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

BMC Genomics
Maria A NilssonBjörn M Hallström

Abstract

The 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 element (SINE) retroposons. The 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...Continue Reading

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Citations

Aug 25, 2015·Veterinary Immunology and Immunopathology·Beata Ujvari, Katherine Belov
Feb 6, 2017·Genome Biology and Evolution·Cibele G Sotero-CaioDavid A Ray
Nov 6, 2017·Journal of Molecular Evolution·Maxwell P Gold, Jacques R Fresco
Jan 13, 2018·Genome Biology and Evolution·Kenji K Kojima
Mar 7, 2021·International Journal of Molecular Sciences·Anna Maria PappalardoTeresa Capriglione

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Datasets Mentioned

BETA
FN666604
FN666605

Software Mentioned

Repeatmasker
TreeFinder
WSINE
RepeatModeler
TinT
RTE
EMBOSS
DFTD
perl
MD

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