Sequencing of plant genomes – a review

Abstract

The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second-and third-generation sequencing platforms called "next-generation" sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome the challenges that arose mainly in plant genomes with large size, high CG content, heterozygosity, transposable elements, repetitive DNA, and homopolymers or polyploidy, as may be the case with the most important crops. There is no doubt that the rest of the species will also benefit from such breakthroughs, which also include direct RNA sequencing without requiring cDNA synthesis. In fact, we are not in a postgenomic era as is sometimes stated, but rather in the beginning of a genomic revolution.

Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance in Alopecurus aequalis

“…Whole-transcriptome sequencing (RNA-Seq) technology is a powerful tool to unravel the genetic basis of the herbicide stress response in weeds (Unver et al, 2010 ; An et al, 2014 ), and to identify the genetic differences between the resistant and sensitive plants, before and after a herbicide application (Metzker, 2010 ). This exceptionally accurate technology has been applied to many non-model plant species, including weeds (Gaines et al, 2014 ; Türktaş et al, 2015 ). Recently, by using RNA-Seq, several genes were identified in weeds that confer NTSR to different herbicides, such as in rye-grass ( Lolium rigidum Gaudin) (Gaines et al, 2014 ; Duhoux et al, 2015 , 2017 ), black-grass ( Alopecurus myosuroides Huds.)…”

De Novo Characterization of the Mung Bean Transcriptome and Transcriptomic Analysis of Adventitious Rooting in Seedlings Using RNA-Seq

“…Many genes are not represented on the microarrays, while genes from large and highly similar families may yield ambiguous expression results due to non-specific hybridization [ 11 ]. Recently, a high-throughput deep-sequencing technology (i.e., next-generation sequencing, NGS), RNA-Seq, has been widely used to explore transcriptomic data and study gene expression at the whole genome level in model and non-model organisms [ 12 , 13 ]. Emerging de novo short read assembly technology has been successfully applied to identify gene expression profiles and discover new genes without a reference genome sequence [ 13 , 14 ].…”

“…Recently, a high-throughput deep-sequencing technology (i.e., next-generation sequencing, NGS), RNA-Seq, has been widely used to explore transcriptomic data and study gene expression at the whole genome level in model and non-model organisms [ 12 , 13 ]. Emerging de novo short read assembly technology has been successfully applied to identify gene expression profiles and discover new genes without a reference genome sequence [ 13 , 14 ]. This technology platform enables the precise elucidation of transcripts present within a particular sample and can be used to calculate gene expression based on absolute transcript abundance [ 15 ].…”

In silico gene expression profiling in Cannabis sativa

“…Like in other plants, the cannabis genome is highly redundant and difficult to resolve 29 . It is very likely that false negatives have caused important transcripts to still be missing.…”