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As a result, TopHat performs best on mammalian transcripts with relatively high abundance, but can stumble in more compact genomes and with non-canonical junctions.
It could be also generalized that theoretically species having increased genome sizes may resist various viral infections stronger than related organisms with more compact genomes.
Although a lot of this variability can be attributed to varying metabolic complexity, it also suggests that some species have more compact genomes than others.
In contrast, bacteriophages have frequently been isolated from nature and used as model laboratory systems due to their much more compact genomes and the corresponding relative ease for assessing molecular responses to selection.
In fugu and Tetraodon, which have more compact genomes, aqp1a and aqp1b were 1.4 1.5 kb and 1.1 1.2 kb in length, respectively, both loci being separated by only 4.1 4.7 kb.
Whilst no apparent relationship exists between the median sizes of the different types of IGR and the AT content, there is, as expected, a strong relationship (R between 0.86-0.93 0.86-0.93 genome density, i.e. more compact genomes have proportionally smaller IGR.
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This is possibly due to their small genome sizes and evolutionary pressure towards a more compact genome [ 26, 27].
Takai and Jones hypothesized that divergent gene organization might stem from the evolution of the human genome from a more compact genome [ 31].
Previous studies have shown that reductions of IGS regions are caused by gene loss, which has led to a more compact genome [ 35, 36].
Ciona intestinalis is a chordate with a simpler and more compact genome than found in vertebrates or even cephalochordates, making it a useful model for studying chordate evolution.
Although the integer representation results in a more compact genome, it still encounters problems as it needs to define the number of gene knockouts a priori [ 7].
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