Allopolyploidization

One of the most prominent methods for bringing out the new lineages of plant species is allopolyploidization, which involves the merger of two divergent genomes (Leitch and Bennett 1997; Soltis and Soltis 1999). Polyploidy is the condition where two or more complete chromosome sets co-occur within the same nucleus (Madlung et al., 2013). It has been found that in plants polyploidy often occurs via autoppolyploidy or allopolyloidy (Ramsey and Schemske, 2002 and Madlung et al., 2013). Both auto and allopolyploids contain duplicated genomes (Madlung et al., 2012) with certain significant differences. In autoploids the duplicaton occurs within the same genome (Obbard et al., 2006). On the other hand, allopolyploidy is the result of intergeneric

In general polyploidy has been recognized as the event that has occurred at least once in the evolutionary history of all angiosperms (Jiao et al., 2011). The extent to which the polyploidy is evolutionary advantageous has been experimentally tested in some cases, but reliable answers are still lacking (Madlung, 2013). Tracing the origins and the evolution of the constituent genomes of allopolyploids has been challenging due to certain factors like the size and the complexity of the duplicated genome (Blanc and Wolfe, 2004; Chen, 2007; Soltis and Soltis, 2009., Doyle et al., 2008) and the pattern in which the different species evolve. For example, Few allopolyploids showed rapid changes in their genome; allopolyploid cotton being an exception ((Liu et al., 2001), few went through hoemlog loss (Doyle et al., 2008., Gaeta et al., 2007; Soltis et al., 2009 ;) whereas in others the gene expression changes seemed to prevail (Lee and Chen, 2001 ; Wang et al., 2006 ; Flagel and Wendel, 2010). For understanding the allopolyploid genome evolution in a better way, genomic data are needed from many more allopolyploids and their progenitor

Over the time chloroplast sequences have been used successfully to interpret the relationships at all taxonomic levels, including the deepest-level relationships of land plants and angiosperms (Chase et al., 1993 ; Borsch et al., 2003 ; Hilu et al., 2003 ; Moore et al., 2010), the intermediate taxonomic levels of orders and families (Downie et al., 2000 ; Potter et al., 2007 ; Chin et al., 2014 ), as well as the relationships among closely related species or populations Soltis et al., 1997 , 2006 ; Schaal et al., 1998 ; Shaw and Small, 2004 ; Morris et al., 2008). cp DNA is therefore being used as a reference DNA while carrying out the phylogenetic studies in plants. Taking all this into account the chloroplast genome (cpDNA) has been recognised as a robust, versatile and cost effective tool for evaluating the phylogenetic relationships and genetic diversity among species. The conventional methods for cpDNA genotyping include Random Amplified Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP) and chloroplast simple sequence repeats (cpSSRs; Provan et al., 2001; Van Den Berg et al., 2002). Genotyping of cpDNA can also be carried out via sequence alignments of the selected hypervariable cpDNA regions