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Review
. 2015 Dec 16:6:1074.
doi: 10.3389/fpls.2015.01074. eCollection 2015.

Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants

Chibuikem I N Unamba  1 , Akshay Nag  2 , Ram K Sharma  2
Affiliations
Review

Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants

Chibuikem I N Unamba et al. Front Plant Sci. .

Abstract

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.

Keywords: genomics; next generation sequencing; non-model; transcriptome; whole genome.

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Figures

Figure 1
Figure 1
Flow chart of NGS enabled genomic analysis in non-model plants.
See this image and copyright information in PMC

References

    1. Achard P., Herr A., Baulcombe D. C., Harberd N. P. (2004). Modulation of floral development by a gibberellin-regulated microRNA. Development 131, 3357–3365. 10.1242/dev.01206 - DOI - PubMed
    1. Ahmadvand R., Poczai P., Hajianfar R., Kolics B., Gorji A. M., Polgár Z., et al. . (2014). Next generation sequencing based development of intron-targeting markers in tetraploid potato and their transferability to other Solanum species. Gene 540, 117–121. 10.1016/j.gene.2014.02.045 - DOI - PubMed
    1. Albert V. A., Barbazuk W. B., Der J. P., Leebens-Mack J., Ma H., Palmer J. D., et al. . (2013). The Amborella genome and the evolution of flowering plants. Science 342:1241089. 10.1126/science.1241089 - DOI - PubMed
    1. Al-Dous E. K., George B., Al-Mahmoud M. E., Al-Jaber M. Y., Wang H., Salameh Y. M., et al. . (2011). De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat. Biotechnol. 29, 521–527. 10.1038/nbt.1860 - DOI - PubMed
    1. Alwine J. C., Kemp D. J., Stark G. R. (1977). Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc. Natl. Acad. Sci. U.S.A. 74, 5350–5354. 10.1073/pnas.74.12.5350 - DOI - PMC - PubMed

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