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The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal.

Sunil M, Hariharan AK, Nayak S, Gupta S, Nambisan SR, Gupta RP, Panda B, Choudhary B, Srinivasan S - DNA Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.

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Karyotype of A. hypochondriacus, the species selected for sequencing, showing diploidy with 32 chromosomes in mitotic root tips. The karyotype shows 32 chromosomes under 100× magnification stained with 0.2% aceto-orcein, as would be expected from the diploid root tips of A. hypochondriacus. This figure appears in colour in the online version of DNA Research.
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DSU021F2: Karyotype of A. hypochondriacus, the species selected for sequencing, showing diploidy with 32 chromosomes in mitotic root tips. The karyotype shows 32 chromosomes under 100× magnification stained with 0.2% aceto-orcein, as would be expected from the diploid root tips of A. hypochondriacus. This figure appears in colour in the online version of DNA Research.

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.


The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal.

Sunil M, Hariharan AK, Nayak S, Gupta S, Nambisan SR, Gupta RP, Panda B, Choudhary B, Srinivasan S - DNA Res. (2014)

Karyotype of A. hypochondriacus, the species selected for sequencing, showing diploidy with 32 chromosomes in mitotic root tips. The karyotype shows 32 chromosomes under 100× magnification stained with 0.2% aceto-orcein, as would be expected from the diploid root tips of A. hypochondriacus. This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263292&req=5

DSU021F2: Karyotype of A. hypochondriacus, the species selected for sequencing, showing diploidy with 32 chromosomes in mitotic root tips. The karyotype shows 32 chromosomes under 100× magnification stained with 0.2% aceto-orcein, as would be expected from the diploid root tips of A. hypochondriacus. This figure appears in colour in the online version of DNA Research.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.

Show MeSH