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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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Rooted phylogram of PEPC 1, 2, 3, and 4. Branches labelled A780S are C4-specific PEPC isoforms containing alanine to serine mutation at residue 780 of Z. mays C4-specific gene with accession CAA33317. All the bacterial-type PEPC isoforms including A. hypochondriacus 4 and B. vulgaris 4 cluster in one clade. All the C4-specific PEPC genes from monocots cluster together. Among dicots, C4-specific PEPC genes are split into two clades representing Asterids and Caryophyllales. There is only one C4-specific PEPC gene in A. hypochondriacus as is also found in other C4 plants. In the figure, the protein sequence of PEPC taken from GenBank (gb ADO15315.1) has been labelled as A. hypochondriacus gb and the one extracted from the genomic scaffolds is labelled as A. hypochondriacus 1. This figure appears in colour in the online version of DNA Research.
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DSU021F9: Rooted phylogram of PEPC 1, 2, 3, and 4. Branches labelled A780S are C4-specific PEPC isoforms containing alanine to serine mutation at residue 780 of Z. mays C4-specific gene with accession CAA33317. All the bacterial-type PEPC isoforms including A. hypochondriacus 4 and B. vulgaris 4 cluster in one clade. All the C4-specific PEPC genes from monocots cluster together. Among dicots, C4-specific PEPC genes are split into two clades representing Asterids and Caryophyllales. There is only one C4-specific PEPC gene in A. hypochondriacus as is also found in other C4 plants. In the figure, the protein sequence of PEPC taken from GenBank (gb ADO15315.1) has been labelled as A. hypochondriacus gb and the one extracted from the genomic scaffolds is labelled as A. hypochondriacus 1. This figure appears in colour in the online version of DNA Research.

Mentions: We have identified full-length cDNA sequences for all the four PEPC isoenzymes from the genome of A. hypochondriacus with only one harbouring the A780S mutation. In order to check if all PEPC genes across various species harbouring A780S mutation result from divergent or convergent evolution, we have created a phylogenetic tree using the multiple sequence alignment of all the PEPC isoenzymes from representative species under various major plant orders including many C3 and C4 from both dicots and monocots (Fig. 9). All PEPC isoenzymes harbouring the A780S mutation, among monocot species, cluster together, suggesting C4 evolution predating speciation in monocots. However, the PEPC gene harbouring the A780S mutation in C4 dicots (represented by A. hypochondriacus and Mollugo cerviana from Caryophyllales and Flaveria trinervia from Asterids), clusters in distal clades. Based on this observation, there can be two hypotheses: (i) the C4-specific mutation occurred independently under Asterid and Caryophyllales; (ii) all C3 dicot plants have selectively lost an ancestral C4-specific isoform during the course of evolution. The first hypothesis has been reported in the literature65 and our observation supports the same. In other words, C4 switch in dicots is a convergent evolution.65 For the second hypothesis to be true, one would need to show that at least one C3 dicot plant continues to retain a C4-specific PEPC gene.Figure 9.


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)

Rooted phylogram of PEPC 1, 2, 3, and 4. Branches labelled A780S are C4-specific PEPC isoforms containing alanine to serine mutation at residue 780 of Z. mays C4-specific gene with accession CAA33317. All the bacterial-type PEPC isoforms including A. hypochondriacus 4 and B. vulgaris 4 cluster in one clade. All the C4-specific PEPC genes from monocots cluster together. Among dicots, C4-specific PEPC genes are split into two clades representing Asterids and Caryophyllales. There is only one C4-specific PEPC gene in A. hypochondriacus as is also found in other C4 plants. In the figure, the protein sequence of PEPC taken from GenBank (gb ADO15315.1) has been labelled as A. hypochondriacus gb and the one extracted from the genomic scaffolds is labelled as A. hypochondriacus 1. This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4263292&req=5

DSU021F9: Rooted phylogram of PEPC 1, 2, 3, and 4. Branches labelled A780S are C4-specific PEPC isoforms containing alanine to serine mutation at residue 780 of Z. mays C4-specific gene with accession CAA33317. All the bacterial-type PEPC isoforms including A. hypochondriacus 4 and B. vulgaris 4 cluster in one clade. All the C4-specific PEPC genes from monocots cluster together. Among dicots, C4-specific PEPC genes are split into two clades representing Asterids and Caryophyllales. There is only one C4-specific PEPC gene in A. hypochondriacus as is also found in other C4 plants. In the figure, the protein sequence of PEPC taken from GenBank (gb ADO15315.1) has been labelled as A. hypochondriacus gb and the one extracted from the genomic scaffolds is labelled as A. hypochondriacus 1. This figure appears in colour in the online version of DNA Research.
Mentions: We have identified full-length cDNA sequences for all the four PEPC isoenzymes from the genome of A. hypochondriacus with only one harbouring the A780S mutation. In order to check if all PEPC genes across various species harbouring A780S mutation result from divergent or convergent evolution, we have created a phylogenetic tree using the multiple sequence alignment of all the PEPC isoenzymes from representative species under various major plant orders including many C3 and C4 from both dicots and monocots (Fig. 9). All PEPC isoenzymes harbouring the A780S mutation, among monocot species, cluster together, suggesting C4 evolution predating speciation in monocots. However, the PEPC gene harbouring the A780S mutation in C4 dicots (represented by A. hypochondriacus and Mollugo cerviana from Caryophyllales and Flaveria trinervia from Asterids), clusters in distal clades. Based on this observation, there can be two hypotheses: (i) the C4-specific mutation occurred independently under Asterid and Caryophyllales; (ii) all C3 dicot plants have selectively lost an ancestral C4-specific isoform during the course of evolution. The first hypothesis has been reported in the literature65 and our observation supports the same. In other words, C4 switch in dicots is a convergent evolution.65 For the second hypothesis to be true, one would need to show that at least one C3 dicot plant continues to retain a C4-specific PEPC gene.Figure 9.

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