However, 23S rRNA has lost favor to 16S rRNA in phylogenetic analysis and is rarely used in taxonomic classification because of the lack of established broad-range sequencing primers and the difficulty of sequencing larger genes with early sequencing technology.
Single SNP differences between related alleles in the non-assayed exons could have potential regulatory or immunologic consequences, although few studies have examined such correlations due to the difficulty of sequencing the additional regions.
This discrepancy might be due to the non-random distribution of these repeat motifs, the biases introduced in the process of library construction, and the difficulty of sequencing long stretches of self-complimentary (AT n repeats which appeared in BAC ends or small-insert genomic libraries using the single pass sequencing strategy.
Next-generation sequencing (NGS) technologies, such as 454 [ 62] and Illumina [ 64- 67], greatly reduced the cost and difficulty of sequencing plastid genomes, and consequently, the number of plastid genomes available on GenBank increased nearly six-fold from 2006 to 2012 [ 68].
For example, genome size directly influences the cost and difficulty of sequencing projects, and is therefore a primary consideration in choosing future sequencing subjects (Gregory 2005 a, b; Gregory et al. 2007) as species with large DNA amounts or genome sizes make such genome projects prohibitively expensive (Fay et al. 2005).
While these findings may be an underestimate due to the difficulty of sequencing through repetitive elements, they nonetheless indicate that while the majority of the ~750,000 HNF4α-Alu elemayts may not be accessible in most cell types, a sizeable portion of HNF4α-Alu elements are in regions of open chromatin and hence may be transcriptionally active.
The low yield reflects the stringency of the initial mapping, the difficulty of sequencing the 18 nt oligo-dT/dA tract present in each 3′ end tag, and the frequency with which PATs mapped to multiple genomic positions; these latter tags were segregated for separate analysis (see Additional file 1: Table S1).
Genome size directly influences the cost and difficulty of sequencing projects, and was a primary consideration in choosing subjects for early whole-genome analyses (Gregory 2001, 2005), including those of algae where small DNA content (haploid genomes ∼100 Mbp) has been a major criterion (Peters et al. 2004; Waaland et al. 2004).
To minimize the difficulties of sequence homology-based genome annotation, data mining was started with screening Selaginella moellendorffii, Physcomitrella patens and Chlamydomonas reinhardtii EST databases for sequences with similarity to cDNAs encoding Arabidopsis thaliana APx, GPx and Prx using BLASTN and TBLASTX [ 29].
