Gold Genome

• Genome backbone: 10x Pacbio Sequel or nanopore ultra long read data.
• Genome error correction: 80-100x Illumina short read data (150x2bp reads). (Multiple insert size library: 500,800,1200,1800 pooled)
• Scaffolding: 20 Kb Mate-pair Library + Filtered Ultra long reads (>15kb)
• Pseudomolecules: GBS/ddRAD based biparental Linkage Mapping on 96 samples and further scaffolding of scaffolds into pseudomolecules.

Standard Bioinformatics includes:

• Hybrid assembly
• Scaffolding
• Pseudomolecule generation.
• Genome Annotation & Comparative Genomics
• Gene prediction & annotation using: Ab-initio, homology based, cDNA based.
• BLASTP alignment to KEGG, SwissProt, and TrEMBL databases.
• Motifs and domains using InterProScan against protein databases, including ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE.
• non-coding RNA (ncRNA) prediction, rRNA, transfer RNAs (tRNAs), snRNA and microRNAs annotations.
• Syntenic blocks and gene collinearity analysis with 6 major plant species. Synonymous (Ks) and non-synonymous (Ka) substitution rates for orthologous gene pairs.
• Phylogenomics analysis for sequenced land races/ wild populations to identify selective sweeps. IBD analysis. LD analysis. Population structure analysis.