molting, metamorphosis, ecdysis, diapause, reproduction, and behavior. Fluctuation of whitefly ecdysteroid levels and the identity of the whitefly molting hormone (20-hydroxyecdysone) have only been reported within the last few years. An ecdysteroid commitment peak that is associated with the reprogramming of tissues for a metamorphic molt in many holometabolous and some hemimetabolous insect species was not observed in last nymphal instars of either the sweet potato whitefly, Bemisia tabaci (Biotype B), or the greenhouse whitefly, Trialeurodes vaporariorum. Ecdysteroids reach peak levels 1-2 days prior to the initiation of the nymphal-adult metamorphic molt. Adult eye and wing differentiation which signal the onset of this molt begin earlier in 4th instar T. vaporariorum (Stages 4 and 5, respectively) than in B. tabaci (Stage 6), and the premolt peak is 3-4 times greater in B. tabaci ( approximately 400 fg/microg protein) than in T. vaporariorum ( approximately 120 fg/microg protein). The JH of B. tabaci nymphs and eggs was found to be JH III, supporting the view that JHs I and II are, with rare exception, only present in lepidopteran insects. In B. tabaci eggs, JH levels were approximately 10 times greater on day 2/3 (0.44 fg/egg or 0.54 ng/g) than on day 5 (0.04 fg/egg or 0.054 ng/g) post-oviposition. Approximately, 1.4 fg/2nd-3rd instar nymph (0.36 ng/g) was detected. It is probable that the relatively high level of JH in day 2/3 eggs is associated with the differentiation of various whitefly tissues during embryonic development.     

Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

Background

Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequencing technique and data analysis pipeline. We compared the suitability of two benchtop next-generation sequencers for whole genome influenza A quasispecies analysis: the Illumina MiSeq sequencing-by-synthesis and the Ion Torrent PGM semiconductor sequencing technique.

Results

We first compared the accuracy and sensitivity of both sequencers using plasmid DNA and different ratios of wild type and mutant plasmid. Illumina MiSeq sequencing reads were one and a half times more accurate than those of the Ion Torrent PGM. The majority of sequencing errors were substitutions on the Illumina MiSeq and insertions and deletions, mostly in homopolymer regions, on the Ion Torrent PGM. To evaluate the suitability of the two techniques for determining the genome diversity of influenza A virus, we generated plasmid-derived PR8 virus and grew this virus in vitro. We also optimized an RT-PCR protocol to obtain uniform coverage of all eight genomic RNA segments. The sequencing reads obtained with both sequencers could successfully be assembled de novo into the segmented influenza virus genome. After mapping of the reads to the reference genome, we found that the detection limit for reliable recognition of variants in the viral genome required a frequency of 0.5% or higher. This threshold exceeds the background error rate resulting from the RT-PCR reaction and the sequencing method. Most of the variants in the PR8 virus genome were present in hemagglutinin, and these mutations were detected by both sequencers.

Conclusions

Our approach underlines the power and limitations of two commonly used next-generation sequencers for the analysis of influenza virus gene diversity. We conclude that the Illumina MiSeq platform is better suited for detecting variant sequences whereas the Ion Torrent PGM platform has a shorter turnaround time. The data analysis pipeline that we propose here will also help to standardize variant calling in small RNA genomes based on next-generation sequencing data.     

Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes

Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes.     

Exploring the relationship between canopy height and terrestrial plant diversity

A relatively small number of broad-scale patterns describe the distribution of biodiversity across the earth. All of them explore biodiversity focusing on a mono or bi-dimensional space. Conversely, the volume of the forests is rarely considered. In the present work, we tested a global correlation between vascular plant species richness (S) and average forest canopy height (H), the latter regarded as a proxy of volume, using the NASA product of Global Forest Canopy Height map and the global map of plant species diversity. We found a significant correlation between H and S both at global and macro-climate scales, with strongest confidence in the tropics. Hence, two different regression models were compared and discussed to provide a possible pattern of the H–S relation. We suggested that the volume of forest ecosystems should be considered in ecological studies as well as in planning and managing natural sites, although in this first attempt, we cannot definitively prove our hypothesis. Again, high-resolution spatial data could be highly important to confirm the H–S relation, even at different scales.     

