Rukam S. Tomar

Draft Genome Sequence of the Methyl Parathion (Pesticide) Degrading Bacterium Pseudomonas spp. MR3.

Pseudomonas spp. MR3 was isolated from the surrounding soil of pesticide manufacturing industries of Ankleshwar, Gujarat. Under laboratory conditions these microbes were able to degrade up to 500xa0ppm of methyl parathion within 72xa0h. Genome sequencing of Pseudomonas spp. MR3 was carried out inIon Torrent (PGM), next generation sequencer. The data obtained revealed 1,268 contigs with genome size of 2.99xa0Mb and Gxa0+xa0C content of 60.9xa0%. The draft genome sequence of strain MR3 will be helpful in studying the genetic pathways involved in the degradation of several pesticides.

Functional characterization of PGPR and its identification through 16 S rRNA sequencing

Plant growth promoting rhizobacteria are known to rapidly colonize the rhizosphere and suppress soil borne pathogens at the root surface. These organisms can also be beneficial to the plant by stimulating growth. Pseudomonas spp. have been studied mainly because of their widespread distribution in soil, their ability to colonize the rhizosphere of host plants and ability to produce a wide range of compounds inhibitory to number of serious plant pathogens.For performing this study, soil sample was collected from six different locations of Junagadh district.Total thirty six bacteria were isolated from the collected soil samples by using general microbiological media, among them ten prominent phosphate solubilizer were selected for studying other plant growth promoting potentials and biochemical characterization. Most efficient Plant growth promoting rhizobia was identified at their strain level by using 16 S rRNA sequencing technology. INTRODUCTION The rhizosphere, representing the thin layer of soil surroundingplant roots and the soil occupied by the roots, supports largeactive groups of bacteria (Villacieroset al., 2003) known asplant growth promoting rhizobacteria (PGPR) (Kloepperet al.,1980).Plant growth promoting rhizobacteria are known torapidly colonize the rhizosphere and suppress soil bornepathogens at the root surface (Rangajaranet al., 2003). These organisms can also be beneficial to the plant by stimulatinggrowth (Bloemberg and Lugtenberg, 2001; Moeinzadehet al.,2010). PGPR can affect plant growth by different direct and indirect mechanisms (Glick 1995; Gupta et al. 2000). Some examples of these mechanisms are (1) increased mineral nutrient solubilization and nitrogen fixation, making nutrients available for the plant; (2) repression of soil borne pathogens (by the production of hydrogen cyanide, siderophores, antibiotics, enzymes like chitinase and/or competition for nutrients); (3) improving plant stress tolerance to drought, salinity, and metal toxicity; and (4) production of phytohormones such as indole-3-acetic acid (IAA) (Gupta et al. 2000). The bacteria presenting one or more of these characteristics are known as plant growth promoting rhizobacteria. Pseudomonas spp. have been studied mainly because of their widespread distribution in soil, their ability to colonize the rhizosphere of host plants and ability to produce a wide range of compounds inhibitory to a number of serious plant pathogens (Weller 1988). The soil bacteria that aggressively colonize the root zone and promote plant growth are generally termed as Plant Growth Promoting Rhizobacteriaand primarily Pseudomonas fluorescence s is identified as an important organism with ability for plant growth promotion and effective disease management properties (Mazzolaet al., 1992). Their applicability as biocontrol agents has drawn wide attention because of the production of secondary metabolites such as siderophore, antibiotics, volatile compounds, Hydrogen Cyanide, enzymes and phyto-hormones (Nagarajkumaret al., 2004). In vitro antibiosis of P. fluorescence strains towards the rice sheath rot pathogen S. oryzaedemonstrated that this pathogen is sensitive to P. fluorescence (Sakthivel and Gnanamanickam, 1987). The biocontrol mechanism to suppress fungal pathogens by Pseudomonas spp. normally involves the production of antibiotics and P. fluorescence s has a gene cluster that produces a suite of antibiotics, including compounds such as 2,4-diacetylphloroglucinol (DAPG), phenazine, pyrrolnitrin, pyoluteorin and bio-surfactantantibiotics (Angayarkanniet al., 2005). Fluorescence t Pseudomonas is uniquely capable of synthesizing many of these antibiotics, not only to enhance its own fitness but also to help in the maintenance of soil health and bioprotection of crops from pathogens (Gaur et al., 2004). Presently, there are number of commercial isolates of Pseudomonas available in the market. MATERIALS AND METHODS ISOLATION AND PURIFICATION Collection of soil sample: The soil sample was collected for the Isolation of plant growth promoting rhizobiafrom rhizosphere of Junagadh district fields of Gujarat. Intact root system was plowed out and the rhizospheric soil samples were carefully taken in sterilized plastic bags. Samples were collected from six different points within area and mix thoroughly; likewise six different locations were selected from the Junagadh district. Isolation of bacteria: For the isolation, 1 gram of each soil samples collected from the various collection sites was dissolved in 10 ml sterile distilled water and mix well for 10 minutes. Serial dilution was made from each sample and appropriate dilution was spread on Nutrient agar plate and incubated at 37±0.1 0C for 24hrs. From the mixed population of microbes, microbial strains were isolated by single colony isolation from the nutrient agar medium. Out of total 57 microbial isolates, 36 isolates were selected for the test of phosphate solubilizing activity. Streak plate method was used for obtaining pure culture, as and when required.

