With the recent technological advances in genomics research, utilizing genomics for enhancing the precision and efficiency of crop breeding has become a possibility. And a paradigm shift from marker assisted breeding to “genomics-assisted breeding” is under way.

Initial microbial sequencing projects focused on model organisms or those with practical applications, i.e. medically or industrially important species. This biased focus on single species and strains ignored the extreme diversity of the microbial world where even the most closely related species/strains can vary greatly in the composition of their ‘dispensable genes’.

However, the advent of low cost and high-throughput sequencing platforms was ideally employed to resequence microbial whole genomes. Forty years of genome sequencing has thus resulted in an abundance of publically available genome sequences stored in online databases. This catalog of genomes—containing representatives from nearly all phyla—provides a bank of reference species to which reads are aligned to reconstruct the genome of the target organism.

Data and analysis workflow for microbiome analysis (Weinstock, 2012)

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