p257

Footnote 53 Addendum

Fig 5.4 Is it still OK for large C number organisms?

The figure is based on the organisms whose genomes were read by 2007. Does this relation really hold for all organisms? The author’s colleague Elbert Branscomb paused a question whether the relation holds even with the so-called C number paradox. The C number is the quantity of DNA per genome, and is uncorrelated with the usual notion of higher or lower organisms; an extreme example may be Liliaceae (see below): in a single family the C numbers can change about 2 orders.

 The genomes of organisms with extremely many repetitive portions as amphibians, plants like Liliaceae, termites and cockroaches, have been avoided. Branscomb for example used B. K. Peterson et al., Big genomes facilitate the comparative identification of regulatory elements, PLoS ONE 4, e4688 (2009) (Fig. 1) to exhibit the breadth of the C number distributions.

 Strictly speaking, Fig. 5.4 should describe the ratio of the regulatory elements and the protein coding genes. Here, the former is represented by the total amount of ncDNA (this amount is used as a surrogate of the amount of the regulatory elements). It may well be the case that for the organisms with extreme C numbers (in a given group) the relation suggested in Fig. 5.4 does not hold accurately. However, the genomes of such organisms have never been read, so fortunately or unfortunately such organisms are excluded from Fig. 5.4. 

Reference about the C numbers of Liliaceae

Liliaceae giant DNA

LEITCHPunctuated genome size evolution in Liliaceae

J Evol Biol  20 2296 (2007)

(BG) Most angiosperms possess small genomes (mode 1C = 0.6 pg, median 1C = 2.9 pg). Those with truly enormous genomes (i.e. $\ge$ 35 pg) are phylogenetically restricted to a few families and include Liliaceae - with species possessing some of the largest genomes so far reported for any plant as well as including species with much smaller genomes.

* 78 species were superimposed onto a phylogenetic tree.

* Genome size in Liliaceae followed a punctuated rather than gradual mode of evolution and that most of the diversification evolved recently.

Fig. 1 of this paper clearly shows that more than 2 orders the C number can change in a family.

Fundamental difference between Prokaryote and Eukaryote from the complexity point of view