Transcriptomic signature of drought response in pearl millet ( Pennisetum glaucum (L.) and development of web-genomic resources

Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource (http://webtom.cabgrid.res.in/pmdtdb/) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.

Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton (Gossypium hirsutum L.)

Cytoplasmic Male Sterility is maternally inherited trait in plants, characterized by failure to produce functional pollen during anther development. Anther development is modulated through the interaction of nuclear and mitochondrial genes. In the present study, differential gene expression of floral buds at the sporogenous stage (SS) and microsporocyte stage (MS) between CGMS and its fertile maintainer line of cotton plants was studied. A total of 320 significantly differentially expressed genes, including 20 down-regulated and 37 up-regulated in CGMS comparing with its maintainer line at the SS stage, as well as and 89 down-regulated and 4 up-regulated in CGMS compared to the fertile line at MS stage. Comparing the two stages in the same line, there were 6 down-regulated differentially expressed genes only induced in CGMS and 9 up-regulated differentially expressed gene only induced in its maintainer. GO analysis revealed essential genes responsible for pollen development, and cytoskeleton category show differential expression between the fertile and CGMS lines. Validation studies by qRT-PCR shows concordance with RNA-seq result. A set of novel SSRs identified in this study can be used in evaluating genetic relationships among cultivars, QTL mapping, and marker-assisted breeding. We reported aberrant expression of genes related to pollen exine formation, and synthesis of pectin lyase, myosine heavy chain, tubulin, actin-beta, heat shock protein and myeloblastosis (MYB) protein as targets for CMS in cotton. The results of this study contribute to basic information for future screening of genes and identification of molecular portraits responsible for CMS as well as to elucidate molecular mechanisms that lead to CMS in cotton.

Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence

Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25–80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73u2009Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

Author Correction: Transcriptomic signature of drought response in pearl millet ( Pennisetum glaucum (L.) and development of web-genomic resources

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Genome Sequencing Analysis of Macrophomina Phaseolina Resistant and Susceptible Castor Genotype

Published by Oriental Scientific Publishing Company

Assessment of genetic variability among Muskmelon (Cucumis melo L.) genotypes through biometrical traits and molecular markers

Fifty genotypes of muskmelon ( Cucumis melo L .) were evaluated for variability through yield attributing characters and molecular markers. Analysis of variance for yield attributing character showed significant variation for all the traits, indicating presence of sufficient variability. D 2 values distributed all the genotypes in seven clusters. Maximum genetic distance was obtained between clusters II and V, while clusters III and VII displayed the lowest degree of divergence. Total soluble sugars followed by total soluble solids and fruit yield per plant contributed the most towards divergence. Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) analysis using 130 and 62 primers generated 1108 and 462 discrete markers, respectively ranging from 200-1800 bp in size. The UPGMA analysis showed that genotypes were distributed in different groups based on similarities matrix. The dendrogram obtained by combining the data of both the molecular marker revealed genetic similarities ranging between 57% to 81% with highest genetic similarity between MM-68 and MMM-61. These results suggest that RAPD and ISSR markers are useful for muskmelon genetic diversity analysis from different region of India, which will be helpful for further genetic improvement program of plant. Knowledge on the genetic diversity of muskmelon can be used to future breeding programmes to improve fruit quality.

Draft Genome Sequence of the Endophytic Bacterium Enterobacter spp. MR1, Isolated from Drought Tolerant Plant (Butea monosperma)

Enterobacter sp. MR1 an endophytic plant growth promoting bacterium was isolated from the roots of Butea monosperma, a drought tolerant plant. Genome sequencing of Enterobacter spp. MR1 was carried out in Ion Torrent (PGM), Next Generation Sequencer. The data obtained revealed 640 contigs with genome size of 4.58xa0Mb and G+C content of 52.8xa0%. This bacterium may contain genes responsible for inducing drought tolerance in plant, including genes for phosphate solubilization, growth hormones and other useful genes for plant growth.