Repeat element annotation
We identified repetitive elements by integrating homology and de novo
predictions. Homology-based transposable elements (TEs) annotation were
obtained by interrogating a genome assembly with known repeats in the
Repbase database v16.02 (Bao, Kojima, & Kohany, 2015) using
RepeatMasker v4.0.5 (DNA-level) (Tarailo-Graovac & Chen, 2009) and
RepeatProteinMask (protein-level; implemented in RepeatMasker). De novo
TE predictions were obtained using RepeatModeler v1.1.0.4 (Smit &
Hubley, 2010) and LTRharvest v1.5.8 (Ellinghaus, Kurtz, & Willhoeft,
2008) to generate database for a RepeatMasker run. Tandem Repeat Finder
(v4.07) (Benson, 1999) was used to find tandem repeats (TRs) in the
genome. A non-redundant repeat annotation set was obtained by combining
the above data. Genome sequences of other marsupials were also
interrogated using the repeat element annotation pipeline. The following
were downloaded from DNA Zoo [Virginia opossum (Didelphis
virginiana ; dv-2k (Olga Dudchenko et al., 2018))], the NCBI Reference
Sequence Database (Release 86) (Pruitt, Tatusova, & Maglott, 2007)
[gray short-tail opossum (Monodelphis domestica ; MonDom5;
GCF_000002295.2), koala (Phascolarctos cinereus ;
phaCin_unsw_v4.1; GCA_002099425.1), Tasmanian devil
(Sarcophilus harrisii; Devil_ref v7.0, also known as sarHar1;
GCA_000189315.1), Tammar wallaby (Notamacropus eugenii ;
Meug_1.1; GCA_000004035.1), and common wombat (Vombatus
ursinus ; GCF_900497805.2)], and the GigaScience Database [brown
antechinus (Antechinus stuartii ; (Brandies et al., 2020a;
Brandies, Tang, Johnson, Hogg, & Belov, 2020b)].