The Draft Genome and Transcriptome of Amaranthus hypochondriacus

The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal DNA Res dsu021

First published online July 28, 2014 doi:10.1093/dnares/dsu021 (18 pages) Full paper available here

o    Meeta Sunil, Arun K. Hariharan, Soumya Nayak, Saurabh Gupta, Suran R. Nambisan, Ravi P. Gupta, Binay Panda, Bibha Choudhary, and Subhashini Srinivasan


Grain amaranths, edibleC4dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essentialaminoacids in cereals andC4photosynthesis beingoneof themost sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n 5 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution.

Key words: Caryophyllales; grain amaranth; Amaranthus hypochondriacus; lysine biosynthesis; C4 photosynthesis