Limits...
Transposable elements: powerful contributors to angiosperm evolution and diversity.

Oliver KR, McComb JA, Greene WK - Genome Biol Evol (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia.

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.

Show MeSH

Related in: MedlinePlus

Summary of the effect of TEs on angiosperm adaptation and evolution. (A) Types of TEs implicated in the generation of traits in flowering plants. (B) Types of events mediated by TEs underlying flowering plant domestication and diversification. (C) Types of events mediated by TEs underlying wild traits in flowering plants. Based on the published data shown in tables 2 and 3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3814199&req=5

evt141-F1: Summary of the effect of TEs on angiosperm adaptation and evolution. (A) Types of TEs implicated in the generation of traits in flowering plants. (B) Types of events mediated by TEs underlying flowering plant domestication and diversification. (C) Types of events mediated by TEs underlying wild traits in flowering plants. Based on the published data shown in tables 2 and 3.

Mentions: Tables 2 and 3 list 65 known instances in which TEs have altered or created individual plant genes and thus were directly implicated at a genomic level in the origin of various traits, both domesticated and wild. Notably, DNA-TEs were the major contributors to these traits, accounting for nearly two thirds of the total (fig. 1A). The autonomous hAT and CACTA elements and nonautonomous MITE DNA-TEs were particularly prevalent contributors, whereas LTR retro-TEs were responsible for the remaining one third of traits. This suggests that DNA-TEs may be particularly effective at facilitating evolution, at least via active TE-Thrust (Oliver and Greene 2011), which accords with findings in disparate lineages, including the vespertilionid bats (Ray et al. 2008; Pagán et al. 2012; Mitra et al. 2013). Traits associated with cultivated plants were most commonly a consequence of gene disruption (50%; fig. 1B and table 2) rather than due to the creative effects of TEs. Although gene disruptions by TEs occur in natural populations, they generally result in a reduction of fitness and were therefore expected to be relatively uncommon. However, gene disruption features prominently in domesticated plant traits due to humans having selected for desirable phenotypes. By contrast, traits facilitated by TEs that could be of value in wild populations were more diverse in origin and most commonly were the result of regulatory changes to plant genes (33%; fig. 1C and table 3). As outlined below, TE-generated traits in angiosperms could be classified into one of the four phenotypic groups, which are not necessarily mutually exclusive.Fig. 1.—


Transposable elements: powerful contributors to angiosperm evolution and diversity.

Oliver KR, McComb JA, Greene WK - Genome Biol Evol (2013)

Summary of the effect of TEs on angiosperm adaptation and evolution. (A) Types of TEs implicated in the generation of traits in flowering plants. (B) Types of events mediated by TEs underlying flowering plant domestication and diversification. (C) Types of events mediated by TEs underlying wild traits in flowering plants. Based on the published data shown in tables 2 and 3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814199&req=5

evt141-F1: Summary of the effect of TEs on angiosperm adaptation and evolution. (A) Types of TEs implicated in the generation of traits in flowering plants. (B) Types of events mediated by TEs underlying flowering plant domestication and diversification. (C) Types of events mediated by TEs underlying wild traits in flowering plants. Based on the published data shown in tables 2 and 3.
Mentions: Tables 2 and 3 list 65 known instances in which TEs have altered or created individual plant genes and thus were directly implicated at a genomic level in the origin of various traits, both domesticated and wild. Notably, DNA-TEs were the major contributors to these traits, accounting for nearly two thirds of the total (fig. 1A). The autonomous hAT and CACTA elements and nonautonomous MITE DNA-TEs were particularly prevalent contributors, whereas LTR retro-TEs were responsible for the remaining one third of traits. This suggests that DNA-TEs may be particularly effective at facilitating evolution, at least via active TE-Thrust (Oliver and Greene 2011), which accords with findings in disparate lineages, including the vespertilionid bats (Ray et al. 2008; Pagán et al. 2012; Mitra et al. 2013). Traits associated with cultivated plants were most commonly a consequence of gene disruption (50%; fig. 1B and table 2) rather than due to the creative effects of TEs. Although gene disruptions by TEs occur in natural populations, they generally result in a reduction of fitness and were therefore expected to be relatively uncommon. However, gene disruption features prominently in domesticated plant traits due to humans having selected for desirable phenotypes. By contrast, traits facilitated by TEs that could be of value in wild populations were more diverse in origin and most commonly were the result of regulatory changes to plant genes (33%; fig. 1C and table 3). As outlined below, TE-generated traits in angiosperms could be classified into one of the four phenotypic groups, which are not necessarily mutually exclusive.Fig. 1.—

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia.

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.

Show MeSH
Related in: MedlinePlus