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Supplemental material, sj-docx-1-bbi-10.1177_11779322211025332 for Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India by Samrat... more
Supplemental material, sj-docx-1-bbi-10.1177_11779322211025332 for Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India by Samrat Ghosh, Aditya Narayan Sarangi, Mayuri Mukherjee, Deeksha Singh, Madduluri Madhavi and Sucheta Tripathy in Bioinformatics and Biology Insights
Additional file 6. Functional annotation for differentially regulated genes. (A) KEGG pathway enrichment data for upregulated DEGs (B) Top ten abundant domains present in the upregulated genes, obtained using Blast2GO (C) the pathway... more
Additional file 6. Functional annotation for differentially regulated genes. (A) KEGG pathway enrichment data for upregulated DEGs (B) Top ten abundant domains present in the upregulated genes, obtained using Blast2GO (C) the pathway reconstruction result of upregulated differentially expressed genes, based on KEGG, generated using BLASTKOALA.
Additional file 4. Differentially expressed genes unique to IR64 cold shock 2 h transcriptome data.
Additional file 3. Gene details for differentially regulated Transcription factors, components of Redox pathway, and other cold-responsive genes.
Additional file 1. Table containing detailed analysis of cold shock (2 h at 4 °C) significantly upregulated and downregulated genes, compared to control conditions, in IR64 seedlings.
Diverse CCNVs revealed by BIC-seq analysis (upper graph for each panel) and a read-depth analysis for heterozygous allele ratios using 10 Kb long non-overlapping sliding window (lower graph). A concatenated view of the 30 largest... more
Diverse CCNVs revealed by BIC-seq analysis (upper graph for each panel) and a read-depth analysis for heterozygous allele ratios using 10 Kb long non-overlapping sliding window (lower graph). A concatenated view of the 30 largest scaffolds with the total length of 30Â MB, which corresponding to approximately a half of the total genome of Phytophthora ramorum, are shown. Scaffolds numbers for large CCNV regions are indicated with pink bars, and those for copy number neutral LOH are shown with blue bars. Scales show log (base 2) fold difference between sample isolates and reference isolates for BIC-seq analysis and log (base 2) ratios of alleles of sample isolates for the heterozygous allele ratio analysis. At each heterozygous locus, a read count ratio (more-abundant allele/less-abundant allele) was calculated. A) A re-isolate 9D1 from a log of coast live oak showing a small copy number change at scaffold 9 in comparison to its original isolate Pr-1556 (wt, bay) used as a reference. ...
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Allele sizes for the 15 multilocus genotypes (MLGs) identified in 30 Washington State isolates of P. ramorum. (PDF 48 kb)
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Mean values for irregularity index and relative lesion area of Phytophthora ramorum isolates identified in K-means analysis. Isolates in Cluster 3 were significantly different from those in Clusters 1 and 2. Bars with different letters... more
Mean values for irregularity index and relative lesion area of Phytophthora ramorum isolates identified in K-means analysis. Isolates in Cluster 3 were significantly different from those in Clusters 1 and 2. Bars with different letters are significantly different at pÂ
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Heuristic picture connoting the green synthesis of iron substituted hydroxyapatite nanoparticles having versatile properties.
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possesses a complex heteroxenic life cycle where infective metacyclic promastigotes are pre-adapted to infect their host and cope up with intracellular stress. Exploiting the similarities between cultured and sandfly derived... more
possesses a complex heteroxenic life cycle where infective metacyclic promastigotes are pre-adapted to infect their host and cope up with intracellular stress. Exploiting the similarities between cultured and sandfly derived promastigotes, we used early and late passage cultured promastigotes to show specific changes at genome level which compromise pathogen fitness reflected in gene expression and infection studies. The pathogen loses virulence mostly transcriptional and translational regulations and long-time cultivation makes them struggle to convert to virulent metacyclics. At the genomic level very subtle plasticity was observed between the early and the late passages mostly in defense-related, nutrient acquisition and signal transduction genes. Chromosome Copy number variation is seen in the early and late passages involving several genes that may be playing a role in pathogenicity. Our study highlights the importance of ABC transporters and calpain like cysteine proteases in ...
