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Research into cyanobacterial diversity dates back to more than 150 years. Advancement in modern molecular, ultrastructural, ecophysiological and in vitro culture techniques broadened our understanding in the cyanobacterial diversity. Molecular data, especially 16S rRNA gene sequence provide basic criteria for present day cyanobacterial taxonomy. As more DNA sequence data become available it came into notice that morphology-based taxonomic classification is unreliable and it could not infer evolutionary relationships. Some strains belonging to the previously assembled taxa which were classified based on traditional morphological distinctness appeared phylogenetically unrelated when their 16S rRNA gene was sequenced. Therefore, this editorial note was written with the objective of highlighting the necessity in revising present system of cyanobacterial classification and importance in establishment of universal criteria for future taxonomic proposals for cyanobacteria. A cyanobacterial phylogenetic tree was reconstructed using past and present 16S rRNA sequence assemblages from the database and from our studies. Phylogenetic tree revealed polyphyletic origin of unicellular order Chroococcales and filamentous order Oscillatoriales. Strains in the genera Pseudanabaena from the present study were phylogenetically more distant from rest of the Oscillatorialeans in the database and may have independently diverged from the common ancestor at an early stage in the evolution. On the other hand, two Leptolyngbya strains from the present study clustered with Leptolyngbya accessions from the database, although two strains shared only 89% sequence identity. It appears that those two strains could be distinct species belong to the genera of Leptolyngbya and each may have independent evolutionary history. This hypothesis was supported by distinct morphological characters shown in axenic cultures. Present study highlight the importance in understanding that molecular data alone could only provide insights into genetic variability and phylogenetic relatedness, but could not recognize phenotypic variability and their ecological importance and ongoing diversification of strains etc. Thus, construction of an accurate taxonomic classification system requires a ‘polyphasic’ approach that combines molecular data with phenotypic, biochemical and ecophysiological data. Also it is necessary to revisit all past assemblages of taxa available in the database in order to avoid future taxonomic mislabelling.

Additional file 4. Chemosensory receptor sequences.

Additional file 7. Complete ATP-binding cassette transporter (ABC) and carboxylesterase sequences.

Additional file 1. Supplementary notes, figures and small tables.

Additional file 6. Complete and partial cytochrome p450 (CYP) sequences.

Additional file 5. Neuropeptide and protein hormone peptide sequences with highlighted features.

Soil contaminated with used lubricant oil (ULO) has become an emerging environmental threat. Phytoremediation is a cost effective, environmentally friendly and novel technique with great potential for remediation of soils contaminated with used lubricating oil (ULO). Therefore, the aim of this study was to investigate the phytoremediation potentials of Crotalaria retusa L. and Impatiens balsamina for ULO contaminated soil. A randomized block pot experiment was conducted for each species under plant house conditions in soil contaminated with ULO at a concentration of 5,000 mg kg−1 (0.5% w/w)-30,000 mg kg−1 (3% w/w). The percentage biodegradation of ULO in the rhizosphere soil of both species following 90 days exposure indicated significant (p

Screening of plant species with an ability to grow on contaminated soil is the most critical step in the planning of a phytoremediation program. While flourishing growth of Impatiens balsamina L. and Crotalaria retusa L. has been observed in areas adjacent to automobile service stations in Sri Lanka, no systematic study of their tolerance to used lubricating oil (ULO) contaminated soil has been carried out. Therefore, the aim of the present study was to investigate the comparative responses of I. balsamina L. and C. retusa L. to soil contaminated with ULO. Both species exhibited 100% seed germination in soils treated with 1%-5% w/w ULO. After 120 h exposure, root lengths and biomass of germinated seedlings of both species were significantly (p 0.05) reduced in all treatments above 3% w/w ULO. The measured growth parameters of plants following 90 d exposure to 0.5-3% w/w ULO, indicated significant (p 0.05) negative effects on I. balsamina and C. retusa at1% w/w and2% w/w ULO, respectively. There were no significant effects on chlorophyll content or root anatomy of either species under any treatments. Therefore, we concluded that I. balsamina can tolerate up to 1% of ULO and C. retusa up to 2% w/w ULO without displaying any negative effects. Comparatively higher biodegradation of ULO in the rhizosphere, root nodule formation, increases in root length and root hair density are all possible strategies for the exhibited higher tolerance of C. retusa. Therefore, the overall results indicate that C. retusa has the greater potential to be used in phytoremediation of ULO contaminated soils. The findings of the present study will be beneficial in planning phytoremediation program for ULO contaminated soil.

