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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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Unrooted phylogram of monofunctional aspartate kinases, the first enzyme in the asparate family pathway. The tree shows that A. hypochondriacus AK gene is in the same clade as AK1 (A. thaliana 1) of A. thaliana, B. vulgaris, and V. vinifera. The AK2 and AK3 (A. thaliana 2 and 3) cluster with V. vinifera 3. The sequences that could not be annotated to any of AK 1/2/3 are labelled as x1, x2, and so on. This figure appears in colour in the online version of DNA Research.
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DSU021F10: Unrooted phylogram of monofunctional aspartate kinases, the first enzyme in the asparate family pathway. The tree shows that A. hypochondriacus AK gene is in the same clade as AK1 (A. thaliana 1) of A. thaliana, B. vulgaris, and V. vinifera. The AK2 and AK3 (A. thaliana 2 and 3) cluster with V. vinifera 3. The sequences that could not be annotated to any of AK 1/2/3 are labelled as x1, x2, and so on. This figure appears in colour in the online version of DNA Research.

Mentions: There are varying numbers of monofunctional AK isoenzymes with varying lysine sensitivity in plants. For example, AK1, AK2, and AK3 genes of A. thaliana vary significantly in their affinity to lysine, with AK1 being the least sensitive.69 In this context, it is of interest to know if the lysine sensitivity of the only monofunctional AK gene of A. hypochondriacus compares with AK1 or the other two enzymes of A. thaliana. Phylogenetic analysis (Fig. 10) using the multiple sequence alignment of protein sequences of AK gene paralogs from diverse species, clusters the AK gene of A. hypochondriacus in the same clade as the AK1 gene of A. thaliana, suggesting that the AK gene of A. hypochondriacus is similar in lysine sensitivity to the AK1 gene. Loss of orthologs of the two lysine-sensitive AK2 and AK3 genes in A. hypochondriacus may be one of the reasons for the high-lysine phenotype in A. hypochondriacus, thus providing a testable hypothesis.Figure 10.


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)

Unrooted phylogram of monofunctional aspartate kinases, the first enzyme in the asparate family pathway. The tree shows that A. hypochondriacus AK gene is in the same clade as AK1 (A. thaliana 1) of A. thaliana, B. vulgaris, and V. vinifera. The AK2 and AK3 (A. thaliana 2 and 3) cluster with V. vinifera 3. The sequences that could not be annotated to any of AK 1/2/3 are labelled as x1, x2, and so on. 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

DSU021F10: Unrooted phylogram of monofunctional aspartate kinases, the first enzyme in the asparate family pathway. The tree shows that A. hypochondriacus AK gene is in the same clade as AK1 (A. thaliana 1) of A. thaliana, B. vulgaris, and V. vinifera. The AK2 and AK3 (A. thaliana 2 and 3) cluster with V. vinifera 3. The sequences that could not be annotated to any of AK 1/2/3 are labelled as x1, x2, and so on. This figure appears in colour in the online version of DNA Research.
Mentions: There are varying numbers of monofunctional AK isoenzymes with varying lysine sensitivity in plants. For example, AK1, AK2, and AK3 genes of A. thaliana vary significantly in their affinity to lysine, with AK1 being the least sensitive.69 In this context, it is of interest to know if the lysine sensitivity of the only monofunctional AK gene of A. hypochondriacus compares with AK1 or the other two enzymes of A. thaliana. Phylogenetic analysis (Fig. 10) using the multiple sequence alignment of protein sequences of AK gene paralogs from diverse species, clusters the AK gene of A. hypochondriacus in the same clade as the AK1 gene of A. thaliana, suggesting that the AK gene of A. hypochondriacus is similar in lysine sensitivity to the AK1 gene. Loss of orthologs of the two lysine-sensitive AK2 and AK3 genes in A. hypochondriacus may be one of the reasons for the high-lysine phenotype in A. hypochondriacus, thus providing a testable hypothesis.Figure 10.

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