Junk DNA goodbye!: In plant evolution (Introduction)

by David Turell , Monday, May 16, 2016, 22:00 (3113 days ago) @ David Turell

Transposable elements in plants have helped direct evolution, a problem Darwin was troubled by: - http://gbe.oxfordjournals.org/content/5/10/1886.full.pdf+html: - From the abstract: - "Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution
of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's “abominable mystery”: the spectacular success of the angiosperms. - Article: - Although once said to be “junk,” or “parasitic,” DNA (Doolittle and Sapienza 1980; Orgel and Crick 1980), a recent large and rapid accumulation of evidence indicates
that transposable elements (TEs) have been a significant factor in the evolution of a wide range of eukaryotic taxa (Bennetzen 2000; Kazazian 2004; Bie´mont and Vieira 2006; Feschotte and Pritham 2007; Bo¨ hne et al. 2008; Hua-Van et al. 2011). We have proposed TEs as powerful facilitators of evolution (Oliver and Greene 2009), formalized this proposal into the TE-Thrust hypothesis (Oliver and Greene 2011),
and more recently, expanded and strengthened this hypothesis (Oliver and Greene 2012). The TE-Thrust hypothesis has great explanatory power with regard to adaptation and evolution and was developed from empirical evidence among the metazoans, principally mammals. It has offered an explanation for the great fecundity of some lineages and the paucity of species in other lineages, for
stasis, and for “living fossils” (Oliver and Greene 2009, 2011, 2012). Owing to variable TE activity over time, TE-Thrust also suggests strong support for punctuated equilibrium (Eldredge andGould 1972; Gould 2002). - *** - "By assessing the available evidence, we conclude that TE-Thrust operates in, and has been crucial to, the evolution of flowering plants. The additional involvement of TEs in the artificial arena of plant domestication provides direct and relatively recent evidence for the importance of TEs in the generation of selectable variation in angiosperms. TE-Thrust is therefore potentially a general phenomenon that may have
very widespread significance to many lineages of life on earth. Nevertheless, TE-Thrust is only one of the many facilitators of evolution, and its relative importance may vary from lineage to lineage and from age to age. A comprehension of the full magnitude of the contributions that TEs have made to angiosperm evolution will require complete genome sequencing and detailed trait characterization in a wide range of plant species, including nondomesticated species of angiosperms and species from other plant phyla. However, any measure of TE impact will likely be an underestimate owing to important contributions having been made by ancient TEs that have been lost or are no longer recognizable." - Comment: As usual more research ,less junk