Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

Murchison, Elizabeth P.; Schulz-Trieglaff, Ole; Ning, Zemin; Alexandrov, Ludmil B.; Bauer, Markus; Fu, Beiyuan; Hims, Matthew M.; Ding, Zhihao; Ivakhno, Sergii; Stewart, Caitlin M.; Ng, Bee Ling; Wong, Wendy S. W.; Aken, Bronwen; White, Simon; Alsop, Amber E.; Becq, Jennifer; Bignell, Graham R.; Cheetham, R. Keira; Cheng, William; Connor, Thomas R.; Cox, A.J.; Feng, Zhiping; Gu, Yong; Grocock, Russell; Harris, Simon R.; Khrebtukova, Irina; Kingsbury, Zoya; Kowarsky, Mark; Kreiss, Alexandre; Luo, Shujun; Marshall, John; McBride, David J.; Murray, Lisa; Pearse, Anne-Maree; Raine, Keiran; Rasolonjatovo, Isabelle; Shaw, Richard J.; Tedder, Philip; Tregidgo, Carolyn; Vilella, Albert J.; Wedge, David C.; Woods, Gregory M.; Gormley, Niall; Humphray, Sean; Schroth, Gary P.; Smith, Geoffrey; Hall, Kevin P.; Searle, Stephen M. J.; Carter, Nigel P.; Papenfuss, Anthony T.; Futreal, P. Andrew; Campbell, Peter J.; Yang, Fengtang; Bentley, David; Evers, Dirk; Stratton, Michael R.

doi:10.1016/j.cell.2011.11.065

Cited by 312 publications

(452 citation statements)

References 63 publications

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“…The thylacine sequence data was then used to assemble contigs de novo. The resulting assembly was comparable to other draft marsupial genomes [10][11][12] , with an N50 contig length of ~3.2 kilobases (Kb) and a total assembly size of ~3. 16 Gb, suggesting the thylacine genome size was similar to previously sequenced marsupials.…”

Section: Resultsmentioning

confidence: 72%

“…Contaminating sequences were depleted by mapping to a database containing microbial and fungal genomes, leaving ~151 Gb (Supplementary Table 1). We assessed the quality of the data by mapping reads to the genome of the Tasmanian devil (Sarcophilus harrisii) 10 , the most closely related species available. Approximately 89.3% of the retained reads mapped to the complete unmasked Tasmanian devil assembly.…”

Section: Resultsmentioning

confidence: 99%

“…The Tasmanian devil has experienced a recent catastrophic population decline due to an extreme lack of genetic diversity, causing widespread susceptibility to devil facial tumour disease 10 . Previous studies of mitochondrial DNA suggested that thylacine populations in Tasmania were even less genetically diverse at the time of their extinction than modern Tasmanian devils 7 .…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

“…We reconstructed thylacine genes by mapping the thylacine sequence data to the Tasmanian devil genome 10 and generating a reference-based assembly. The Tasmanian devil genome annotations were then used to extract thylacine genes.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

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Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

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Section: Resultsmentioning

confidence: 72%

Section: Resultsmentioning

confidence: 99%

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

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Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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“…17 He reported on their recent finding that Tasmanian Devils were able to generate potent anti-tumour responses following immunisation with xenogeneic K562 cells, and that cytotoxicity generated was most likely from natural killer cells. 18 Further studies revealed that inflammatory stimuli could induce the generation of cytotoxic responses against DFTD cells.…”

Section: Australian Stories-transmissible Tumours and Hendra Virus (Hev)mentioning

confidence: 99%

4th Australasian Vaccines and Immunotherapeutic Development Meeting

Engwerda

Belz

2012

Immunol Cell Biol

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Genome Sequence of an Australian Kangaroo,Macropus eugenii

Deakin

2013

Encyclopedia of Life Sciences

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The tammar wallaby ( Macropus eugenii ) is a model marsupial species that has been intensively used for research into various aspects of marsupial biology. Recently, it became one of only three marsupial species to have its genome sequenced. Comparisons of genome sequence from all three marsupials with those of other vertebrates have made it possible to begin identifying marsupial‐specific genome features. Our knowledge of the biology of the tammar wallaby has informed the interpretation of these unique features and provided insight into their evolution. Among these unique features are genes involved in the sophisticated marsupial lactation system and genes encoding for potent antimicrobial peptides. Comparisons of genome organisation have also provided insight into marsupial genome evolution. Key Concepts: Uncovering the genetic basis of unique marsupial features is now possible due to the availability of genome sequences for three marsupial species. The tammar wallaby is a model species used for studies into marsupial biology, making it possible to link genomic features with the biological characteristics. As the tammar wallaby genome was only lightly sequenced, other genomic resources such as transcriptome sequences and genome maps have enhanced the genome assembly. A number of novel genes are associated with the complex marsupial lactation system and immunity. Five novel genes have been identified on the marsupial Y chromosome. The organisation of the tammar wallaby major histocompatibility complex is vastly different to that of any other species studied to date. A decades old debate over chromosome number in the ancestral marsupial has been resolved by comparing genome organisation among the sequenced marsupials species and the outgroup species human and chicken. The wallaby genome assembly in combination with other genomic resources are proving valuable for the discovery of marsupial‐specific features.

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Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

Cited by 312 publications

References 63 publications

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

4th Australasian Vaccines and Immunotherapeutic Development Meeting

Genome Sequence of an Australian Kangaroo,Macropus eugenii

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