A5054548116- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Phytochemicals and Medicinal Plants
- Subterranean biodiversity and taxonomy
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Protist diversity and phylogeny
- Moringa oleifera research and applications
- Essential Oils and Antimicrobial Activity
- Plant biochemistry and biosynthesis
- Chromosomal and Genetic Variations
- Physiological and biochemical adaptations
- RNA and protein synthesis mechanisms
- Aquaculture disease management and microbiota
- Fish Biology and Ecology Studies
- Aquaculture Nutrition and Growth
- Marine Invertebrate Physiology and Ecology
- Animal Genetics and Reproduction
- Cassava research and cyanide
- Marine Biology and Ecology Research
- Biological Research and Disease Studies
- Ichthyology and Marine Biology
- Cephalopods and Marine Biology
- MicroRNA in disease regulation
Institute of Molecular and Cell Biology
2017-2022
Agency for Science, Technology and Research
2017-2022
Genome Institute of Singapore
2022
National Centre for Biological Sciences
2011-2020
Manipal Academy of Higher Education
2011-2015
Tata Institute of Fundamental Research
2010-2013
SASTRA University
2011
King Abdullah University of Science and Technology
2011
Abstract Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient their timing in relation to cyclostome-gnathostome divergence remained contentious. Here we generate de novo long-read-based chromosome-scale assemblies for Japanese lamprey elephant shark. Using these other representative genomes developing algorithms probabilistic macrosynteny model, reconstruct high-resolution...
Krishna Tulsi, a member of Lamiaceae family, is herb well known for its spiritual, religious and medicinal importance in India. The common name this plant 'Tulsi' (or 'Tulasi' or 'Thulasi') considered sacred by Hindus. We present the draft genome Ocimum tenuiflurum L (subtype Tulsi) report. paired-end mate-pair sequence libraries were generated whole sequenced with Illumina Hiseq 1000, resulting an assembled 374 Mb, coverage 61 % (612 Mb estimated size). have also studied transcriptomes...
Abstract The evolutionary history of horseshoe crabs, spanning approximately 500 million years, is characterized by remarkable morphological stasis and a low species diversity with only four extant species. Here we report chromosome-level genome assembly for the mangrove crab ( Carcinoscorpius rotundicauda ) using PacBio reads Hi-C data. spans 1.67 Gb contig N50 7.8 Mb 98% assigned to 16 chromosomes. contains five Hox clusters 34 genes, highest number reported in any invertebrate. Detailed...
Cytidine deaminases of the AID/APOBEC family catalyze C-to-U nucleotide transitions in mRNA or DNA. Members APOBEC3 branch are involved antiviral defense, whereas AID contributes to diversification antibody repertoires jawed vertebrates via somatic hypermutation, gene conversion, and class switch recombination. In extant jawless vertebrate, lamprey, two members implicated generation diversity variable lymphocyte receptors (VLRs). Expression studies linked CDA1 CDA2 genes assembly VLRA/C...
Abstract Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability genomic resources these species will be valuable in planning appropriate conservation measures. Whole‐genome sequences are currently available three species. In this study, we generated a chromosome‐level genome assembly the fourth Asian coastal horseshoe crab ( Tachypleus gigas ; size...
Three-dimensional domain swapping is a unique protein structural phenomenon where two or more chains in oligomer share common segment between individual chains. This observed an array of structures oligomeric conformation. Protein swapped conformations perform diverse functional roles and are also associated with deposition diseases humans. We have performed in-depth literature curation bioinformatics analyses to develop integrated knowledgebase proteins involved 3D swapping. The hallmark...
Background 3D domain swapping is an oligomerization process in which structural elements get exchanged between subunits. This mechanism grasped interest of many researchers due to its association with neurodegenerative diseases like Alzheimer's disease, spongiform encephalopathy etc. Despite the biomedical relevance, very little known about understanding this mechanism. The quest for ruling principles behind curious phenomenon that could enable early prediction provided impetus our...
