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. Author manuscript; available in PMC: 2013 Mar 31.
Published in final edited form as: Annu Rev Genet. 2012;46:651–675. doi: 10.1146/annurev-genet-110711-155616

Table 1.

Transposon content and activities in various genomes

Organism Genome composition Transposon activity References
Plants
Physcomitrella patens Moss; a model for evolutionary biology, manipulable genome 480-Mb genome; more than half of the genome are transposon elements High LTR activity; Helitron less active (108)
Selaginella moellendorffii Lycophyte and oldest extant vascular plant; useful model in evolutionary biology 106-Mb genome; approximately one-third derived from transposon activity LTRs predominate (5)
Arabidopsis thaliana Dicotyledonous flowering plant; its small size and short generation time led to its extensive use in genetics and developmental biology 125-Mb genome; transposons account for approximately 10% LTRs highly active; DNA transposons (mutator-like elements, MULEs and Basho) also active; LINEs and SINEs relatively quiescent (50, 89, 97, 104, 139, 143)
Zea mays Maize; organism in which transposons were discovered 2.3-Gb genome; nearly 85% composed of transposable elements LTRs are highly active; TIRs and Helitrons less active (14, 46, 71–73, 79, 84, 88, 109–111, 122, 124, 128, 129, 140)
Oryza sativa Rice; major calorie source for human 420-Mb gnome; ~25% of the genome is of transposon origin High LTR activity; TIRs less active; low LINEs and SINEs activity (56, 58, 99, 137, 138)
Animals (invertebrates)
Hydra magnipapillata Freshwater cnidarian; a model for tissue patterning, transplantation, and regeneration 1–1.5-Gb genome; transposons compose approximately 60% of the genome CR1 non-LTR retrotransposons most abundant; followed by mariner and hAT DNA transposons (18)
Caenorhabditis elegans Nematode; a model for genetics, neurobiology, and development; manipulated by RNAi 97-Mb genome; 12% of the genome is transposon derived TIRs are highly active, particularly Tc1 and Tc3 transposons; LTRs less active (9, 37, 49, 96)
Drosophila melanogaster Fruit fly; extensively used model for development and genetics; meiotic recombination is female specific and tractable through use of balancer chromosomes 180-Mb genome; 4%–9% of the genome transposon derived TIRs are highly active; LTRs, LINEs, SINEs, and Helitrons less active (6, 8, 10, 23, 27, 30, 35, 42, 43, 54, 66, 77, 80, 94, 98, 101, 114)
Animals (vertebrates)
Takifugu rubripes Pufferfish; relatively compact genome valuable in comparative genomics 365-Mb genome; interspersed repeats comprise only 2.7% Many types of transposable elements appear recently active, show low nucleotide divergence; LINE-like Mauis are the single-most common; SINE-FR and DNA transposons (Tc1_FR, Tc2_FR, and Chaplin) are also common (3)
Anolis carolinensis Lizard/green anole; the first nonavian reptilian genome sequenced 2.2-Gb genome; ~20% transposons Multiple families of non-LTRs are recently active. DNA transposons (hAT, Tc1, Helitron, Chapaev) show low divergence from consensus. LTR activity also present. (92, 93, 100)
Ornithorhynchus anatinus Platypus; a monotreme useful for studies of mammalian and reptilian evolution 2.3-Gb genome; 50% interspersed repeats LINE2 and companion SINEs (MIR and Mon-1) are highly active; no L1 activity (126)
Myotis lucifugus Brown bat 2.3-Mb genome; ~25% transposons TIRs are highly active; Helitrons second-most active; LINEs and SINEs are inactive (95, 102, 105, 106)
Rattus norvegicus Rat; first mammalian species domesticated for scientific research 2.75-Gb genome; 40% interspersed repeats LINEs and SINEs, followed by LTRs are highly active; 12% of the genome reflects rat-specific L1 insertions, not shared by mouse (1, 40, 67, 125)
Mus musculus Mouse; an especially genetically tractable mammalian model 2.5-Gb genome; 37% interspersed repeats LINEs, SINEs, and LTRs are highly active, with numerous species and strain-specific insertions characterized; ancestral repeats have a high rate of sequence divergence in mouse versus human (1, 2, 44, 127, 142)
Homo sapiens Human 2.9-Gb genome; 46% interspersed repeats LINEs and SINEs are highly active with L1, AluY, and SVA sequences polymorphic in populations; LTRs recently active; DNA transposons inactive (7, 12, 13, 15, 19, 25, 31, 32, 47, 53, 55, 57, 63, 69, 112, 118, 134, 136)

Abbreviations: LINE, long interspersed element; LTR, long terminal repeat; SINE, short interspersed element; TIR, terminal inverted repeat.