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

The pungency, lineament of chilli, is conferred by a set of compounds known as capsaicinoids which are synthesized only in fruits of capsicum genus. Accumulation of capsaicinoids in the fruits may be influenced by various environmental factors beyond their optimal range for the plant. A few studies have investigated the impact of abiotic stress on capsaicinoids production. In present study, the impact of salt stress on capsaicin accumulation was evaluated in three capsicum cultivars. To accomplish this objective three capsicum cultivars (CO1, K2 and G4) having different sensitivity level against salt were subjected to various salt concentrations (25mM, 50mM, 100mM, 150mM and 200mM). However, capsaicin accumulation was depended on stress severity, fruit age as well as the genotypes. Capsaicin accumulation was increased in fruits plants treated with low salt concentration as compared to control plants while it was found to be decreasing in fruits of plant

Impact of Salt on Capsaicin Synthesis in Three Capsicum Cultivars.

Bi-Functional Aspects of Peptide Decorated PLGA Nanocarriers for Enhanced Translocation Across the Blood-Brain Barrier through Macropinocytosis

A pilot-scale study of the integrated phycoremediation-photolytic ozonation based municipal solid waste leachate treatment process.

Various Bacillus spp. capable of producing enzymes with industrially desirable properties have been isolated from adverse environments. Here, we announce the 3.91-Mbp draft genome sequence of a moderately salt-resistant Bacillus vallismortis strain, TD3, capable of producing several industrially relevant enzymes.

Genome Sequence of Bacillus vallismortis TD3, a Salt-Tolerant Strain Isolated from the Sediments of a Solar Saltern in Tamil Nadu, India.

Evolving disease resistance rice variety has become a continuous encounter from plant pathologists’ point of view, against the changing scenario in the severity of various fungal, bacterial and viral diseases. Although we are successful to some extent in developing some varieties through conventional and molecular breeding, the recent genome level  data indicate that we have only disclosed the tip of an iceberg. The strategy of introducing single foreign gene for every disease crop plants like rice, suffers not only from regulatory issues of genetically modified rice but also lack of sustainability under field tests. This is attributed to the fact that pathogen resistance is mediated by complex networking of genes and their protein products. Transcription factors that control expression of hundreds of other genes offer themselves as valid  candidate for key gene transgenics. Rice transcription factors like Osmyb4 is observed to regulate many PR protein genes and genes involved in post infection defense. Hence, over-expressing these gene(s) in cultivated variety(s) would result in transgenic rice resistant to multiple diseases. The level of constitutive expression of these genes should however be evaluated in major cultivated varieties of rice and a correlation of their native level of resistance/susceptibility to diseases may complement the  approach.

Kodiveri Muthukaliannan Gothandam

Papers

Impact of Salt on Capsaicin Synthesis in Three Capsicum Cultivars.

Bi-Functional Aspects of Peptide Decorated PLGA Nanocarriers for Enhanced Translocation Across the Blood-Brain Barrier through Macropinocytosis

A pilot-scale study of the integrated phycoremediation-photolytic ozonation based municipal solid waste leachate treatment process.

Genome Sequence of Bacillus vallismortis TD3, a Salt-Tolerant Strain Isolated from the Sediments of a Solar Saltern in Tamil Nadu, India.

‘Master switch’ genes for disease resistance in rice: lessons learnt and lessons to learn