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Research Interests: Genetics, Genomics, Comparative Genomics, Biology, Cell Adhesion, and 15 moreAbiotic Stress, Biological Sciences, Environmental Sciences, Gene Order, Genome, Gene, Enzyme, Carbohydrate metabolism, Antifungal Agents, Genome sequence, Base Sequence, Gene Family, Differential expression, Cadherins, and Gene Rearrangement
The genome of the soybean pathogen Phytophthora sojae contains nearly 400 genes encoding candidate effector proteins carrying the host cell entry motif RXLR-dEER. Here, we report a broad survey of the transcription, variation, and... more
The genome of the soybean pathogen Phytophthora sojae contains nearly 400 genes encoding candidate effector proteins carrying the host cell entry motif RXLR-dEER. Here, we report a broad survey of the transcription, variation, and functions of a large sample of the P. sojae candidate effectors. Forty-five (12%) effector genes showed high levels of polymorphism among P. sojae isolates and significant evidence for positive selection. Of 169 effectors tested, most could suppress programmed cell death triggered by BAX, effectors, and/or the PAMP INF1, while several triggered cell death themselves. Among the most strongly expressed effectors, one immediate-early class was highly expressed even prior to infection and was further induced 2- to 10-fold following infection. A second early class, including several that triggered cell death, was weakly expressed prior to infection but induced 20- to 120-fold during the first 12 h of infection. The most strongly expressed immediate-early effect...
Research Interests: Genetics, Plant Biology, Biology, Medicine, Animals, and 15 moreCell Death, Programmed cell death, Gene, Oomycetes, Phytophthora, Microarray Analysis, Effectors, Plant cell, Amino Acid Sequence, Phytophthora sojae, PLANT PROTEINS, Biochemistry and cell biology, Gene Expression Regulation, Molecular Sequence Data, and Agrobacterium tumefaciens
ABSTRACT Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH prototype test probe with B-form, tetrameric DNA... more
ABSTRACT Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH prototype test probe with B-form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH-like ion interacting with (G-C)4, (A-T)4, and [(G-C)·(A-T)]2 deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH-like ion is near known alkylation sites. The results of the Az+ … [(G-C)·(A-T)]2 interaction are virtually identical to those found for the CH-like ion. Aqueous solvation energetics have little effect on the physical association of Az+ with [(G-C)·(A-T)]2.
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These are all ffn files containing CDS sequences of 120 Phytophthora genomes.
Research Interests: Genome and Phytophthora
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing... more
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of...
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Details of NA1 P. ramorum isolates used in this study. Other names, source, geographical location, year of isolation, SSR multilocus genotypes, colony phenotype, relative radial growth rate, relative lesion size, irregularity index,... more
Details of NA1 P. ramorum isolates used in this study. Other names, source, geographical location, year of isolation, SSR multilocus genotypes, colony phenotype, relative radial growth rate, relative lesion size, irregularity index, K-means cluster, CCNV type and contact scientists for isolates are shown. (XLSX 19 kb)
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Pathogens secrete effector molecules that facilitate the infection of their hosts. A number of effectors identified in plant pathogenic Phytophthora species possess N-terminal motifs (RXLR-dEER) required for targeting these effectors into... more
Pathogens secrete effector molecules that facilitate the infection of their hosts. A number of effectors identified in plant pathogenic Phytophthora species possess N-terminal motifs (RXLR-dEER) required for targeting these effectors into host cells. Here, we bioinformatically identify >370 candidate effector genes in each of the genomes of P. sojae and P. ramorum . A single superfamily, termed avirulence homolog ( Avh ) genes, accounts for most of the effectors. The Avh proteins show extensive sequence divergence but are all related and likely evolved from a common ancestor by rapid duplication and divergence. More than half of the Avh proteins contain conserved C-terminal motifs (termed W, Y, and L) that are usually arranged as a module that can be repeated up to eight times. The Avh genes belong to the most rapidly evolving part of the genome, and they are nearly always located at synteny breakpoints. The superfamily includes all experimentally identified oomycete effector and...
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The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously... more
The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.
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Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional... more
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Beside...
1 The Key Laboratory of Plant Immunity/Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China, 2 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F... more
1 The Key Laboratory of Plant Immunity/Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China, 2 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China, 3 Structural Biology & Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India, Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen... more
It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen Phytophthora ramorum NA1 revealed considerable genetic variation in the form of Structural Variants (SVs). To better understand how SVs arise and their significance to the California NA1 population, we studied the evolutionary histories of SVs and the forest conditions associated with their emergence. Ancestral state reconstruction suggests that SVs arose by somatic mutations among multiple independent lineages, rather than by recombination. We asked if this unusual phenomenon of parallel evolution between isolated populations is transmitted to extant lineages and found that SVs persist longer in a population if their genetic background had a lower mutation load. Genetic parallelism was also found in geographically distant demes where forest conditi...
