MRI is characterized by a specific base composition within a region under analysis.
Although the genome is not organized in discrete isochores as in some fungal genomes [ 37], we observe some large-scale variation (>100 kb) in base composition within chromosomes, as well as finer-scale fluctuations (Additional file 4A).
To date, there seems to be little taxonomic consistency in mitochondrial genome base composition within ciliates: Tetrahymena pyriformis has an AT content similar to O. trifallax at 79% (Burger et al. 2000), whereas P. tetraurelia (Pritchard et al. 1990) and E. minuta (de Graaf et al. 2009) have a considerably lower AT content at 59%and64%4%, respectively.
The 70% AT base composition is within the range described for other arthropods.
With an A + T content of 65.5%, the Floydiella genome falls within the range of base composition observed for the four completely sequenced chlorophycean cpDNAs (table 1) but deviates significantly from Volvox cpDNA (57% A + T).
The expected frequency,, of a homopolymer tract of length N randomly occurring is calculated by the formula: where base frequency is the fractional base composition of the tract base i within the DNA for that file, and N is the tract length.
Within a range (±5) of the base composition of the R. felis genome (32.5% GC), only seven pRF genes deviate from the average base composition (pRF02, pRF04, pRF14, pRF25, pRF51, pRF65, pRF67).
The comparison of sequence coverage among intended targets within each library was influenced by the base composition of the targets.
The base composition of the J-strand of the Dendrolinus species fell within the range of other Bombycoidea species, and their nucleotide compositions were significantly biased toward A and T (Additional file 8).
The data show that there are no significant departures from an equilibrium base composition, either across the entire phylogeny or within any of the individual lineages (Table 2).
