The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal.
Bottom Line: 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.
Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.Show MeSH
Mentions: We obtained the domesticated grains of A. hypochondriacus from farmers in northern Karnataka growing this as a crop for consumption in the name of ‘Rajgira’ or ‘Rajeera’ throughout southern India. We purchased the seeds of other grain species, A. cruentus and A. caudatus, from Park Seeds sold in the names of ‘Autumn's Touch’ and ‘Love-Lies-Bleeding’, respectively. These three types of seeds were grown in campus grounds in three separate lots for taxonomic purposes (Fig. 1). Large numbers of seeds from the first round from each grain species were whitish or pinkish for A. hypochondriacus, whitish for A. cruentus, and reddish for A. caudatus (shown inset in Fig. 1). Amaranthus hypochondriacus produced two types of plants—one with white and the other with red inflorescences. Separating the seeds of white and red varieties of A. hypochondriacus and growing for over two generations retained the inflorescence of the parent plants in the successive generations, thus suggesting purity of lines obtained from farmers. Also, repeated generations produced not only 100% white seeds for the white plants of A. hypochondriacus, but also the plants looked very similar in size, inflorescence, and yield. We have used the tissues from the plants of A. hypochondriacus with white inflorescence after two generations for sequencing both the genome and the transcriptomes reported here.Figure 1.
Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.