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: The seeds of the plants selected for sequencing were allowed to germinate in water for 24 h. The root tips were incubated at 4°C for 4 h and then fixed using Carnoy's solution. The processed root tips were excised and treated with 1 N HCl for 1 min, followed by treatment with 45% acetic acid for 10 min, staining with 0.2% aceto-orcein along with gentle heat fixing over a spirit lamp, squashing with the thumb, and mounting using 50% glycerol on a microscopic glass slide. The image was captured at 100× magnification under a compound light microscope. As shown in Fig. 2, the number of chromosomes in the selected diploid plant was confirmed to be 32 (n = 16) for sequencing purposes.Figure 2.
Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.