Furthermore, the combination of repeat length polymorphisms and the inherent difficulties of sequencing long stretches of microsatellite-like repeats have resulted in sequence gaps (N's) in the DPP domain of many animal genome sequencing projects.
Heterochromatic regions are the dark matter in genomes and even for well studied organisms we still do not have a complete genomic sequence due to the difficulties of sequencing these regions.
Years later the genome sequence of D. melanogaster became available (Adams et al. 2000), but unfortunately it was not very informative on the Y-linked paralogs of Mst77F (" Mst77Y" hereafter), in part because of the general difficulties of sequencing and annotation of Y-linked genes (Carvalho et al. 2009), and mostly because these genes were severely misassembled (Krsticevic et al. 2010).
This process increased the complexity of the fish genome and the difficulty of sequence assembly and annotation.
The difficulty of sequence assembly is the most significant factor explaining the relatively small number of plant species with finished genome sequences.
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).
