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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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Sixteen supercontigs of A. hypochondriacus corresponding to 16 haploid chromosomes drawn in centiMorgan scale showing the location of respective scaffolds anchored using 355 linkage SNPs out of the 411 reported. The red labels represent scaffolds containing the 355 SNPs and those in blue show the scaffolds that only map to one side of the SNPs with high confidence.
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DSU021F3: Sixteen supercontigs of A. hypochondriacus corresponding to 16 haploid chromosomes drawn in centiMorgan scale showing the location of respective scaffolds anchored using 355 linkage SNPs out of the 411 reported. The red labels represent scaffolds containing the 355 SNPs and those in blue show the scaffolds that only map to one side of the SNPs with high confidence.

Mentions: Table 1 includes the statistics from the assembly of genomic reads into scaffolds. The total ATGC content, without Ns, within the assembled scaffolds is 273 million bases. Addition of MP reads improved the size of the largest scaffold by 20 folds to 485,353 from 24,878 bases and scaffold N50 to 35,089 from contig N50 of 1,884. The genome of A. hypochondriacus was found to be AT-rich with 66% AT content (Supplementary Fig. S2), which compares with the genomes of other plants.47 Figure 3 shows the uniform coverage of the 16 chromosomes by genomic scaffolds, which harbour 355 (86%) SNPs of the 411 linkage SNPs reported for grain amaranths.18Table 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)

Sixteen supercontigs of A. hypochondriacus corresponding to 16 haploid chromosomes drawn in centiMorgan scale showing the location of respective scaffolds anchored using 355 linkage SNPs out of the 411 reported. The red labels represent scaffolds containing the 355 SNPs and those in blue show the scaffolds that only map to one side of the SNPs with high confidence.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU021F3: Sixteen supercontigs of A. hypochondriacus corresponding to 16 haploid chromosomes drawn in centiMorgan scale showing the location of respective scaffolds anchored using 355 linkage SNPs out of the 411 reported. The red labels represent scaffolds containing the 355 SNPs and those in blue show the scaffolds that only map to one side of the SNPs with high confidence.
Mentions: Table 1 includes the statistics from the assembly of genomic reads into scaffolds. The total ATGC content, without Ns, within the assembled scaffolds is 273 million bases. Addition of MP reads improved the size of the largest scaffold by 20 folds to 485,353 from 24,878 bases and scaffold N50 to 35,089 from contig N50 of 1,884. The genome of A. hypochondriacus was found to be AT-rich with 66% AT content (Supplementary Fig. S2), which compares with the genomes of other plants.47 Figure 3 shows the uniform coverage of the 16 chromosomes by genomic scaffolds, which harbour 355 (86%) SNPs of the 411 linkage SNPs reported for grain amaranths.18Table 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