The evolution of two transmissible cancers in Tasmanian devils

Abstract

Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumor 1 (DFT1) and devil facial tumor 2 (DFT2). We investigated the genetic diversity and evolution of these clones by analyzing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled, chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982 to 1989) and DFT2 in 2011 (2009 to 2012). Subclone analysis documents transmission of heterogeneous cell populations. DFT2 has faster mutation rates than DFT1 across all variant classes, including substitutions, indels, rearrangements, transposable element insertions, and copy number alterations, and we identify a hypermutated DFT1 lineage with defective DNA mismatch repair. Several loci show plausible evidence of positive selection in DFT1 or DFT2, including loss of chromosome Y and inactivation of MGA , but none are common to both cancers. This study reveals the parallel long-term evolution of two transmissible cancers inhabiting a common niche in Tasmanian devils.

Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution

“…We called the resulting assembly DasViv_v1.0. The assembly size was ∼3.14 Gb, comparable to that of related marsupials, and scaffolds were nearly free of internal gaps (Supplementary Table S2) 23; 24 . The assembly was composed of only 76 scaffolds, of which the seven largest corresponded to the conserved karyotype found across all known dasyurids: six autosomes plus the X chromosome (Fig.…”

“…Together, the seven chromosome-scale scaffolds accounted for 99.34% of the total assembly size. Homology between eastern quoll chromosome-scale scaffolds and those of the related Tasmanian devil ( Sarcophilus harrisii ) and yellow-footed antechinus ( Antechinus flavipes ) was confirmed by the high overlap of orthologous gene annotations (>95%) and their similar total lengths (Supplementary Table S3) 23; 24 . Recovery of complete single-copy mammalian BUSCOs (Benchmarking Universal Single-Copy Orthologs) was 92.2%, second only to the koala ( Phascolarctos cinereus ) among marsupial reference genomes currently available on NCBI (Fig.…”

“…We first sought to compare ASIP orthologs from our eastern quoll genome (DasViv_v1.0) and the reference genomes of the Tasmanian devil (mSarHar1.11) with those from several other dasyuromorph species by aligning their coding sequences (Supplementary File S1 and Supplementary Table S6) 23; 24; 43-45 . Notably, while extracting orthologs from each reference genome, we failed to identify the first exon of ASIP from mSarHar1.11, despite the assembly being of high-quality and containing few gaps 24 .…”

“…We first sought to compare ASIP orthologs from our eastern quoll genome (DasViv_v1.0) and the reference genomes of the Tasmanian devil (mSarHar1.11) with those from several other dasyuromorph species by aligning their coding sequences (Supplementary File S1 and Supplementary Table S6) 23; 24; 43-45 . Notably, while extracting orthologs from each reference genome, we failed to identify the first exon of ASIP from mSarHar1.11, despite the assembly being of high-quality and containing few gaps 24 . To rule out the possibility that this region is present in the Tasmanian devil genome, but not reliably assembled during the construction of mSarHar.1.11, we aligned the nanopore long reads used to produce this genome against our eastern quoll genome.…”

Agential autonomy and biological individuality

“…Another important and problematic locus is the symbiont microbes that live on and in multicellular organisms. molluscs and some mammals such as Tasmanian devils (Stammnitz et al, 2023).…”