Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil

Abstract

The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.

Keywords: DNA transposon; Sarcophilus; retrotransposon.

Fig. 1.

Structural organization of non-LTR retrotransposons (A, B) and DNA transposons (C) identified in the Tasmanian devil genome. ORFs are disrupted by frameshifts, nonsense mutations, and indels. We investigated L1-1_MD from opossum and L1-1_SH from Tasmanian devil. WSINE1 from Tasmanian devil and SINE1_Mdo from opossum are both CORE-SINEs and share a homologous head and body-region. Presented copy numbers of the different elements were published in Nilsson et al. (2012), Gentles et al. (2007), and Gilbert et al. (2013). For the nonautonomous non-LTR retrotransposons, the green rectangle indicates the tRNA-region, the pink rectangle is the CORE sequence, whereas the brown rectangle shows the opossum specific sequence. The 5′- and 3′-ends of RCHARR1 are 99% identical to the 5′ and 3′ of the hAT-1_MEu sequence (blue and yellow boxes). ORF1/2, open reading frames 1 and 2; EN, endonuclease; ITR, inverted terminal repeats; AB, A and B box of the RNA polymerase III promoter; AAA, poly(A)tail. *RTE elements do not include a poly(A)tail at their 3′-ends, but TAAGTATC tandem repeats.

Fig. 2.

(A) L1 copy lengths plotted against the respective L1 copy numbers identified in four mammals (human, mouse, dog, and opossum) with retrotranspositionally active L1 elements, (B) L1 copy lengths plotted against the respective L1 copy numbers identified in four mammals (ground squirrel [Platt and Ray 2012], Black flying fox [Pteropus alecto], Large flying fox [Pteropus vampyrus] [Cantrell et al. 2008; Zhang et al. 2013], and Tasmanian devil), in which functional L1 elements have not been identified. Peaks in the range of 6,000–6,500 nt indicating full-length L1 elements are only observed in the genomes of those mammals with functional, retrotransposition-competent L1 elements but are absent from the genomes of those mammals devoid of any functional L1 elements.

Fig. 3.

Length distribution of RT-encoding ORFs found in two HMM pattern searches in the opossum and Tasmanian devil genomes. All ORFs longer than 300 aa were screened in both marsupial genomes. (A) A non-LTR HMM pattern was derived from 42 phylogenetically diverse ORF2 sequences (from LINE1, LINE2, LINE3, RTE, and Penelope) and screened in opossum and Tasmanian devil genomes. (B) In total, 268 RT domain sequences from the Gypsy Database 2.0 were used to create an HMM pattern. The copy number was plotted against length for each HMM pattern and species. See table 1 for additional information regarding the resulting distribution of element classes from each HMM pattern.

Fig. 4.

Phylogenetically informative retrotransposon insertions for the order Dasyuromorphia. Each circle represents a phylogenetically informative retrotransposon insertion. Colors refer to the element type. Two large deletions of more than 100 nt were found and are indicated as black triangles. Numbat, Myrmecobius fasciatus; Fat-tailed dunnart, Sminthopsis crassicaudata; Planigale, Planigale sp.; Quoll, Dasyurus geoffroii; Dibbler, Parantechinus apicalis; Mardo, Antechinus flavipes.

Fig. 5.

A time-calibrated tree of dasyuromorphian phylogeny (divergence times from Krajewski et al. 2000; Meredith et al. 2008; Nilsson et al. 2012). The WSINE1 inactivation event, DNA transposon transmissions, and the occurrence of the newly identified ERV1 have been mapped on the tree.

Fig. 6.

A repeat landscape of the Tasmanian devil genome showing the expansion and decline of transposable elements. The x axis shows the percentage of CpG adjusted Kimura-2-parameter substitutions to the consensus sequences in 1% bins. The y axis shows the relative amount of genome sequence covered by each transposable element group. The youngest elements have the least amount of substitutions whereas evolutionary older elements will have acquired more mutations. Trends showing a decline in various non-LTR retrotransposon groups have been indicated by arrows and numbers. (1) L3 inactivation, (2) L2 inactivation, (3) RTE inactivation, (4) SINE inactivation, (5) possible L1 inactivation. As in most mammals, the percentage of ERVs and DNA transposons relative to the entire genome is low. The colored circles refer to different types of elements found in the Tasmanian devil genome.