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

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.

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

“…Significance is identified and expressed as posterior probability of differential expression (PPDE) $0.95 (Leng et al, 2013; Supplemental Files S1-S3, S6). RT-qPCR was not used to validate gene expression due to the prerequisite for highly characterized sequence data (Unamba et al, 2015). A number of criteria need to be met for qPCR reference genes to be regarded as reliable (Chervoneva et al, 2010), importantly, traditional "housekeeping" genes (such as b-actin and 18S) have been extensively acknowledged as unstable in numerous biological systems (Gorzelniak et al, 2001;Solanas et al, 2001;Glare et al, 2002;Raaijmakers et al, 2002;Brunner et al, 2004;Gonçalves et al, 2005;Nicot et al, 2005;González-Verdejo et al, 2008;Barsalobres-Cavallari et al, 2009;Paolacci et al, 2009;Xu et al, 2012b;Jiang et al, 2014;Llanos et al, 2015).…”

De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

“…The transcriptome analysis identified three unique putative genes for AACT (e-value: 1e −48 to 0) and four for HMGS (e-value: 1e −30 to 0) in rose-scented geranium. A total of thirteen unique putative transcripts represented NADPH-dependent enzyme- HMGR (e-value: 3e −21 to 0) in rose-scented geranium, which catalyzes the biosynthesis of mevalonate from HMG-CoA [17, 31]. The sequence analysis of putative AACT, HMGS and HMGR genes suggested that they contain full-length open reading frames (ORFs).…”

“…Sangwan et al [16] provided a process for isolation of proteins and catalytically active enzymes from rose-scented geranium. Next-generation sequencing (NGS) technologies have accelerated transcriptome investigations in several plant species, exploring qualitative and quantitative insights of global gene regulation [17]. In SRA database, raw sequencing reads are available for a total of 13 Pelargonium species: P. tetragonum , P. fulgidum , P. transvaalense, P. incrassatum , P.austral , P. cotyledonis , P. nanum , P. citronellum , P. dichondrifolium , P. myrrhifolium , P. echinatum , P. exstipulatum , and Pelargonium x hortorum .…”

Cytotoxic and Antioxidant Effects in Various Tissue Extracts of Plumbago zeylanica: Implications for Anticancer Potential

“…20 Different concentrations (3.65-500μg in 20μl of ethanol) were prepared and mixed with (180μl) 50 µM DPPH. Plumbagin in different concentration (0.83-100μM) was used as the reference-standard.…”