The full-length article about “genome size” [attached left pdf file] was shared with all of GEITP on Aug 31st, and that analysis is re-posted furthest below. The editorial commentary [attached right pdf file] was intended to accompany the full-length article. However, re-approaching this intriguing topic a second time is (in my humble opinion) worthwhile. It is well known that GENOME SIZE varies by many orders of magnitude across plants, fungus and animals –– but resolving the most important evolutionary forces driving this variation –– remains an active debate. As mentioned before, the human genome typically comprises coding DNA (~1.0-1.5%; i.e. “the exome”), noncoding (‘selfish’) repetitive sequences (~45%), and conserved noncoding sequences (~53-54%) that likely contain important heritable information that we do not yet understand.
We know that EUKARYOTIC (organisms carrying pairs of chromosomes) GENOME SIZE variation is not simply associated with complexity of the organism. Thus, genetic drift (process of change in the frequency of an allele (gene variant) in a population over time, caused by chance, or random events, rather than by natural selection) of the amount of noncoding DNA is one possible reason to explain genome size –– implicating population and species history as key drivers of shifts in DNA content. Alternatively, directional selection (i.e. the opposite of genetic drift) could be acting on DNA content. Because the predominant component of many eukaryotic genomes comprises selfish genetic elements such as transposable elements (TEs) and regions subject to meiotic drive (preferential production of certain gametes (egg, sperm) that alters segregation of genes from the Mendelian prediction) –– factors that influence their differential success across populations and species could account for much of the variation in genome size.
Authors [see attached article] capitalize on the remarkable genome size variation in maize and its wild relatives, which differs by 40% to 70% within and between subspecies. It is estimated that ~85% of the maize genome is composed of TEs, B chromosomes, and heterochromatic knobs subject to meiotic drive –– highlighting the success of selfish genetic elements in this lineage (compare ~85% in maize with ~45% for the human genome). Nevertheless, clines of genome size along with phenotypic and environmental variables in Zea mays spp. have often been described, with a number of studies showing evidence of genome reductions, including the loss of knobs and B chromosomes, in regions where the maize is grown at higher altitudes and latitudes.
Authors use whole-genome-sequence data from three altitudinal clines (populations that have adapted to three varying altitudes) to obtain detailed information, not only about the kinship and structure of their samples, but also about the contribution of each type of repeat to overall genome size. Using this approach to test for local adaptation, authors are able to reject the hypothesis of the neutral model –– concluding that genome size differences among the altitudinal clines are too extreme to be explained solely by genetic drift. Authors instead found a strong correlation of TE copy-number with genome size and altitude. These data strongly support the likelihood that environmental adaptation (i.e. growth at higher altitudes and higher latitudes) could be an important determinant of transposable element abundance, mediated through its effects on genome size.
PLoS Genet May 2o18; 14: e1007249.