Genome Data



Primary Details

Genome ID GEN2
Plant Name Withania somnifera
Description Draft frame of Ashwagandha (Withania somnifera) genome. Abstract: Illumina Hi seq 4000 paired-end De-novo sequencing of NEXTFLEX rapid DNA sequencing kit derived paired-end libraries of cultivated annual inbred CWS11 of W. somnifera.

About Genome

Field Data Plant Image
Platform Illumina HiSeq4000
Strategy De novo RNA Seq
Source Genomic
Library Name CWS11
Layout Paired end
Spot Value 302
Bases 62.9 Gb
Size 25.8 Gb
GC Content Percentage 39.4
Publish Data 2020-08-11
External Database ID PRJNA483387
DNA C-Value 4.40
Submitted By Dr. Tripta Jhang, CSIR-Central Institute of Medicinal & Aromatic Plants, Lucknow, Uttar Pradesh, India

Images

Description Details

Materials & Method
Whole genome sequencing (WGS) library was prepared with Illumina-compatible NEXTflex Rapid DNA sequencing kit (BIOO Scientific, Austin, Texas, U.S.A.) at Genotypic Technology Pvt. Ltd., Bangalore, India. Briefly, DNA was shearedusing Covaris S2 sonicator (Covaris, Woburn, Massachusetts, USA) to generate approx. fragment size distribution from 300 bp to 500bp.The fragment size distribution was checkedon Agilent TapeStation and subsequently purified using Highprepmagnetic beads (Magbio). Purified fragments were end-repaired, adenylated and ligated to Illumina multiplexbarcode adaptorsas per NEXTFlex Rapid DNAsequencing kit protocol. Adapter-ligatedDNA was purified usingHighprepbeads. Resultant fragments were amplified for 5cyclesof PCR using Illumina-compatible primers provided in the NEXTFlexRapid DNA sequencing kit.Final PCR product (sequencing library) was purified withHighprepbeads, followed by library quality control check. Illumina-compatible sequencing library wasquantified by Qubit fluorometer (Thermo Fisher Scientific, MA, USA) and its fragment size distribution was analyzed on Agilent 2200 Tapestation.
SRA database IDs (NCBI, USA)
SRA database Run ID: SRR7760127; Experiment ID: SRX4615795; Biosample ID: SAMN09737281 (SRS3718800); Bioproject ID: PRJNA483387; SRA Study ID: SRP158960

Genomic Data

Raw Data
Raw Sequence File Raw Genome Data Download SRA (NCBI) Link VIEW DOWNLOAD

Pathway Analysis Report Data

Transcript id KO id Description Pathway Pathway function Organism

Predicted SSR Report Data

Scaffold id Type of ssr Pattern of ssr Size ssr start position ssr end position

Functional Annotation Report Data

query_id query_length subject_id subject_length percentage_identity alignment_length query_coverage subject_coverage noof_mismatches noof_gaps query_start query_end subject_start subject_end e_value score_entry entry_name protein_description gene_names ec_number organism_name pathway_name protein_existence protein_family go_bp go_mf go_cc