1. A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis 
Michael Freeling, Jie Xu, Margaret Woodhouse, Damon Lisch 
Molecular Plant 
Volume 8, Issue 6, Pages (June 2015)
DOI: /j.molp
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2. Figure 1 The C-Value Paradox Exhibited by Sequenced Grasses.
The sequenced grass family 1C DNA values, when corrected for ploidy, excellently demonstrate the C-value paradox. This crude cladogram begins with the pre-grass tetraploidy (homeolog Ks = ca. 90%) before the major split between the two grass subfamilies (homeolog Ks ca. 65%, perhaps 50–70 million years ago). This graphic of sequenced grasses was redrawn from the all-plant tree in CoGePedia (instance ), the up-to-date encyclopedia supporting the CoGe comparative genomics toolbox ( Lyons and Freeling, 2008):
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

3. Figure 2 The Idea of Balance Per Se Conveyed with a Ballast Metaphor.
For these cargo ships carrying junk (little boxes), junk is ballast. Junk must be distributed in balance to prevent malfunction. While a heavy load of junk might increase stability and decrease agility (upper), a light load permits function as well (middle). If the balance is off, largely independent of load (bottom), the ship lists to the heavy side and dumps its junk into the sea. Here, the ship is the organism and its cargo is junk DNA, where junk DNA functions in bulk as ballast. If all junk was removed, the ship would still function. The junk is excess but functional. If you find metaphors tedious, then see the text for an example of how the level (dosages) of a regulatory trimeric protein ABC responds to varying levels of B product (Birchler and Veitia, 2007). Over production of B only leads to nonproductive subcomplexes and hypermorphic dominant dysfunction. This example illustrates balance per se about as effectively as these cargo ships (art by M.W.).
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

4. Figure 3 Comparing the Genomes of Rice and Sorghum.
(A) Exemplary distribution of the difference (junk) between the orthologous genomes of the grasses Japonica rice v6.1 (x axis, in bp) and sorghum v1.4 (y axis in bp) rendered graphically in the SynMap dot-plot application of CoGe with gene pairs (dots) color coded by synonymous substitution frequency, Ks. The lower Ks line, colored purple, is the syntenic line of orthologous pairs. Other lines are derived from gene pairs reflecting the pre-grass tetraploidy (blue), and even more ancient (light blue) dicot lineage polyploidies. Note the swooping lines, explained because sorghum has far more transposons at its centromers than rice, but the pile-up of this junk is clearly gradual.
(B) A blow up (from A) of sorghum chromosome 4 (y axis) and rice chromosome 2 (x axis), shows dramatically the graded nature of junk DNA (swooping) in sorghum.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

5. Figure 4 Comparing a Chromosomal Segment between Rice and Sorghum.
Two exemplary regions of orthologous rice (lower panel)-sorghum (upper panel) chromosomes, compared using blastn in GEvo (in CoGe), showing the distribution of intergenic noncoding DNA. Orthologous coding sequences are connected by orange lines and all noncoding sequences are hard-masked (colored pink) in sorghum.
(A) Two 1.1-Mb orthologous regions far out from the centromere of sorghum chromosome 1 and its rice orthologous 1.1 Mb. Note the three small inversions, these being common. There is about a 2.5-Mb excess of DNA, presumably junk, in sorghum.
(B) A 1300-kb stretch of sorghum chromosome 9 near the centromere paired with its 140-kb orthologous rice chromosomal segment; sorghum’s genes in this region are separated by about 10× more junk DNA than are the orthologous genes in rice.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

6. Figure 5
SmRNA Coverage around Genes Is Greater on the Recessive Subgenomes (of B. rapa Chiifu) than on the Dominant Subgenome.
Average number of unique 24-bp RNAs (y axis) within a 100-bp sliding window targeting uniquely Brassica rapa DNA within 5 kb upstream and downstream of the transcriptional unit (orange model between dashed lines).
(A) All B. rapa genes (red line) or all genes except TE DNA are hardmasked (green line).
(B) All B. rapa annotated genes separated by a subgenome. Data for genes in the chromosomal segments from the dominant (LF) subgenome are color coded red. Data for genes in either MF1 or MF2, the recessive subgenomes, are color coded blue. Note that genes on the recessive subgenomes have more 24-bp RNA (silencing RNA) targeting both 5′ and 3′ of the transcriptional unit. Scanned from the corrected Figure 2 in Woodhouse et al. (2014) (republished by permission).
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions