title: The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal.
abstract: Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most 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 = 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.
authors: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Meeta
authors: M
authors: Sunil
authors: GANIT Labs: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Arun K
authors: AK
authors: Hariharan
authors: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Soumya
authors: S
authors: Nayak
authors: GANIT Labs: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Saurabh
authors: S
authors: Gupta
authors: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Suran R
authors: SR
authors: Nambisan
authors: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Ravi P
authors: RP
authors: Gupta
authors: GANIT Labs: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Binay
authors: B
authors: Panda
authors: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.
authors: Bibha
authors: B
authors: Choudhary
authors: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India ssubha@ibab.ac.in.
authors: Subhashini
authors: S
authors: Srinivasan
mesh_terms: D027721:Amaranthus / Q000235:genetics* / Q000378:metabolism; D002523:Edible Grain / Q000235:genetics* / Q000378:metabolism; D018745:Genome, Plant / Q000502:physiology*; D008239:Lysine / Q000096:biosynthesis / Q000235:genetics; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome / Q000502:physiology*
chemical_list: D008239:Lysine
keywords: Amaranthus hypochondriacus; C4 photosynthesis; Caryophyllales; grain amaranth; lysine biosynthesis