Next generation complex genome assembly

• Main Authors: Baruch, Kobi, Barad, Omer, Zvi, Gil Ben, Ronen, Gil
• Format: Article
• Language: deu
• Published: Julius Kühn-Institut 2016-07-01
• Series: Julius-Kühn-Archiv
• Online Access: http://pub.jki.bund.de/index.php/JKA/article/view/6473/6075

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.