Genome assembly, annotation and evolutionary insights from the draft genome of wild pomegranate.

Abstract

Wild pomegranate is a potent medicinal plant known for its medicinal and nutritional attributes. Despite its healing and curative properties, the genome of this wild species remains elusive, thus limiting our understanding on the genetic processes involved in the biosynthesis of functional molecules. This study presents the annotation of a de novo genome assembly of wild pomegranate, with a genome size of 279.0 Mb. From the assembly, 34.8 GB of the data was retained, encompassing 72,055 scaffolds. A total of 49,178 genes were predicted, with an average of 5.36 exons per gene and a GC content of 49%. About 14,400 genes were annotated in biological, cellular and molecular processes related mostly to carbohydrate metabolism, intracellular signal transduction, mRNA binding and DNA helicase activity. KEGG enrichment analysis revealed maximum number of genes associated with biosynthesis of secondary metabolites mainly phenypropanoid pathway, followed by ribosome and plant hormone signal transduction. From the identified functional genes, 230 genes scaffolds encoded for transcription factors belonging to 25 families with highest recorded for MYB gene family. Study of annotated transposable elements unveiled the existence of long terminal repeats and retrotransposons. Additionally, our investigation involves the comparative analysis and identification of orthologous genes among the genomes of wild and cultivated species of Punica granatum and also across selected five plant species Eucalyptus grandis, Vitis vinifera, Jatropha curcas, Theobroma cacao and Gossypium raimondii, revealing the functional and evolutionary dynamics across species. To the best of our knowledge, this is the first report on the genome assembly, annotation and gene prediction in wild pomegranate. Also, information regarding the terpenoid pathway genes has been unravelled for the first time in the present study. Inclusively, the current study offers thorough details on important aspects of the wild pomegranate genome that would be useful in comprehending its genetics and will facilitate discovery of genes against various biotic and abiotic stresses.