Illumina HiSeq Sequencing was selected to provide a deep coverage of identified genes as the large number of reads allows quantification of gene expression by mapping to reference genome, and is usually sufficient to detect most expressed gene even at low expression level [ 25], which is an ideal choice at a cost-performance perspective.
These technologies promise a deeper coverage of polymorphic sequence information and therefore increase the likelihood of identifying polymorphisms more closely linked to a character, if not the causal polymorphism itself, thus providing a manageable shortlist of gene candidates to be functionally tested.
Performing a second sequencing run only increased the number of genes identified by ~30%, indicating that massively parallel pyrosequencing provides deep coverage of the A. annua trichome transcriptome.
Using messenger RNA (mRNA) derived from Arabidopsis seedlings, Weber and colleagues [ 20] identified 541,852 ESTs which accounted for nearly 17,449 gene loci and thus provided very deep coverage of the transcriptome.
Performing a second sequencing run increased the number of genes identified by approximately 30% (Table 3), suggesting that two pyrosequencing runs detect a substantial fraction of genes expressed in glandular trichomes and provide deep coverage of the A. annua trichome transcriptome.
This provides a deeper understanding of various hydration product formations.
For an anatomical controlled vocabulary, biocurators selected from 2 774 terms from the MeSH 'Anatomy [A]' branch, which provided a deep and robust coverage of body systems and cell types.
However, the sequencing costs incurred to reach a sufficiently deep coverage of large genomes remain currently an issue.
As studies begin to define both the modern and ancient human microbiomes we should focus on providing deeper coverage of these communities and consider the effects of important covariates such as diet, sex, geographical and temporal placement, and signatures of disease.