Tospoviruses are among the most devastating viruses of horticultural and field crops. Capsicum chlorosis virus (CaCV) has emerged as an important pathogen of capsicum and tomato in Australia and South-east Asia. Present knowledge about CaCV protein functions in host cells is lacking. We determined intracellular localization and interactions of CaCV proteins by live plant cell imaging to gain insight into the associations of viral proteins during infection. Proteins were transiently expressed as fusions to autofluorescent proteins in leaf epidermal cells of Nicotiana benthamiana and capsicum. All viral proteins localized at least partially in the cell periphery suggestive of cytoplasmic replication and assembly of CaCV. Nucleocapsid (N) and non-structural movement (NSm) proteins localized exclusively in the cell periphery, while non-structural suppressor of silencing (NSs) protein and Gc and Gn glycoproteins accumulated in both the cell periphery and the nucleus. Nuclear localization of CaCV Gn and NSs is unique among tospoviruses. We validated nuclear localization of NSs by immunofluorescence in protoplasts. Bimolecular fluorescence complementation showed self-interactions of CaCV N, NSs and NSm, and heterotypic interactions of N with NSs and Gn. All interactions occurred in the cytoplasm, except NSs self-interaction was exclusively nuclear. Interactions of a tospoviral NSs protein with itself and with N had not been reported previously. Functionally, CaCV NSs showed strong local and systemic RNA silencing suppressor activity and appears to delay short-distance spread of silencing signal. Cell-to-cell movement activity of NSm was demonstrated by trans-complementation of a movement-defective tobamovirus replicon. CaCV NSm localized at plasmodesmata and its transient expression led to the formation of tubular structures that protruded from protoplasts. The D155 residue in the 30K-like movement protein-specific LxD/N50-70G motif of NSm was critical for plasmodesmata localization and movement activity. Compared to other tospoviruses, CaCV proteins have both conserved and unique properties in terms of in planta localization, interactions and protein functions which will effect viral multiplication and movement in host plants.

Thrips palmi is a widely distributed major agricultural pest in the tropics and subtropics, causing significant losses in cucurbit and solanaceous crops through feeding damage and transmission of tospoviruses. Thrips palmi is a vector of capsicum chlorosis virus (CaCV) in Australia. The present understanding of transmission biology and potential effects of CaCV on T. palmi is limited. To gain insights into molecular responses to CaCV infection, we performed RNA-Seq to identify thrips transcripts that are differentially-abundant during virus infection of adults. De-novo assembly of the transcriptome generated from whole bodies of T. palmi adults generated 166,445 contigs, of which ~24% contained a predicted open reading frame. We identified 1,389 differentially-expressed (DE) transcripts, with comparable numbers up- (708) and down-regulated (681) in virus-exposed thrips compared to non-exposed thrips. Approximately 59% of these DE transcripts had significant matches to NCBI non-redundant proteins (Blastx) and Blast2GO identified provisional functional categories among the up-regulated transcripts in virus-exposed thrips including innate immune response-related genes, salivary gland and/or gut-associated genes and vitellogenin genes. The majority of the immune-related proteins are known to serve functions in lysosome activity and melanisation in insects. Most of the up-regulated oral and extra-oral digestion-associated genes appear to be involved in digestion of proteins, lipids and plant cell wall components which may indirectly enhance the likelihood or frequency of virus transmission or may be involved in the regulation of host defence responses. Most of the down-regulated transcripts fell into the gene ontology functional category of 'structural constituent of cuticle'. Comparison to DE genes responsive to tomato spotted wilt virus in Frankliniella occidentalis indicates conservation of some thrips molecular responses to infection by different tospoviruses. This study assembled the first transcriptome in the genus Thrips and provides important data to broaden our understanding of networks of molecular interactions between thrips and tospoviruses.

Background Capsicum chlorosis virus (CaCV) is an emerging pathogen of capsicum, tomato and peanut crops in Australia and South-East Asia. Commercial capsicum cultivars with CaCV resistance are not yet available, but CaCV resistance identified in Capsicum chinense is being introgressed into commercial Bell capsicum. However, our knowledge of the molecular mechanisms leading to the resistance response to CaCV infection is limited. Therefore, transcriptome and expression profiling data provide an important resource to better understand CaCV resistance mechanisms. Methodology/Principal Findings We assembled capsicum transcriptomes and analysed gene expression using Illumina HiSeq platform combined with a tag-based digital gene expression system. Total RNA extracted from CaCV/mock inoculated CaCV resistant (R) and susceptible (S) capsicum at the time point when R line showed a strong hypersensitive response to CaCV infection was used in transcriptome assembly. Gene expression profiles of R and S capsicum in CaCV- and buffer-inoculated conditions were compared. None of the genes were differentially expressed (DE) between R and S cultivars when mock-inoculated, while 2484 genes were DE when inoculated with CaCV. Functional classification revealed that the most highly up-regulated DE genes in R capsicum included pathogenesis-related genes, cell death-associated genes, genes associated with hormone-mediated signalling pathways and genes encoding enzymes involved in synthesis of defense-related secondary metabolites. We selected 15 genes to confirm DE expression levels by real-time quantitative PCR. Conclusion/Significance DE transcript profiling data provided comprehensive gene expression information to gain an understanding of the underlying CaCV resistance mechanisms. Further, we identified candidate CaCV resistance genes in the CaCV-resistant C. annuum x C. chinense breeding line. This knowledge will be useful in future for fine mapping of the CaCV resistance locus and potential genetic engineering of resistance into CaCV-susceptible crops.