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Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species... more
Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes.Results: The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulat...
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Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many... more
Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenom...
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Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had... more
Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a ‘highly repetitive’ component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive...
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Abstract In the present investigation, nano hydroxyapatite (HAp) and fluorine substituted hydroxyapatite (FHAp) with varying fluorine concentrations have been successfully prepared by hydrothermal method. The as synthesized powders were... more
Abstract In the present investigation, nano hydroxyapatite (HAp) and fluorine substituted hydroxyapatite (FHAp) with varying fluorine concentrations have been successfully prepared by hydrothermal method. The as synthesized powders were characterized using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), high resolution transmission electron microscope (HRTEM) and ion chromatography (IC) for fluorine content analysis. XRD results showed shifting of HAp peaks with increasing fluorine substitution and detected calcium fluoride (CaF2) phase in the synthesized powders where theoretically 100% or more OH ions substituted by F ions. The crystallinity of HAp powder gradually increased and cell volume decreased with fluorine substitution. HRTEM of the synthesized powders showed the nano rod like morphology. The IC was carried out to understand the degree fluoridation in the synthesized powder. The IC result of in vitro fluorine ion leaching showed that fluorine concentration in aqueous medium depends on the degree of fluoridation in the synthesized powder. The as synthesized powders were checked for antimicrobial activity by using both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) strains. The powder having ~33% fluorine substitution showed bactericidal effect. The in vitro fluorine ion release study showed significantly high fluorine concentration in aqueous medium for the HAp powders having more than 50% fluorine substituted. The in vitro cell viability assay using mouse osteoblast cell line (MC3T3-E1) confirmed that the powders were non-cytotoxic.
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Next generation sequencing techniques produce enormous data but its analysis and visualization remains a big challenge. To address this, we have developed Genome Annotator Light(GAL), a Docker based package for genome analysis and data... more
Next generation sequencing techniques produce enormous data but its analysis and visualization remains a big challenge. To address this, we have developed Genome Annotator Light(GAL), a Docker based package for genome analysis and data visualization. GAL integrated several existing tools and in-house programs inside a Docker Container for systematic analysis and visualization of genomes through web browser. GAL takes varieties of input types ranging from raw Fasta files to fully annotated files, processes them through a standard annotation pipeline and visualizes on a web browser. Comparative genomic analysis is performed automatically within a given taxonomic class. GAL creates interactive genome browser with clickable genomic feature tracks; local BLAST-able database; query page, on-fly downstream data analysis using EMBOSS etc. Overall, GAL is an extremely convenient, portable and platform independent. Fully integrated web-resources can be easily created and deployed, e.g. www.eumicrobedb.org/cglab, for our in-house genomes. GAL is freely available at https://hub.docker.com/u/cglabiicb/.
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Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome... more
Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. Compared to other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organised in 1919 contigs and 1898 scaffolds, encompassing 11741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and CRN effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (P. multivor...
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Accumulating evidence suggests that genome plasticity allows filamentous plant pathogens to adapt to changing environments. Recently, the generalist plant pathogen Phytophthora ramorum has been documented to undergo irreversible... more
Accumulating evidence suggests that genome plasticity allows filamentous plant pathogens to adapt to changing environments. Recently, the generalist plant pathogen Phytophthora ramorum has been documented to undergo irreversible phenotypic alterations accompanied by chromosomal aberrations when infecting trunks of mature oak trees (genus Quercus). In contrast, genomes and phenotypes of the pathogen derived from the foliage of California bay (Umbellularia californica) are usually stable. We define this phenomenon as host-induced phenotypic diversification (HIPD). P. ramorum also causes a severe foliar blight in some ornamental plants such as Rhododendron spp. and Viburnum spp., and isolates from these hosts occasionally show phenotypes resembling those from oak trunks that carry chromosomal aberrations. The aim of this study was to investigate variations in phenotypes and genomes of P. ramorum isolates from non-oak hosts and substrates to determine whether HIPD changes may be equival...