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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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Relationship among recent CORE-SINEs in marsupial genomes. A hypothetical evolutionary scenario of the relationships among short CORE-SINEs, particularly WSINE1 and WALLSI2, found in marsupials. The short CORE (beige) is only found in a few SINEs, suggesting a common evolutionary origin. Insertions into the tRNA-related part (green) of CORE-SINEs are rare; thus, the 7-nt insert (black) shared between WSINE1a/1b and WALLSI2 is likely to have a common evolutionary origin. Elements in parentheses are those responsible for the retroposition of the respective SINES. Green: tRNA-related sequence, beige: CORE sequence, dark grey: LINE3-like tail sequence, purple: RTE-like tail sequence, pink: origin unknown of the tail sequence, black: 7-nt insertion, red: 11-nt insertion, red AAAA: indicates that the SINE uses a poly(A)-tail for propagation via LINE1.
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Figure 5: Relationship among recent CORE-SINEs in marsupial genomes. A hypothetical evolutionary scenario of the relationships among short CORE-SINEs, particularly WSINE1 and WALLSI2, found in marsupials. The short CORE (beige) is only found in a few SINEs, suggesting a common evolutionary origin. Insertions into the tRNA-related part (green) of CORE-SINEs are rare; thus, the 7-nt insert (black) shared between WSINE1a/1b and WALLSI2 is likely to have a common evolutionary origin. Elements in parentheses are those responsible for the retroposition of the respective SINES. Green: tRNA-related sequence, beige: CORE sequence, dark grey: LINE3-like tail sequence, purple: RTE-like tail sequence, pink: origin unknown of the tail sequence, black: 7-nt insertion, red: 11-nt insertion, red AAAA: indicates that the SINE uses a poly(A)-tail for propagation via LINE1.

Mentions: Comparative indel analysis of 75,000 full-length WSINE1s showed that there are two over-represented insertions. One is located at position 80 and the other at position 120 (Figure 3). It has been shown that the insert at position 80 is most likely the result of a duplication [30]. Alignments of the tRNA-related parts from several CORE-SINEs, both young and old, indicate that insertions and deletions are very infrequent in this region. No deletions were observed. Insertions were found in only three other CORE-SINEs (Mar1a_Mdo, MAR1, and WALLSI2) (data not shown). WSINE1 has no inserts, and can be considered ancestral to both WSINE1a (11-nt and 7-nt inserts) and WSINE1b (7-nt insert) (Figure 5). After screening the different marsupial SINEs, it is evident that the distinguishing 7-nt-long insert found in WSINE1a and WSINE1b is also present in WALLSI2 [30]. Insertions in the CORE-SINE tRNA region appear to be highly infrequent, therefore the presence of a 7-nt insert in a homologous position in WALLSI2 and WSINE1a/b indicates a common evolutionary ancestry. WSINE1a and WSINE1b share the 7-nt insert but 1a has received an additional 11-nt insert. Thus the acquisition of the 11-nt insert in WSINE1a would suggest an origin after 1b.


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

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

Relationship among recent CORE-SINEs in marsupial genomes. A hypothetical evolutionary scenario of the relationships among short CORE-SINEs, particularly WSINE1 and WALLSI2, found in marsupials. The short CORE (beige) is only found in a few SINEs, suggesting a common evolutionary origin. Insertions into the tRNA-related part (green) of CORE-SINEs are rare; thus, the 7-nt insert (black) shared between WSINE1a/1b and WALLSI2 is likely to have a common evolutionary origin. Elements in parentheses are those responsible for the retroposition of the respective SINES. Green: tRNA-related sequence, beige: CORE sequence, dark grey: LINE3-like tail sequence, purple: RTE-like tail sequence, pink: origin unknown of the tail sequence, black: 7-nt insertion, red: 11-nt insertion, red AAAA: indicates that the SINE uses a poly(A)-tail for propagation via LINE1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Relationship among recent CORE-SINEs in marsupial genomes. A hypothetical evolutionary scenario of the relationships among short CORE-SINEs, particularly WSINE1 and WALLSI2, found in marsupials. The short CORE (beige) is only found in a few SINEs, suggesting a common evolutionary origin. Insertions into the tRNA-related part (green) of CORE-SINEs are rare; thus, the 7-nt insert (black) shared between WSINE1a/1b and WALLSI2 is likely to have a common evolutionary origin. Elements in parentheses are those responsible for the retroposition of the respective SINES. Green: tRNA-related sequence, beige: CORE sequence, dark grey: LINE3-like tail sequence, purple: RTE-like tail sequence, pink: origin unknown of the tail sequence, black: 7-nt insertion, red: 11-nt insertion, red AAAA: indicates that the SINE uses a poly(A)-tail for propagation via LINE1.
Mentions: Comparative indel analysis of 75,000 full-length WSINE1s showed that there are two over-represented insertions. One is located at position 80 and the other at position 120 (Figure 3). It has been shown that the insert at position 80 is most likely the result of a duplication [30]. Alignments of the tRNA-related parts from several CORE-SINEs, both young and old, indicate that insertions and deletions are very infrequent in this region. No deletions were observed. Insertions were found in only three other CORE-SINEs (Mar1a_Mdo, MAR1, and WALLSI2) (data not shown). WSINE1 has no inserts, and can be considered ancestral to both WSINE1a (11-nt and 7-nt inserts) and WSINE1b (7-nt insert) (Figure 5). After screening the different marsupial SINEs, it is evident that the distinguishing 7-nt-long insert found in WSINE1a and WSINE1b is also present in WALLSI2 [30]. Insertions in the CORE-SINE tRNA region appear to be highly infrequent, therefore the presence of a 7-nt insert in a homologous position in WALLSI2 and WSINE1a/b indicates a common evolutionary ancestry. WSINE1a and WSINE1b share the 7-nt insert but 1a has received an additional 11-nt insert. Thus the acquisition of the 11-nt insert in WSINE1a would suggest an origin after 1b.

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