The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal.
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.
Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.Show MeSH
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.
Affiliation: Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, Karnataka 560100, India.