RNA-seq based on next-generation sequencing technology is expected to overcome the fixed-genome limitations of microarray technology.
However, consultation of the F. vesca genome has limitations, particularly for F. x ananassa-specific genome regions or genome regions derived from other progenitors.
EST-SSRs are useful for genetic analysis, but their relatively low polymorphism and the high possibility of no gene-rich regions in the genome are limitations to their use.
Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle.
It is likely that the genome size limitation for packaging was exceeded, resulting in less efficient virus production.
With the completion and availability of the sorghum genome this limitation has now been overcome and we are now in a position to undertake genome-scale comparative studies between evolutionarily related monocotyledonous genomes.
Although all soybean sequences were sequentially placed in relation to the A. thaliana genome, a limitation on map precision means that separation into uniquely delimited map entries does not occur within a 400 bp range.
Nevertheless, it is important to note that phylogenetic analyses based on mt genomes show limitations (particularly when addressing deep phylogenetic relationships but not only), and can render odd results that are incongruent with other evidences [ 29- 31].
The conservation of these sequences in significant number of bacterial genomes despite limitation on their genomic size during evolution have therefore suggested their functions are essential in regulation of cellular activities in prokaryotes, as in their eukaryotic counterparts.
However, it is difficult to clarify the functions of all genes by only genetic techniques because estimation of functions from genome sequences has limitations.
