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)

The recent successes of genome-wide expression profiling in biology tend to overlook the power of genetics. We here propose a merger of genomics and genetics into ‘genetical genomics’. This involves expression profiling and marker-based fingerprinting of each individual of a segregating population, and exploits all the statistical tools used in the analysis of quantitative trait loci. Genetical genomics will combine the power of two different worlds in a way that is likely to become instrumental in the further unravelling of metabolic, regulatory and developmental pathways.

Genetical genomics : the added value from segregation

Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO2 or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.

Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review.

https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00087-8.pdf

Signaling Mechanisms in Pattern-Triggered Immunity (PTI)

Background

The control of plant anthocyanin accumulation is via transcriptional regulation of the genes encoding the biosynthetic enzymes. A key activator appears to be an R2R3 MYB transcription factor. In apple fruit, skin anthocyanin levels are controlled by a gene called MYBA or MYB1, while the gene determining fruit flesh and foliage anthocyanin has been termed MYB10. In order to further understand tissue-specific anthocyanin regulation we have isolated orthologous MYB genes from all the commercially important rosaceous species.

Results

We use gene specific primers to show that the three MYB activators of apple anthocyanin (MYB10/MYB1/MYBA) are likely alleles of each other. MYB transcription factors, with high sequence identity to the apple gene were isolated from across the rosaceous family (e.g. apples, pears, plums, cherries, peaches, raspberries, rose, strawberry). Key identifying amino acid residues were found in both the DNA-binding and C-terminal domains of these MYBs. The expression of these MYB10 genes correlates with fruit and flower anthocyanin levels. Their function was tested in tobacco and strawberry. In tobacco, these MYBs were shown to induce the anthocyanin pathway when co-expressed with bHLHs, while over-expression of strawberry and apple genes in the crop of origin elevates anthocyanins.

Conclusions

This family-wide study of rosaceous R2R3 MYBs provides insight into the evolution of this plant trait. It has implications for the development of new coloured fruit and flowers, as well as aiding the understanding of temporal-spatial colour change.

An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae

Regulation of gene expression at the level of transcription controls many crucial biological processes. Transcription factors (TFs) play a great role in controlling cellular processes and MYB TF family is large and involved in controlling various processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense etc. Here, we review MYB TFs with particular emphasis on their role in controlling different biological processes. This will provide valuable insights in understanding regulatory networks and associated functions to develop strategies for crop improvement.

/pdf/myb-transcription-factor-genes-as-regulators-for-plant-1xuf8cbdfx.pdf

MYB transcription factor genes as regulators for plant responses: an overview

A step towards genotype-independent regeneration of cotton (Gossypium hirsutum L.) was achieved by selection for regeneration potential (RG) in commercial seed of elite cultivars. A callus induction medium (MCIM) empirically determined for the cultivar `Maxxa' paved the way for RG selection among individual genotypic variants within a cultivar. MCIM consists of a basal Murashige-Skoog medium, supplemented with a unique combination of two synthetic auxins. Hypocotyl explants of `Coker 312', `Maxxa' and `Riata' seedlings cultured on MCIM successfully produced a high quality, friable callus as defined by its color, texture, size, and organization. Based on the number of fertile plants regenerated on a per seedling basis, RG was estimated as 17.4%, 44.4% and 80% in Acala cotton cultivars `Maxxa', `Ultima', and `Riata', respectively. The high RG of the cultivar Riata, a Round-up Ready® transgenic cultivar in a Maxxa genetic background, is likely due to additional RG alleles introgressed from the transgenic parent. Genotypic differences between cultivars for RG was reflected by the need for supplemental kinetin to efficiently regenerate `Ultima' plantlets via somatic embryogenesis. RG selection pressure through two cycles of selection resulted in development of advanced highly regenerable `Max-R' lines in an elite genetic background with immediate potential as suitable germplasm for breeding and biotechnology applications. Based on the results presented here, strategies for genotype-independent transformation and regeneration of cotton are proposed that integrate selection and introgression of regeneration potential in improvement programs.

Development of a highly regenerable elite Acala cotton (Gossypium hirsutum cv. Maxxa): a step towards genotype-independent regeneration

An efficient and reproducible protocol is required to achieve high frequency transformation from transformed calli. We report here high frequency plant regeneration from mature seed derived embryogenic calli of two recalcitrant indica rice cultivars HKR-46 and HKR-126 after partial desiccation treatment. Embryogenic and nodular callus was initiated on MS basal medium supplemented with 2.5 mg l -1 2,4-D, 500 mg l -1 proline, 500 mg l -1 casein hydrolysate, 30 g l -1 sucrose and 2.5 g l -1 gelrite. Several media with different combinations of growth regulators were tried. Maximum shoot regeneration frequency (63%) was observed in partially desiccated calli for 48 h in cv. HKR 46 and 82.1 per cent in cv. HKR-126 on the MS modified medium supplemented with 2 mg l -1 kinetin + 0.5 mg l -1 NAA + 30 gl -1 sucrose + 6 g l -1 gelrite followed by in the medium supplemented with 1 mgl -1 2ip + 30 g l -1 sucrose + 6 g l -1 gelrite (61% in cv. HKR-46 and 79.2 % in cv. HKR-126). Highly significant regeneration differences were observed in partially desiccated calli (48 h) in comparison to non-dehydrated (0 h desiccation) calli. Shoot regeneration frequency increased from 1.2 to 5.6 fold after 48 h of desiccation in both the cultivars on different regeneration media. Shoot regeneration frequency declined at 72 h desiccation treatment as compared to 48 h treatment. Well-developed plantlets were hardened and transferred to the green house. Key words: Plant regeneration; indica rice; mature embryo; partial desiccation. African Journal of Biotechnology Vol.3(5) 2004: 256-259

/pdf/high-frequency-plant-regeneration-from-desiccated-calli-of-vlxaqzsrm5.pdf

High frequency plant regeneration from desiccated calli of indica rice (Oryza Sativa l.)

Plant biotechnology has great potential for improving target traits in crops. This can be achieved by the production of transgenic crops and marker-assisted breeding. Marker-assisted breeding has gained momentum in recent times since it does not need biosafety regulations. Several kind of molecular markers are available for use in crop breeding, such as restriction fragment length polymorphism, microsatellites, sequence characterized amplified region, sequence-tagged site, inter-simple sequence repeat amplification, amplified fragment length polymorphism and single nucleotide polymorphism. Sequence-related amplified polymorphism is a novel molecular marker system which is based on open reading frames (ORFs) developed from genome sequence data of Arabidopsis. It provides a unique combination of forward and reverse primers which can be selected arbitrarily giving a large number of primer combinations. Since this is an ORF-based marker system, it targets functional genes and has potential for their application in crop breeding. This marker system was first used and demonstrated by Li and Quiros in Brassica oleracea in 2001, and since then there have been several reports in different plant species ranging from field crops to tree species for assessing genetic diversity, mapping and tagging of genes, hybrid identification and sex determination. This review provides an overview of SRAP markers and their applications in crop improvement.

Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement

Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications.

/pdf/nanotechnology-based-approaches-for-detection-and-delivery-1v7llmuo42.pdf

Neelam R. Yadav

Papers

MYB transcription factor genes as regulators for plant responses: an overview

Development of a highly regenerable elite Acala cotton (Gossypium hirsutum cv. Maxxa): a step towards genotype-independent regeneration

High frequency plant regeneration from desiccated calli of indica rice (Oryza Sativa l.)

Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement

Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection