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

Nilsson MA, Janke A, Murchison EP, Ning Z, Hallström BM - BMC Genomics (2012)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: LOEWE-Biodiversity and Climate Research Center, BiK-F, Senckenberganlage 25, Frankfurt am Main D-60325, Germany. maria.nilsson-janke@senckenberg.de

ABSTRACT

Background: 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.

Results: 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 genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago.

Conclusions: The 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.

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SINE Transposition in Transposition. TinT (Transposition in Transposition) of the most abundant marsupial-specific SINEs and non-autonomous LINEs in the Tasmanian devil genome. The chronological order of SINE activity goes from bottom (oldest) to top (most recent), with WSINE1 representing the most recently active SINE. The length of the bars indicates the length of time a SINE was active, with MIR3/Ther-2 having the longest activity period and P7SL_MD and WALLSI1 the shortest. The color-coding indicates the types of elements responsible for the respective SINE retropositions. The * indicates truncation of the CORE sequence.
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Figure 2: SINE Transposition in Transposition. TinT (Transposition in Transposition) of the most abundant marsupial-specific SINEs and non-autonomous LINEs in the Tasmanian devil genome. The chronological order of SINE activity goes from bottom (oldest) to top (most recent), with WSINE1 representing the most recently active SINE. The length of the bars indicates the length of time a SINE was active, with MIR3/Ther-2 having the longest activity period and P7SL_MD and WALLSI1 the shortest. The color-coding indicates the types of elements responsible for the respective SINE retropositions. The * indicates truncation of the CORE sequence.

Mentions: For comparative genomics and in particular evolutionary purposes, it is useful to be able to estimate the relative order of activities of different groups of integrated SINEs found in the genome. TinT (transposition in transposition) is an algorithm that screens the genome for nested retroposon insertions (i.e., retroposons inserted within another retroposon) and calculates its relative time frame of activity based on the fact that old inactive retroposons cannot insert into younger active retroposons [34]. Screening of the Tasmanian devil genome with the TinT program [34] revealed 17,928 nested insertions for the most frequent SINEs and non-autonomous LINEs (Figure 2) ( Additional file 1: Table S2). The most recently active element is the WSINE1. The TinT pattern from the Tasmanian devil is reasonably similar to those previously observed in the opossum and wallaby [35].


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

Nilsson MA, Janke A, Murchison EP, Ning Z, Hallström BM - BMC Genomics (2012)

SINE Transposition in Transposition. TinT (Transposition in Transposition) of the most abundant marsupial-specific SINEs and non-autonomous LINEs in the Tasmanian devil genome. The chronological order of SINE activity goes from bottom (oldest) to top (most recent), with WSINE1 representing the most recently active SINE. The length of the bars indicates the length of time a SINE was active, with MIR3/Ther-2 having the longest activity period and P7SL_MD and WALLSI1 the shortest. The color-coding indicates the types of elements responsible for the respective SINE retropositions. The * indicates truncation of the CORE sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3403934&req=5

Figure 2: SINE Transposition in Transposition. TinT (Transposition in Transposition) of the most abundant marsupial-specific SINEs and non-autonomous LINEs in the Tasmanian devil genome. The chronological order of SINE activity goes from bottom (oldest) to top (most recent), with WSINE1 representing the most recently active SINE. The length of the bars indicates the length of time a SINE was active, with MIR3/Ther-2 having the longest activity period and P7SL_MD and WALLSI1 the shortest. The color-coding indicates the types of elements responsible for the respective SINE retropositions. The * indicates truncation of the CORE sequence.
Mentions: For comparative genomics and in particular evolutionary purposes, it is useful to be able to estimate the relative order of activities of different groups of integrated SINEs found in the genome. TinT (transposition in transposition) is an algorithm that screens the genome for nested retroposon insertions (i.e., retroposons inserted within another retroposon) and calculates its relative time frame of activity based on the fact that old inactive retroposons cannot insert into younger active retroposons [34]. Screening of the Tasmanian devil genome with the TinT program [34] revealed 17,928 nested insertions for the most frequent SINEs and non-autonomous LINEs (Figure 2) ( Additional file 1: Table S2). The most recently active element is the WSINE1. The TinT pattern from the Tasmanian devil is reasonably similar to those previously observed in the opossum and wallaby [35].

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: LOEWE-Biodiversity and Climate Research Center, BiK-F, Senckenberganlage 25, Frankfurt am Main D-60325, Germany. maria.nilsson-janke@senckenberg.de

ABSTRACT

Background: 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.

Results: 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 genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus