Non-model plants i.e., the species which have one or all of the characters such as long life cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of sequencing projects earlier, due to high running cost of Sanger sequencing. Consequently, the information about their genomics and key biological processes are inadequate. However, the advent of fast and cost effective next generation sequencing (NGS) platforms in the recent past has enabled the unearthing of certain characteristic gene structures unique to these species. It has also aided in gaining insight about mechanisms underlying processes of gene expression and secondary metabolism as well as facilitated development of genomic resources for diversity characterization, evolutionary analysis and marker assisted breeding even without prior availability of genomic sequence information. In this review we explore how different Next Gen Sequencing platforms, as well as recent advances in NGS based high throughput genotyping technologies are rewarding efforts on de-novo whole genome/transcriptome sequencing, development of genome wide sequence based markers resources for improvement of non-model crops that are less costly than phenotyping.

Ipomoea, with enormous economic importance, is a large genus with species that are highly evolutionarily diverged. There is dearth of information regarding the phylogenetic relationships of the Nigerian species of the genus Ipomoea. It is therefore imperative to use contemporary taxonomic evidences to understand the diversity of its distribution in a region and provide enhanced delimitation of the taxa. In this study, 6 genic simple sequence repeat (SSR) markers whose cross transferability have been established among the plant species were selected to appraise their level of polymorphism and used to study the phylogenetic relationships among 11 indigenous Nigerian Ipomoea species. The 6 SSR loci showed varying levels of polymorphism among the genotypes of all 11 species assessed and demonstrated 100% polymorphism when examined across the 11 species. A total of 55 alleles were produced. The PIC of the primers ranged between 0.2223 and 0.874 with an average value of 0.71885. Phylogenetic analysis clustered species into 3 major and 6 sub clusters wherein the species were clearly separated. This study has shown the effectiveness of developed genic SSR markers for establishing phylogenetic relationship in Ipomoea species.