Genotyping Indian patients with primary cardiomyopathies-analysis of database.

INTRODUCTION: Each population has its own unique genotype. Genotyping data on Indian cardiomyopathy patients is lacking. METHODS: We aimed to create and analyse a database of sequence variations in Indian patients with primary cardiomyopathies. This included all data of the cardiomyopathy cohort at the Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh. In addition, all published papers in Pubmed containing sequence variations in Indian cardiomyopathy patients till December 2020 using specific search terms were included. Affected genes and sequence variations, methodologies and quality of clinical data was analysed. Novel sequence variations were documented. RESULTS: A database of 493 datasets including 417 different sequence variations was created. Of these, the PGIMER database had 137 datasets consisting of 94 different variants. Only 63 publications included genotyping data of Indian cardiomyopathy cohort from 2000 to 2020 reporting 335 sequence variations. Five (7.9%) studies were from institutions abroad. Of published variations, 35.1% were novel. Most studies carried out selective genotyping. Comprehensive genotyping using cardiomyopathy panels or whole exome sequencing was reported in only 9 (14.3%) publications. CONCLUSION: Database of 417 different sequence variations in Indian cardiomyopathy patients was analysed. Over a third of all reported sequence variations in Indians were novel.

De novo Transcriptome Analysis Revealed Genes Involved in Flavonoid and Vitamin C Biosynthesis in Phyllanthus emblica (L.).

Phyllanthus emblica is an affluent source of various therapeutic components. A few of them like vitamin C and flavonoids are predominant bioactive compounds that are being used in immense pharmacological applications. In-spite of numerous applications, the genomic information of this plant was limited to a few expressed sequence tags (ESTs) in DNA databases. Herein, we developed in-depth transcriptome information of P. emblica using Illumina Hiseq 2000 platform and characterized. A total of 31,285,965 high-quality reads were assembled into 91,288 contigs with the N50 value 358. Out of them, 47,267 contigs were functionally annotated using BLASTX search against NCBI-non-redundant (NR) protein database. Further, 31,366 contigs showed similarity with various gene ontology (GO) terms, and 1299 were related to different enzymes and biosynthetic pathways. We identified the transcripts related to each gene involved in flavonoid and vitamin C biosynthesis. Several cytochrome P450s (CYPs) and glucosyltransferases (GTs) genes involved in flavonoid biosynthesis and various other metabolic pathways were also documented. Further, 6510 transcription factors and 4420 EST derived simple sequence repeat (SSR) markers were also predicted. The present study enlightened various characteristic features of P. emblica genome, and provided an important resource for future molecular and functional genomics studies.