Shallow Whole Genome Sequencing for the Assembly of Complete Chloroplast Genome Sequence of Arachis hypogaea L.

Abstract

The chloroplast (CP) is a plant organelle originated from cyanobacteria through symbiosis and had become an important component of the plant cell. It is the reaction center for the photosynthesis and also for several steps in the biosynthetic pathways of fatty acids, vitamins, pigments and amino acids. The CP genome is highly conserved in land plants (Raubeson and Jansen, 2005). The CP genome is circular and exhibits a quadripartite genome structure consisting of a large single copy region (LSC) and a small single copy region (SSC), separated by a pair of inverted repeats (IRs) with a few exceptions where loss of an IR or the SSC was observed. The size of the CP genome varies from 19 to 217 Kb in land plants, and the IRs are usually 20–26 kb in length (http://www.ncbi.nlm.nih.gov/genome/organelle/). Lack of recombination makes the CP genome an ideal target for phylogenetic studies (Ravi et al., 2008; Wu and Ge, 2012). Arachis hypogaea L. also known as groundnut is an herbaceous plant belonging to the Fabaceae family. It has an allotetraploid genome (AABB; 2n = 4x = 40) with a size of about 2.8 Gb. There have been many speculations regarding the ancestors of A and B subgenomes of A. hypogaea and proved to have originated through a hybridization event between Arachis ipaensis L. (B subgenome) and Arachis duranensis L. (A subgenome) (Kochert et al., 1996; David et al., 2016). It is one of the major edible oilseed crops in the world, and India is the second largest producer accounting for about 15% of the world production (FAOSTAT, 2015). Kernels of A. hypogaea L. contains 43–50% oil and 23–26% proteins. The oil comprises majorly of palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), arachidic acid (20:0), eicosenoic acid (20:1), behemic acid (22:0), and lignoseric acid (24:0) along with trace amounts of palmitoleic acid (16:1). The mono and poly-unsaturated fatty acids, oleic acid and linoleic acid constitute about 75% of the total oil content (Shiv, 1982). Many attempts have successfully been made to improve the crop yield, drought resistance, disease resistance and other characteristics of A. hypogaea L. using classical breeding as well as genetic engineering using nuclear transformation. Chloroplast transformation by homologous recombination for producing transgenic plants is also possible due to the presence of candidate loci on the CP genome. Additionally, Genetic engineering of chloroplast genome when compared to nuclear transformation is environment-friendly; it minimizes the pleiotropic effects along with containment of the foreign genes (Daniell et al., 2005). Hence, the availability of the complete chloroplast genome of A. hypogaea L. will be an invaluable resource for designing and evaluating efficient chloroplast transformation experiments.