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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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A genome duplication study in A. thaliana, G. max, V. vinifera, S. lycopersicum, A. hypochondriacus, B. vulgaris, O. sativa, S. bicolor, and Z. mays by comparison of the distribution of percentage identities among paralogous pairs from the respective proteomes. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. The Kernel density plot of the density function of the number of paralogous pairs against the percentage identities for the diverse sequenced plant species shows the first peak at 20–40% identity corresponding to the paleaohexaploidy event and the sharp peak at 90–100% identity representing a recent whole genome duplication event. From the plot, it is evident that A. hypochondriacus, like B. vulgaris, did not undergo any recent whole genome duplication.
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DSU021F7: A genome duplication study in A. thaliana, G. max, V. vinifera, S. lycopersicum, A. hypochondriacus, B. vulgaris, O. sativa, S. bicolor, and Z. mays by comparison of the distribution of percentage identities among paralogous pairs from the respective proteomes. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. The Kernel density plot of the density function of the number of paralogous pairs against the percentage identities for the diverse sequenced plant species shows the first peak at 20–40% identity corresponding to the paleaohexaploidy event and the sharp peak at 90–100% identity representing a recent whole genome duplication event. From the plot, it is evident that A. hypochondriacus, like B. vulgaris, did not undergo any recent whole genome duplication.

Mentions: Estimation of 24,829 proteins provided an opportunity to look for any sign of recent whole genome duplication using a method reported by Axelsen et al.59 Figure 7 shows the comparison of proteomes of various species to find levels of divergence among paralogs. The peak near 90% for Z. mays, A. thaliana, and G. max confirms the recent whole genome duplication events reported for these species.60Amaranthus hypochondriacus and B. vulgaris, both species classified under the order Caryophyllales, lack the peak near 90% similar to V. vinifera, suggesting no recent whole genome duplication event in A. hypochondriacus and B. vulgaris. The peak near 30 for all dicot species represent a paleohexaploidy event common to all dicots,50 including the two species of Caryophyllales studied here. Based on this analysis, we have redrawn the place for A. hypochondriacus in Fig. 8, which is reproduced with permission from the authors.61Figure 7.


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)

A genome duplication study in A. thaliana, G. max, V. vinifera, S. lycopersicum, A. hypochondriacus, B. vulgaris, O. sativa, S. bicolor, and Z. mays by comparison of the distribution of percentage identities among paralogous pairs from the respective proteomes. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. The Kernel density plot of the density function of the number of paralogous pairs against the percentage identities for the diverse sequenced plant species shows the first peak at 20–40% identity corresponding to the paleaohexaploidy event and the sharp peak at 90–100% identity representing a recent whole genome duplication event. From the plot, it is evident that A. hypochondriacus, like B. vulgaris, did not undergo any recent whole genome duplication.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU021F7: A genome duplication study in A. thaliana, G. max, V. vinifera, S. lycopersicum, A. hypochondriacus, B. vulgaris, O. sativa, S. bicolor, and Z. mays by comparison of the distribution of percentage identities among paralogous pairs from the respective proteomes. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. The Kernel density plot of the density function of the number of paralogous pairs against the percentage identities for the diverse sequenced plant species shows the first peak at 20–40% identity corresponding to the paleaohexaploidy event and the sharp peak at 90–100% identity representing a recent whole genome duplication event. From the plot, it is evident that A. hypochondriacus, like B. vulgaris, did not undergo any recent whole genome duplication.
Mentions: Estimation of 24,829 proteins provided an opportunity to look for any sign of recent whole genome duplication using a method reported by Axelsen et al.59 Figure 7 shows the comparison of proteomes of various species to find levels of divergence among paralogs. The peak near 90% for Z. mays, A. thaliana, and G. max confirms the recent whole genome duplication events reported for these species.60Amaranthus hypochondriacus and B. vulgaris, both species classified under the order Caryophyllales, lack the peak near 90% similar to V. vinifera, suggesting no recent whole genome duplication event in A. hypochondriacus and B. vulgaris. The peak near 30 for all dicot species represent a paleohexaploidy event common to all dicots,50 including the two species of Caryophyllales studied here. Based on this analysis, we have redrawn the place for A. hypochondriacus in Fig. 8, which is reproduced with permission from the authors.61Figure 7.

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