Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Renfree, Marilyn B.; Papenfuss, Anthony T.; Deakin, Janine E.; Lindsay, James; Heider, Thomas; Belov, Katherine; Rens, Willem; Waters, PD; Pharo, Elizabeth A.; Shaw, Geoff; Wong, Emily S.; Lefevre, CM; Nicholas, KR; Kuroki, Yoshio; Wakefield, Matthew J.; Zenger, Kyall R.; Cw, Wang; Ferguson-Smith, M. E.; Nicholas, F. W.; Hickford, Danielle; Yu, Hongshi; Short, Kirsty R.; Siddle, HV; Frankenberg, Stephen; Chew, KY; Menzies, B.R.; Stringer, Jessica M; Suzuki, Shunsuke; Hore, TA; Delbridge, ML; Patel, Hardip R.; Mohammadi, Amir H.; Schneider, NY; Yq, Hu; O'Hara, William A; Nadaf, Shafagh Al; Wu, Chao-ting; Feng, ZP; Cocks, BG; Jh, Wang; Flicek, Paul; Searle, S.; Fairley, Susan; Beal, Kathryn; Herrero, Javier; Carone, Dawn M.; Suzuki, Yuichiro; Sugano, Shoji; Toyoda, Atushi; Sakaki, Y; Kondo, Shinji; Nishida, Yuichiro; Tatsumoto, Shoji; Mandiou, Ion; Hsu, Arthur; Ka, McColl; Lansdell, Benjamin; Weinstock, George M.; Kuczek, Elizabeth; McGrath, Annette; Wilson, Peter; Men, A.; Hazar-Rethinam, Mehlika; Hall, Anne; Davis, Jayne L.; Wood, Derrick E.; Williams, S. A.; Sundaravadanam, Yogi; Muzny, D. M.; Jhangiani, SN; Lr, Lewis; Mb, Morgan; Okwuonu, GO; Ruiz, SJ; Santibanez, Jireh; Nazareth, Lynne V.; Cree, Andy; Fowler, Gerald R.; Kovar, CL; Dinh, HH; Joshi,; Jing, Chyn; Lara, Francisco J.; Thornton, Rebecca; Chen, L; Jx, Deng; Liu, Y; Shen, Jy; Song, XZ; Edson, Janette; Troon, Carmen; Thomas, D. Wu; Stephens, Amber; Yapa, Lankesha; Levchenko, Tanya; Gibbs, RA; Cooper, D. W.; Speed, TP; Fujiyama, Asao; Graves, Jennifer A. Marshall; O'Neill, R. J.; Pask, Andrew J; Forrest, SM; Worley, Kim C.

doi:10.1186/gb-2011-12-12-414

Cited by 39 publications

(36 citation statements)

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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%

“…Additionally, ~61.6% of reads mapped to the repeatmasked reference assembly, covering ~84.4% of unmasked bases to an average depth of ~42.8× (Supplementary Table 2). For comparison, we mapped the thylacine data to two other marsupial genomes, the tammar wallaby (Macropus eugenii) 11 and the gray short-tailed opossum (Monodelphis domestica) 12 . As expected, the percentage of reads that mapped decreased with increased phylogenetic distance between the reference genome and thylacine ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Reads that mapped to the contaminant database were removed from the dataset and not subjected to further analysis. To further validate that retained reads were composed largely of thylacine DNA, reads were mapped against the repeat-masked genomes of three extant marsupials: the Tasmanian devil (Sarcophilus harrisii) 10 , the tammar wallaby (Macropus eugenii) 11 and the gray short-tailed opossum (Monodelphis domestica) 12 as well as the complete, unmasked genome of the Tasmanian devil (assembly versions given in Supplementary Table 8). The percentage of reads mapping uniquely to each reference genome was graphed (Supplementary Fig.…”

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%

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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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“…CenH3 in maize was shown to interact with long CentC satellite transcripts (Du et al 2010). Interestingly, in the tammar wallaby, small centromeric transcripts align to the same centromeric sequences found specifically within CENP-A nucleosomes (Renfree et al 2011). Conceivably, the small and long RNAs interact with CENP-A at different times during the cell cycle, thereby temporally separating their respective functions.…”

Section: Centromeric Transcriptionmentioning

confidence: 98%

Pericentric and centromeric transcription: a perfect balance required

2012

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The pericentromere and centromere regions of the genome have previously been considered tightly compacted and transcriptionally inert. However, there is mounting evidence that these regions not only actively produce transcripts but that these pericentric and centromeric transcripts are also vital to maintaining genome stability and proper cell division. In this review, we define the pericentromere and centromere of eukaryotic chromosomes in terms of their histone modifications and their nascent transcripts. In addition, we present the currently known roles these transcripts play in heterochromatin formation, development, and differentiation, as well as their interaction with centromeric proteins, and ultimately centromere function. Recent work has added considerable complexity to the theoretical framework defining the innate requirement for pericentric and centromeric transcription. It is clear that maintaining a fine balance of transcriptional output is critical, as deviations from this balance result in centromere disfunction and genomic instability.

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“…Alternatively, genome size can be calculated from the sum of chromosome sizes determined by flow-karyotypic analysis using a flow cytometer [3][4][5][6][7]. For example, the sum of chromosome sizes in human (HSA) [4] and dog [5] by this method gives a value of 3.15 Gb and 2.75 Gb, respectively.…”

Section: Introductionmentioning

confidence: 99%

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

2012

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The genome size in turtles and crocodiles is thought to be much larger than the 1.2 Gb of the chicken ( Gallus gallus domesticus , GGA), according to the animal genome size database. However, GGA macrochromosomes show extensive homology in the karyotypes of the red eared slider ( Trachemys scripta elegans , TSC) and the Nile crocodile ( Crocodylus niloticus , CNI), and bird and reptile genomes have been highly conserved during evolution. In this study, size and GC content of all chromosomes are measured from the flow karyotypes of GGA, TSC and CNI. Genome sizes estimated from the total chromosome size demonstrate that TSC and CNI are 1.21 Gb and 1.29 Gb, respectively. This refines previous overestimations and reveals similar genome sizes in chicken, turtle and crocodile. Analysis of chromosome GC content in each of these three species shows a higher GC content in smaller chromosomes than in larger chromosomes. This contrasts with mammals and squamates in which GC content does not correlate with chromosome size. These data suggest that a common ancestor of birds, turtles and crocodiles had a small genome size and a chromosomal size-dependent GC bias, distinct from the squamate lineage.

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Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Cited by 39 publications

References 1 publication

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

Pericentric and centromeric transcription: a perfect balance required

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

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