UniMelb Thylacine Genomics Repository

This FigShare repository contains genomic datasets for the Thylacine Genomics Project at the University of Melbourne (VIC, Australia). Currently 4 files arising from 2 publications are hosted on this repository. All assemblies arise from NCBI BioSample SAMN06049672

1). Feigin et al. 2018: Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore [https://www.nature.com/articles/s41559-017-0417-y]

a) ThyCyn1.0: This assembly is the first de novo whole-genome assembly for the thylacine. It is a contig-level assembly and thus contains no scaffolds. It was generated from short insert paired-end reads (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=354646). Sequencing and data pre-processing strategy are discussed in the methods of Feigin et al. 2018. This assembly was used exclusively to estimate genome size and G+C content of the thylacine genome.

b) UniMelb_Thylacine_Refassem_1/GCA_007646695.1: Because of the highly-fragmentary nature (low N50) of ThyCyn1.0, UniMelb_Thylacine_Refassem_1 was generated to perform all evolutionary analyses detailed in Feigin et al. 2018. UniMelb_Thylacine_Refassem_1 was generated by mapping thylacine reads against the repeatmasked version of the previous Tasmanian devil draft genome Devil_ref v7.0 and generating reference-guided scaffolds. This is not a complete genome assembly, as it is composed only of non-repetitive genomic regions and does not include indel differences between Thylacine and devil. This was done to preserve the coordinate systems between thylacine and devil, permitting the use of the already-existing Tasmanian devil gene annotations. See methods of Feigin et al. 2018 for details. Assembly is hosted on NCBI under BioProject PRJNA354646.

2) Feigin et al. 2022: A chromosome-scale hybrid genome assembly of the extinct Tasmanian tiger (Thylacinus cynocephalus) [https://www.biorxiv.org/content/10.1101/2022.03.02.482690v1.full]

a) ThyCyn2.0: This assembly is a chromosome-scale hybrid genome for the thylacine. It was generated by producing improved de novo contigs and short read-based scaffolds, which were then aligned to the Tasmanian devil reference genome mSarHar1.11. This assembly represents a substantial improvement in contiguity and completeness over both ThyCyn1.0 and UniMelb_Thylacine_Refassem_1. Assembly is hosted on NCBI under BioProject PRJNA354646.

b) ThyCyn2.0 annotation: Associated with ThyCyn2.0, we have produced a set of homology-based gene annotations using a gene model liftover procedure (see Feigin et al. 2022 for details). Briefly, exons from the Tasmanian devil genome RefSeq annotation were aligned to the thylacine assembly and gene models were created by linking exons together, filtering for those with preserved the intron-exon structure of the reference devil annotation (with an allowable distance scaling factor of 4).