The Draft Genome of a C4 Dicot, Amaranthus hypochondriacus

Grain amaranths, members of Amaranthaceae family of plants, are C4 dicots that are known to produce edible seeds with lysine content as high as milk. Given the obscurity during modern times, it is hard to believe that grain amaranths were domesticated for human consumption some thousands of years ago during the Aztec and the Inca civilization. Lysine being the most limiting essential amino acid in cereals and C4 carbon fixation being one of the most sought after phenotypes in protein rich legumes and nuts, grain amaranths hold the potential to address protein malnutrition problem from multiple fronts using diverse strategies. Furthermore, the Amaranths are classified under Caryophylalles, a clade distal from those containing other edible dicot plants, thus providing the much sought after opportunity to diversify the much needed food base. The economic potential of grain Amaranths demands the benefit of NGS technologies. Here, we present the progress made in deciphering the genome and transcriptomes of Amaranthus hypochondriacus, a grain variety cultivated in the state of Karnataka, India. The species was selected both for the erect seed heads and relatively aggressive growth compared to A. caudatus and A. cruentus, the only other two Amaranthus species producing edible grains. We demonstrate that 80% of the coding regions could be deciphered from the 105X coverage of short reads from a single sequencing platform, Illumina GAIIx. Estimation of the coverage of coding regions based on various criteria will be discussed.