Therefore, we only used data from whole genome and high coverage assemblies.
We report here possible differences that can be examined further in the future when high coverage assemblies become available for more taxa.
Also underway is higher coverage assembly of the model homosporous fern, Ce. richardii (Sessa et al. 2014; Marchant et al. unpublished data).
While most of the genome sequences considered here will eventually be replaced by higher coverage assemblies, other projects parallel this one in certain respects.
However, these plants differ in many ways from the heterosporous land plants that have been examined to date, and higher coverage assemblies are critical for detailed comparative analyses of fern and land plant genome structure.
The genomic basis of divergence was investigated by complete high-coverage assembly of the five genomes and comparison with ancestor (Ferenci et al. 2009).
In addition, as shown by our theoretical analysis, consideration of sequencing error can continue to be important even with high-coverage assemblies, particularly for applications in comparative or population genomics.
This detailed look at the assembly scores shows that adding coverage does not always produce better results, and explains which aspects of some of the high-coverage assemblies contribute to poor scores compared to lower-coverage assemblies.
A relative high proportion of reads (876 839 out of 877 523, 99.92%) was assembled into reliable contigs (containing less than 9% mismatches), which is in agreement with other high-coverage assemblies [ 32].
Luckily, the availability of a high coverage (4×) assembly of the pig genome released in September 2009 now provides an unprecedented chance to explore novel compositional features in the pig genome.
