The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Social Network Analysis

Pentatricopeptide repeat proteins: a socket set for organelle gene expression.

Cytoplasmic male sterility (CMS) and nucleus-controlled fertility restoration are widespread plant reproductive features that provide useful tools to exploit heterosis in crops. However, the molecular mechanism underlying this kind of cytoplasmic-nuclear interaction remains unclear. Here, we show in rice (Oryza sativa) with Boro II cytoplasm that an abnormal mitochondrial open reading frame, orf79, is cotranscribed with a duplicated atp6 (B-atp6) gene and encodes a cytotoxic peptide. Expression of orf79 in CMS lines and transgenic rice plants caused gametophytic male sterility. Immunoblot analysis showed that the ORF79 protein accumulates specifically in microspores. Two fertility restorer genes, Rf1a and Rf1b, were identified at the classical locus Rf-1 as members of a multigene cluster that encode pentatricopeptide repeat proteins. RF1A and RF1B are both targeted to mitochondria and can restore male fertility by blocking ORF79 production via endonucleolytic cleavage (RF1A) or degradation (RF1B) of dicistronic B-atp6/orf79 mRNA. In the presence of both restorers, RF1A was epistatic over RF1B in the mRNA processing. We have also shown that RF1A plays an additional role in promoting the editing of atp6 mRNAs, independent of its cleavage function.

Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing

MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become the subject of intense study. They are a class of post-transcriptional negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in the responses of trees to the stressful environments incurred over their long-term growth. Here, we report the cloning of small RNAs from abiotic stressed tissues of Populus trichocarpa (Ptc) and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, nine families are novel, increasing the number of the known Ptc-miRNA families from 33 to 42. A total of 346 targets was predicted for the cloned Ptc-miRNAs using penalty scores of </=2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six of the selected targets were validated experimentally. The expression of a majority of the novel miRNAs was altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known Ptc-miRNAs identified 19 additional cold stress-responsive Ptc-miRNAs from 14 miRNA gene families. Interestingly, we found that individual miRNAs of a family responded differentially to stress, which suggests that the members of a family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with the long-term growth of tree species and provide useful information for developing trees with a greater level of stress resistance.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2008.03497.x

Stress‐responsive microRNAs in Populus

Accumulating functional genomic data in rice are unveiling the role of regulatory genes and their significance in modulating responses to complex traits like stress tolerance. Rice Osmyb4 is one such gene coding for transcription factor, and the homologous and heterologous ectopic expression has proved increased tolerance to several abiotic stress and few biotic stresses in plants. Nevertheless, the role of this gene in rice plants for disease resistance has not been studied. We attempted to study the correlation of existing bottom-line expression of this gene in selected rice cultivars and their reaction to artificial challenge with the sheath blight pathogen (Rhizoctonia solani) and bacterial leaf blight pathogen (Xanthomonas oryzae pv. oryzae). The study consisted of artificial inoculation of the pathogens and scoring for disease in selected rice cultivars and amplification of Osmyb4 transcripts by a simple reverse transcription PCR. Inoculation studies revealed a higher disease index in cv. IR 50 and lower disease in cvs TRY 3 and IR 36. Reverse transcription PCR in healthy plants revealed significantly higher constitutive expression of this gene in cvs TRY 3 and IR 36 which was not found in IR 50. However, expression of this gene in cv. IR 50 was found to be cold-inducible. The natural expression level of Osmyb4 in disease-resistant rice varieties provides molecular evidences for their possible role in regulating disease resistance.