Rapid identification of adult whiteflies in plant consignments using monoclonal antibodies

A rapid and simple method for the identification of adult whiteflies (Homoptera: Aleyrodidae) would be valuable, both to facilitate pest management decision making and, more importantly, to prevent the introduction of new pests into non-infested areas. Considering the enormous economic losses that have resulted in the recent past from the accidental introduction of harmful species, there is a clear and urgent need for a reliable antibody-based test kit that would allow non-specialist growers, extension workers and customs authorities to identify whiteflies. As a first step in this process, this paper describes the development and characterisation of monoclonal antibodies capable of distinguishing between major pest species of whitefly, and application of these antibodies in an enzyme-linked immunosorbent assay (ELISA). A monoclonal antibody is described that reacts strongly with both male and female Trialeurodes vaporariorum (Westwood) but not with either Bemisia tabaci (Gennadius) or B. argentifolii Bellows & Perring. A second antibody is reported that gives a strong response to female Bemisia sp. that does not react with T. vaporariorum of either sex. The two antibodies used in combination provide a powerful means of distinguishing between adult whitefly, particularly at low levels of infestation in plant consignments, when pupae cannot easily be found.     

Identification of plant chemicals attracting and repelling whiteflies

The harmful side effects of chemical pest control have focused increasing attention on the potential for environmentally friendly, sustainable and efficient methods to control the sweet potato whitefly, Bemisia tabaci (Gennadius). One control method employs a volatile repellent (push), and an alluring volatile trap (pull) to manipulate the distribution and control the whitefly. Here, a Y-tube olfactometer was used to investigate the orientation responses of the whitefly toward the volatile components of six plants: tomato, tobacco, cabbage, cotton, cucumber and celery. Gas chromatography coupled with mass spectrometry was used to identify and quantify extracts from the six plants. Six treatments were conducted to demonstrate the “push–pull” method’s effects on the host selection behaviors of B. tabaci in a greenhouse. Four of the plant extracts tested had exceedingly attractive effects on the adult insects, but not those from celery. B. tabaci exhibited a prominent attraction response to (E)-2-hexenal, 3-hexen-1-ol and mixtures of these compounds, with the response rates exceeding 80 % for all tested proportions. Limonene diluted 500 times had a 62 % greater deterrent effect on adults than was observed in its absence, and it repelled egg-laying by more than 80 % in the greenhouse experiment. These data show that (E)-2-hexenal, 3-hexen-1-ol and limonene can be expected to be used for the “push–pull” method to control B. tabaci.     

Phylogenetic diversity and metagenomics of candidate division OP3

Except for environmental 16S rRNA gene sequences, no information is available for members of the candidate division OP3. These bacteria appear to thrive in anoxic environments, such as marine sediments, hypersaline deep sea, freshwater lakes, aquifers, flooded paddy soils and methanogenic bioreactors. The 16S rRNA phylogeny suggests that OP3 belongs to the Planctomycetes/Verrucomicrobia/Chlamydiae (PVC) superphylum. Metagenomic fosmid libraries were constructed from flooded paddy soil and screened for 16S rRNA gene‐containing fragments affiliated with the PVC superphylum. The screening of 63 000 clones resulted in 23 assay‐positive fosmids, of which three clones were affiliated with OP3. The 16S rRNA gene sequence divergence between the fragments OP3/1, OP3/2 and OP3/3 ranges from 18% to 25%, indicating that they belong to different OP3 subdivisions. The 23S rRNA phylogeny confirmed the membership of OP3 in the PVC superphylum. Sequencing the OP3 fragments resulted in a total of 105 kb of genomic information and 90 ORFs, of which 47 could be assigned a putative function and 11 were conserved hypothetical. Using BLASTP searches, a high proportion of ORFs had best matches to homologues from Deltaproteobacteria, rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of nine ORFs was predicted to encode the bacterial NADH dehydrogenase I. Given the high proportion of homologues present in deltaproteobacteria and anoxic conditions in the natural environment of OP3 bacteria, the detection of NADH dehydrogenase I may suggest an anaerobic respiration mode. Oligonucleotide frequencies calculated for OP3/1, OP3/2 and OP/3 show high intraphylum correlations. This novel sequence information could therefore be used to identify OP3‐related fragments in large metagenomic data sets using marker gene‐independent procedures in the future. In addition to the OP3 fragments, a single metagenomic fragment affiliated with the candidate division BRC1 was obtained and analysed.     

Assembly of flexuous plant viruses and their proteins.

Recent experiments on the disassembly and assembly of some flexuous plant viruses and their proteins are described. The properties of reconstituted potato virus X and those of assembled potato virus Y protein are considered as well as the suitability of other flexuous viruses for reconstitution studies.     

Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA

DNA sequencing technology has proven very valuable for analysing the microbiota of poorly accessible ecosystems such as hydrothermal vents. Using a combination of amplicon and shotgun sequencing of small-subunit rRNA and its gene, we examined the composition and diversity of microbial communities from the recently discovered Jan Mayen vent field, located on Mohn's Ridge in the Norwegian-Greenland Sea. The communities were dominated by the epsilonproteobacterial genera Sulfurimonas and Sulfurovum. These are mesophiles involved in sulphur metabolism and typically found in vent fluid mixing zones. Composition and diversity predictions differed systematically between extracted DNA and RNA samples as well as between amplicon and shotgun sequencing. These differences were more substantial than those between two biological replicates. Amplicon vs. shotgun sequencing differences could be explained to a large extent by bias introduced during PCR, caused by preferential primer-template annealing, while DNA vs. RNA differences were thought to be caused by differences between the activity levels of taxa. Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights.     

Assessing the diversity and specificity of two freshwater viral communities through metagenomics

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.     

Evolution of geminiviruses and their satellites

Geminiviruses and their satellites have circular single stranded DNA genomes, infecting many crops and weeds across the globe. To successfully invade new hosts, break host resistance, move virus particles within and between plants, geminiviruses and their satellites have evolved a coordinated network of protein interactions, showing a possible evolutionary path. Humans have played an important role in the last century to promote the emergence of many geminivirus diseases, thereby impacting their evolution. The greatest molecular diversity of geminiviruses and their satellites resides in Southeast Asia revealing a possible center of origin. This minireview leads us to a possible general grand scheme of their evolution.     

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

Metagenomics generates and tests hypotheses about dynamics and mechanistic drivers in wild populations, yet commonly suffers from insufficient (相似文献   

Exploring the relationship between macrofungi diversity, abundance, and vascular plant diversity in semi-natural and managed forests in north-east Hungary

The diversity of easy-to-study organisms (e.g. vascular plants) is often used as a proxy for the diversity of other organisms whose investigation needs more effort, time and specialist knowledge. Some previous studies have found positive relationships between plant and macrofungal diversity and thus support this approach, while others question this practice. Our aim was to explore the possibility of using plant diversity as surrogate for macrofungal diversity in the forests of the Pannonian ecoregion. A total of 19 permanent plots in north-east Hungary were sampled for vascular plants and macrofungi. The effect on macrofungal abundance and diversity, as well as degradation level, of plant evenness and richness was tested using generalized linear models. Species richness of macrofungi assemblages proved to be independent of the diversity and naturalness of vascular plant communities; however, there was congruence in the composition of the two communities. In contrast to diversity, macrofungi abundance was significantly negatively correlated to plant species richness. There was a hump-backed relationship between the abundance of terricolous macrofungi and the degradation level estimated on the basis of the occurrence of vascular plants, although degradation did not influence the abundance of lignicolous macrofungi. Our results question the reliability of decisions on nature conservation actions based on a few groups of easy-to-observe organisms, and underline the necessity of studying as wide a range of taxonomic groups as possible.     

Evolutionary relationships of primary prokaryotic endosymbionts of whiteflies and their hosts

Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are plant sap-sucking insects that harbor prokaryotic primary endosymbionts (P-endosymbionts) within specialized cells located in their body cavity. Four-kilobase DNA fragments containing 16S-23S ribosomal DNA (rDNA) were amplified from the P-endosymbiont of 24 whiteflies from 22 different species of 2 whitefly subfamilies. In addition, 3-kb DNA fragments containing mitochondrial cytB, nd1, and large-subunit rDNA (LrDNA) were amplified from 17 whitefly species. Comparisons of the P-endosymbiont (16S-23S rDNA) and host (cytB-nd1-LrDNA) phylogenetic trees indicated overall congruence consistent with a single infection of a whitefly ancestor with a bacterium and subsequent cospeciation (cocladogenesis) of the host and the P-endosymbiont. On the basis of both the P-endosymbiont and host trees, the whiteflies could be subdivided into at least five clusters. The major subdivision was between the subfamilies Aleyrodinae and Aleurodicinae. Unlike the P-endosymbionts of may other insects, the P-endosymbionts of whiteflies were related to Pseudomonas and possibly to the P-endosymbionts of psyllids. The lineage consisting of the P-endosymbionts of whiteflies is given the designation "Candidatus Portiera" gen. nov., with a single species, "Candidatus Portiera aleyrodidarum" sp. nov.     

Choosing and using a plant DNA barcode

The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.