Vandna Chawla

Vandna Chawla

PhD

About

68
Publications
3,595
Reads
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221
Citations

Publications

Publications (68)
Article
Full-text available
Background Selection of optimal computational strategies for analyzing metagenomics data is a decisive step in determining the microbial composition of a sample, and this procedure is complex because of the numerous tools currently available. The aim of this research was to summarize the results of crowdsourced sbv IMPROVER Microbiomics Challenge d...
Preprint
Background: Selection of optimal computational strategies for analyzing metagenomics data is a decisive step in determining the microbial composition of a sample, and this procedure is complex because of the numerous tools currently available. The crowdsourced sbv IMPROVER Microbiomics Challenge and extended analyses benchmarked 21 off-the-shelf ta...
Article
Full-text available
Nitrate is the main source of inorganic nitrogen for plants, which also act as signaling molecule. Present study was aimed to understand nitrate regulatory mechanism in Brassica juncea cultivars, with contrasting nitrogen-use-efficiency (NUE) viz. Pusa Bold (PB, high-NUE) and Pusa Jai Kisan (PJK, low-NUE), employing RNA-seq approach. A total of 403...
Article
Full-text available
Tea quality and yield is influenced by various factors including developmental tissue, seasonal variation and cultivar type. Here, the molecular basis of these factors was investigated in three tea cultivars namely, Him Sphurti (H), TV23 (T), and UPASI-9 (U) using RNA-seq. Seasonal variation in these cultivars was studied during active (A), mid-dor...
Article
The AT-rich genome of P. falciparum has uniquely localized G-rich stretches that have propensity to form G-quadruplexes. However, their global occurrence and potential biological roles in the parasite are poorly explored. Our genome-wide analysis revealed unique enrichment of quadruplexes in P. falciparum genome which was remarkably different from...
Article
With the advent of short-reads-based genome sequencing approaches, large number of organisms are being sequenced all over the world. Most of these assemblies are done using some de novo short read assemblers and other related approaches. However, the contigs produced this way are prone to wrong assembly. So far, there is a conspicuous dearth of rel...
Article
Full-text available
Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome o...
Data
Effect of k-mer size on assembling performance of transcriptome using Velvet, SOAPdenovo and ABySS. (XLS)
Data
Assembly validation with known V. inaequalis nucleotide sequences. (XLS)
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Pfam domains predicted to be present in the secretome of V. inaequalis. (XLS)
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Summary of PHI database gene orthologs in V. inaequalis. (DOC)
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Sizes of selected protein families in V. inaequalis and other plant pathogens. (XLS)
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155 experimentally validated nucleotide sequences for V. inaequalis available at GenBank. (TXT)
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Sequences of known effectors of various pathogenic fungi. (TXT)
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Sequences of known V. inaequalis effectors. (TXT)
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Dissimilar sequence groupings for assembled V. inaequalis transcriptome sequences. (XLS)
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Set A transcripts sequences. (ZIP)
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Set B transcripts sequences. (ZIP)
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Candidate RxLR effector summary. (XLS)
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Assembly validation through Sanger Sequencing. (DOC)
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Cell wall degrading enzymes predicted in transcriptome of V. inaequalis. (XLS)
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Protease genes in different fungal genomes, arranged by MEROPS family. (XLS)
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Blast analysis result against Fungal Cytochrome P450 database. (XLS)
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GO annotation of PHI gene orthologs of V. inaequalis. (XLS)
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Number of reference protein sequences of selected phytopathogenic fungi used for Phylogenomics. (DOC)
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Percentage of carbohydrate-degrading enzymes in ascomycetes fungal pathogens, arranged by GH family. (XLS)
Article
Full-text available
Picrorhiza kurrooa Royle ex Benth. is an endangered plant species of medicinal importance. The medicinal property is attributed to monoterpenoids picroside I and II, which are modulated by temperature. The transcriptome information of this species is limited with the availability of few hundreds of expressed sequence tags (ESTs) in the public datab...
Data
Top highly represented functional conserved domains found in unknown sequences.
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Details on all the transcription factor (TF) families analyzed in P. kurrooa.
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Pooled transcriptome data of P. kurrooa. File contains the remaining data of Additional file 1.
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Guanine-cytosine (GC) content analysis of P. kurrooa transcripts. The average GC content of each transcript was calculated and highest proportion of transcripts belongs to the GC content range of 40-49%.
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Reads per exon kilobase per million (RPKM) based expression of annotated cytochrome P450s (CYPs) in P. kurrooa transcriptome.
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Oligonucleotide sequences and polymerase chain reaction (PCR) conditions used in reverse transcriptase (RT-PCR) based expression analysis.
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Experimentally validated expressed sequence tags (ESTs) of P. kurrooa available at dbEST NCBI. Methods section has details including URL used in the present analysis.
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Top 20 most abundant transcription factor (TF) families analyzed in P. kurrooa. Details of all the TFs are mentioned in Additional file 10.
Data
Pooled transcriptome data of P. kurrooa. Due to large amount, data is divided into Additional file 1 and Additional file 2.
Data
Dissimilar sequence groupings for assembled transcriptome sequences. The grouped sequences are dissimilar from each other, and belong to different regions of common genes. This helps reducing the over-representation of total transcripts, usually missed in assembling.
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Simple sequence repeats (SSRs) identified in transcripts of P. kurrooa.
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Comparative plots for top ten highest represented molecular function (A) and biological process (B) categories in A. thaliana and P. kurrooa.
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Reads per exon kilobase per million (RPKM) based gene expression at 15°C and 25°C in different expression categories ranging from > 10 fold increment to 0.5 fold or lower.
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Reads per exon kilobase per million (RPKM) based expression of transcription factors analysed for P. kurrooa transcriptome at 15°C and 25°C.
Data
Reads per exon kilobase per million (RPKM) based expression of targeted genes of mevalonate (MVA), 2-C-methyl-D-erythritol 4-phosphate (MEP) and phenylpropanoid (PP) pathway (pathways associated with picrosides biosynthesis) at 15°C and 25°C.
Data
Reads per exon kilobase per million (RPKM) based expression of annotated glycosyltransferases in P. kurrooa transcriptome.

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