Naturally Existing Levels of Osmyb4 Gene Expression in Rice Cultivars Correlate with their Reaction to Fungal and Bacterial Pathogens

Carotenoids pathway is one of decisive anabolic pathway which is responsible for diverse, vital functions such as absorption, dissipation and transfer of solar energy for photosynthesis. Change in environmental factors causes modulation in molecular as well physiological responses to acclimate altered conditions. The current study is designed to assess the difference in the expression pattern of carotenoid pathway genes as well as accumulation of β-carotene among three capsicum varieties having different sensitivity level against salt. To achieve this objective salt tolerant (G4), moderate, tolerant (K2) and sensitive (CO1) varieties were treated under different NaCl concentration (25, 50, 100, 150 and 200 mM) for 30 days. Differential expressions of five major genes of carotenoid pathway (phytoene synthase, phytoene desaturase, zeta carotene desaturase, lycopene β-cyclase and capsanthin/capsorubin synthase) were examined. Semi-quantitative real time PCR expression data have demonstrated the declined expression of genes under study as the salt concentration gradually increased. We also analyzed the impact of salt on chlorophyll content and β-carotene content.

Expression of Carotenoid Pathway Genes in Three Capsicum Varieties under Salt Stress

This study was undertaken to investigate the phytochemical and anti-bacterial properties of Amorphophallus commutatus var. wynadensis tubers using solvents of increasing polarity (viz: petroleum ether, hexane, and water). The chemical constituents of various extracts were obtained by the phytochemical analysis. For the anti-bacterial studies, both gram positive bacteria ( Streptococcus pyogenes , Streptococcus faecalis and Bacillus cereus ) and gram negative bacteria ( Enterobacter aerogenes, Escherichia coli, Salmonella typhi, and Proteus mirabilis ) were used. Among the various extracts, the petroleum ether extract (PEE) showed maximum zone of Inhibition (ZOI) against S. typhi and P. mirabilis with ZOI as 35 and 34 mm, respectively. The morphological aspects of A. commutatus are also present.

Morphological, phytochemical, and anti-bacterial properties of wild and indigenous plant (Amorphophallus commutatus)

Aims: This study is an endeavor to gain proper understanding about salt tolerance mechanism in plants; an attempt was made to characterize the differential expression of stress responsive genes, sodium potassium content proline content in three capsicum cultivars having different salt sensitivity level. Place and Duration of Study: School of Bio Sciences and Technology, VIT University, Vellore of India between June 2013 to May 2014. Methodology: Capsicum cultivars (salt tolerant, salt moderate sensitive and salt susceptible) were treated with different concentration of NaCl such as 25mM, 50mM, 100mM, 150mM and 200mM. Gene expression studies under different salt treatment were done for the following genes: osmotic adjustment (CaPROX1), osmotin like protein (CaOSM1), aquaporin (CaPIP2), dehydrin responsive gene (CaDREBLP1), ring domain zinc finger protein gene (CaKR1), membrane protein (CaChi2), endoplasmic reticulum ubiquitine ligase (CaRMa1H1) and cell death repressor (CaBI1). Proline Original Research Article Maurya et al.; ARRB, 6(1): xxx-xxx, 2015; Article no.ARRB.2015.064 67 content and sodium and potassium ion content also measured. Results: The result indicated that genes CaDREBLP1, CaRMa1H1, CaKR1, CaOSM1 were up regulated while CaPROX1, CaPIP2 genes were down regulated under salt stress. But no significant difference was noticed in gene expression level of CaBI1 and CaChi 2 gene. Conclusion: The higher gene expression level of stress responsive genes viz. CaDREBLP1, CaRMa1H1, CaKR1, CaOSM1 may involved in different level of salt tolerance among selected cultivars. Thus differential transcript modulation of these genes in capsicum cultivars indicates their role lending the salt tolerance in salt tolerant cultivar than sensitive.

Kodiveri Muthukaliannan Gothandam

Papers

Naturally Existing Levels of Osmyb4 Gene Expression in Rice Cultivars Correlate with their Reaction to Fungal and Bacterial Pathogens

Expression of Carotenoid Pathway Genes in Three Capsicum Varieties under Salt Stress

Morphological, phytochemical, and anti-bacterial properties of wild and indigenous plant (Amorphophallus commutatus)

Analysis of stress responsive genes in capsicum for salinity responses.

Prognostic significance of Lymph Node Ratio (LNR): Clinical insights and strategies for routine clinical practice.