In the past few decades both basic and applied research on common wheat has lagged behind other crop species due to its complex, polyploid genome and difficulties in genetic transformation.
The ability to form these hairpins results in genome instability, difficulties in maintaining clones in Escherichia coli and major problems for most DNA sequencing approaches.
Due to special features of hexaploid wheat with large and complex genome and difficulties for transformation, and of Pst without sexual reproduction and hard to culture on media, the use of most genetic and molecular techniques in studying genes involved in the wheat- Pst interactions has been largely limited.
Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing.
Highly repetitive genomes present difficulties in sequencing and assembly steps of whole genome sequencing projects.
The relatively large number of gene order mutations that have occurred in the Campanulaceae chloroplast genomes causes difficulties when interpreting their phylogenetic significance.
However, gene and genome duplications pose difficulties for functional characterization and translational research.
Understanding how phenylpropanoid metabolism is controlled in the grasses has been complicated by recent genome duplications, the difficulties in making transgenic plants and the absence of mutants in many genes.
Part 2: Methodology discusses the process of sequencing the Neanderthal genome and the difficulties of extracting and analyzing the ancient DNA.
However, the use of buccal DNA for more demanding, large-scale genetic applications can be problematic [5], [6]: for instance, DNA that is of poor quality due to degradation can lead to incorrect or missing genotype calls, discordant results in samples subjected to whole genome amplification, and difficulties in using the samples in DNA-pooling experiments [7], [8].
