Expansion of CORE-SINEs in the genome of the Tasmanian devil

BMC Genomics

Research Article

Björn M Hallström¹  Maria A Nilsson¹  Axel Janke²  Elizabeth P Murchison³  Zemin Ning³ 

[1] LOEWE - Biodiversity and Climate Research Center, BiK-F, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany;LOEWE - Biodiversity and Climate Research Center, BiK-F, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany;Goethe University Frankfurt, BioCampus, Siesmayerstr. 70, 60323, Frankfurt am Main, Germany;Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK;

关键词: SINE;    WSINE1;    Retroposon;    Tasmanian devil;    Sarcophilus;    Genome;    Marsupials;   

DOI  :  10.1186/1471-2164-13-172

 received in 2011-11-29, accepted in 2012-05-06,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed e lement (SINE) retroposons.ResultsThe temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago.ConclusionsThe radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

【 授权许可】

Unknown   
© Nilsson et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.