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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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Photographs of the three grain species of Amaranthus grown on campus grounds. The plants from left to right are: A. hypochondriacus, A. cruentus, and A. caudatus, as identified by their taxonomic features including those of the inflorescence and the leaves. Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). Insets are the corresponding seeds obtained after two generations of growing these species on campus grounds. For A. hypochondriacus (left), the seeds from red plants are at the bottom left and those from white plants are shown at the top right.
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DSU021F1: Photographs of the three grain species of Amaranthus grown on campus grounds. The plants from left to right are: A. hypochondriacus, A. cruentus, and A. caudatus, as identified by their taxonomic features including those of the inflorescence and the leaves. Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). Insets are the corresponding seeds obtained after two generations of growing these species on campus grounds. For A. hypochondriacus (left), the seeds from red plants are at the bottom left and those from white plants are shown at the top right.

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.


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)

Photographs of the three grain species of Amaranthus grown on campus grounds. The plants from left to right are: A. hypochondriacus, A. cruentus, and A. caudatus, as identified by their taxonomic features including those of the inflorescence and the leaves. Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). Insets are the corresponding seeds obtained after two generations of growing these species on campus grounds. For A. hypochondriacus (left), the seeds from red plants are at the bottom left and those from white plants are shown at the top right.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU021F1: Photographs of the three grain species of Amaranthus grown on campus grounds. The plants from left to right are: A. hypochondriacus, A. cruentus, and A. caudatus, as identified by their taxonomic features including those of the inflorescence and the leaves. Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). Insets are the corresponding seeds obtained after two generations of growing these species on campus grounds. For A. hypochondriacus (left), the seeds from red plants are at the bottom left and those from white plants are shown at the top right.
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.

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