Abstract The transcription factor Pax6 is crucial for the development of central nervous system, eye, olfactory system and pancreas, implicated in human disease. While a single gene exists chicken, occurs as family other vertebrates, with two members elephant shark, Xenopus tropicalis Anolis lizard three teleost fish such stickleback medaka. However, complement genes jawless vertebrates (cyclostomes), sister group jawed (gnathostomes), unknown. Using combination BAC sequencing genome...
Various methods have been developed to computationally predict hotspot residues at novel protein-protein interfaces. However, there are various challenges in obtaining accurate prediction. We a method which uses different aspects of protein structure and sequence space residue level highlight interface crucial for the complex formation. ECMIS (Energetic Conservation Mass Index Spatial Clustering) algorithm was able outperform existing identification methods. It achieve around 80% accuracy...
Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms' evolutionary responses to past sea-level fluctuations and estimation of their potential is therefore indispensable in efforts mitigate the effects future change. We sampled tens thousands genomic markers ~300 individuals two four extant horseshoe crab species across complex archipelagic Singapore Straits.
The antigen receptor repertoires of one the smallest vertebrates are organized in a fractal manner.
Protein domain families are usually classified on the basis of similarity amino acid sequences. Selection a single representative sequence for each family provides targets structure determination or modeling and also enables fast searches to associate new members family. Such selection could be challenging since some these exhibit huge variation depending number in family, average length extent divergence within We had earlier created 3PFDB database as repository best sequences, selected...
This protocol describes a stepwise process to identify proteins of interest from query proteome derived NGS data. We implemented this on Moringa oleifera transcriptome involved in secondary metabolite and vitamin biosynthesis ion transport. knowledge-driven identifies using an integrated approach involving sensitive sequence search evolutionary relationships. make use functionally important residues (FIR) specific for the protein family identified through its homologous sequences literature....
Studies of the voltage-gated sodium (Nav) channels extant gnathostomes have made it possible to deduce that ancestral possessed four channel genes derived from a single chordate gene following two rounds genome duplication early in vertebrates. We investigated Nav family species lampreys (the Japanese lamprey
Domain swapping mechanism is a specialised mode of oligomerization proteins in which part protein exchanged non-covalent manner between constituent subunits. This highly affected by several physiological conditions. Here, we present detailed analysis ofthe effect pH on different regions the domain swapped oligomer considering examples are known to be sensitive transiting from monomeric domain-swapped dimeric form. The energetic calculations were performed using specialized method considers...
Singapore's National Flower, Papilionanthe (Ple.) Miss Joaquim 'Agnes' (PMJ) is highly prized as a horticultural flower from the Orchidaceae family. A combination of short-read sequencing, single-molecule long-read sequencing and chromatin contact mapping was used to assemble PMJ genome, spanning 2.5 Gb 19 pseudo-chromosomal scaffolds. Genomic resources chemical profiling provided insights towards identifying, understanding elucidating various classes secondary metabolite compounds...
In this paper, we present the data acquired during transcriptome analysis of plant Moringa oleifera [1] from five different tissues (root, stem, leaf, flower and seed) by RNA sequencing. A total 271 million reads were assembled with an N50 2094 bp. The combined was assessed for transcript abundance across tissues. protein coding genes identified transcripts annotated used orthology analysis. Further, enzymes involved in biosynthesis select medicinally important secondary metabolites,...
Protein domains are the compact, evolutionarily conserved units of proteins that can be utilized for function association large number gene products realised from whole genome sequencing projects. Homology, inferred by sequence similarity, is usually a reason transfer annotation pre-existing domain families to products. Sequence analysis protocols directed reference used homology searches reduce computational time in such large-scale data mining processes. As protein diverse nature, it an...
Available three-dimensional structures of proteins suggest that can engage in limited extent aggregation through a peculiar form ‘hand-shake’ strategy is defined as ‘domain swap...
Pathways of all the 14 important medicinal metabolites Tulsi genome which were studied in detail.