Next generation complex genome assembly

Abstract

Whole genome assembly boosts the discovery of genes and pathways involved in the key metabolites produced in medicinal plants. Many medicinal plants possess large, polyploid and/or heterozygote genomes, thus denovo assembly of these genomes poses a significant challenge both algorithmically and economically. DeNovoMAGIC-2 assembler has successfully reconstructed some of the largest most repetitive, polyploid and heterozygote plant genomes. Using only high coverage of short Illumina reads, DeNovoMAGIC-2 has assembled over 90 % of the genome sequence of the 16 Gb, hexaploid wheat and the 1 Gb, tetraploid and heterozygote mango genome, with N50 of ~7 Mb and ~1 Mb respectively. Assemblies were completed in 14 and 2 days using 1 Tb and 0.512 Tb RAM computers, respectively. BUSCO analysis revealed full intact gene content for over 90 % of the genome, with clear phasing of allelic and paralog genes. Similar employment of DeNovoMAGIC-2 is expected to reconstruct the genome sequences of many medicinal plants, boosting our basic understanding of metabolite production and accumulation, towards industrializing medicine production from plants.