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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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Comparative GO annotation of three species including A. hypochondriacus, V. vinifera and S. lycopersicum. The percentage of genes deciphered for A. hypochondriacus, S. lycopersicum and V. vinifera within each category of GO as annotated by comparison with A. thaliana based on orthology and further normalized for the percentage of genes in A. thaliana shows that annotation of the draft genome is comparable to that of the published genomes. This figure appears in colour in the online version of DNA Research.
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DSU021F6: Comparative GO annotation of three species including A. hypochondriacus, V. vinifera and S. lycopersicum. The percentage of genes deciphered for A. hypochondriacus, S. lycopersicum and V. vinifera within each category of GO as annotated by comparison with A. thaliana based on orthology and further normalized for the percentage of genes in A. thaliana shows that annotation of the draft genome is comparable to that of the published genomes. This figure appears in colour in the online version of DNA Research.

Mentions: An amino acid level comparison of A. thaliana proteome49 against genomic scaffolds of A. hypochondriacus shows that 60.11% of A. thaliana proteins find orthology within the genomic scaffolds using the filter mentioned in the Materials and Methods section. Similar efforts with the scaffolds of two other species, V. vinifera50 and S. lycopersicum,51 finds comparable, 17,311 (63%) and 16,538 (60.32%), respectively, orthology to the A. thaliana proteome. Also, as shown in Fig. 5, the orthology of 14,590 A. thaliana genes common to the genomic scaffolds of V. vinifera, S. lycopersicum, and A. hypochondriacus suggests that functions of these genes are common to all dicots. A GO annotation of the A. thaliana orthologs in V. vinifera, S. lycopersicum, and A. hypochondriacus scaffolds shows that more than 80% of the genes annotated under each GO category in A. hypochondriacus has been deciphered (Fig. 6), and that the coverage of A. hypochondriacus genes within each category is comparable to the other two reported genomes of V. vinifera and S. lycopersicum.Figure 5.


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)

Comparative GO annotation of three species including A. hypochondriacus, V. vinifera and S. lycopersicum. The percentage of genes deciphered for A. hypochondriacus, S. lycopersicum and V. vinifera within each category of GO as annotated by comparison with A. thaliana based on orthology and further normalized for the percentage of genes in A. thaliana shows that annotation of the draft genome is comparable to that of the published genomes. 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

DSU021F6: Comparative GO annotation of three species including A. hypochondriacus, V. vinifera and S. lycopersicum. The percentage of genes deciphered for A. hypochondriacus, S. lycopersicum and V. vinifera within each category of GO as annotated by comparison with A. thaliana based on orthology and further normalized for the percentage of genes in A. thaliana shows that annotation of the draft genome is comparable to that of the published genomes. This figure appears in colour in the online version of DNA Research.
Mentions: An amino acid level comparison of A. thaliana proteome49 against genomic scaffolds of A. hypochondriacus shows that 60.11% of A. thaliana proteins find orthology within the genomic scaffolds using the filter mentioned in the Materials and Methods section. Similar efforts with the scaffolds of two other species, V. vinifera50 and S. lycopersicum,51 finds comparable, 17,311 (63%) and 16,538 (60.32%), respectively, orthology to the A. thaliana proteome. Also, as shown in Fig. 5, the orthology of 14,590 A. thaliana genes common to the genomic scaffolds of V. vinifera, S. lycopersicum, and A. hypochondriacus suggests that functions of these genes are common to all dicots. A GO annotation of the A. thaliana orthologs in V. vinifera, S. lycopersicum, and A. hypochondriacus scaffolds shows that more than 80% of the genes annotated under each GO category in A. hypochondriacus has been deciphered (Fig. 6), and that the coverage of A. hypochondriacus genes within each category is comparable to the other two reported genomes of V. vinifera and S. lycopersicum.Figure 5.

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