The Plant Genome C hloroplasts are important organelles that are responsible for photosynthesis and play a vital role in plant physiology and development in green plants and algae (Raven and Allen, 2003). Chloroplasts have their own DNA, and for most of the land plants, the chloroplast genome exists in circular form with a quadripartite structure comprised of a large single copy (LSC) and a small single copy (SSC) region separated by two inverted repeats (IR; Sugiura, 2003; Wicke et al., 2011). The size of the chloroplast genome varies from 120 to 170 Kb and possessed 60 to 130 genes which are primarily involved in photosynthesis and other metabolic process (Sugiura, 2003; Wicke et al., 2011). The haploid nature, low level of recombination, and maternal inheritance of the chloroplast genome, as well as its low substitution rate compared with the nuclear genome, present chloroplast genomes as valuable

To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions.

Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A’s and G’s in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.

Nature selected certain regions of the genome for encoding proteins. Most of the sequences were used to encode only RNA. What happened to the remaining sections of the genome? It is possible that some sequences were retired and retained as non-functional entities called pseudogenes. Though several evolutionary prospects with functional endpoints exist, we looked at the possibility of hypothetical proteins correlating with the emergence of pseudogenes and potential of such genes to make novel synthetic molecules. In this commentary, we consider two key aspects: (1) does any correlation exist between hypothetical proteins and pseudogenes and (2)-can we make novel and functional proteins from pseudogenes?