TY - JOUR
T1 - A non-LTR retroelement extinction in Spermophilus tridecemlineatus
AU - Platt, Roy N.
AU - Ray, David A.
N1 - Funding Information:
We thank the Broad Institute Genome Sequencing Platform and Genome Sequencing and Analysis Program, F. Di Palma and Kerstin Lindblad-Toh for making the early assembly of S. tridecemlineatus available. This work was supported by the National Science Foundation [ MCB-0841821 and DEB-1020865 ]. Additional support was provided by the Institute for Genomics, Biocomputing and Biotechnology , the College of Agriculture and Life Sciences (both at Mississippi State University) and the Eberly College of Arts and Sciences at West Virginia University . Constructive criticism of the manuscript was provided by F.G. Hoffman, A. Chong, M.P. Ramakodi, M.W. Vandewege, J.D. Smith, A. Sharma, C. Thompson, C. Lavoie, and anonymous reviewers. S. DiFazio provided computational support.
PY - 2012/5/25
Y1 - 2012/5/25
N2 - The typical mammalian genome is dominated by two types of transposable elements (TEs), the autonomous and non-autonomous non-LTR retrotransposons, i.e. LINEs and SINEs, and with few exceptions there is a sole active LINE family (L1). During an ongoing investigation of TEs in rodents we determined that overall transposon activity has been steadily declining in Spermophilus tridecemlineatus. More specifically, the typically ubiquitous L1 activity of mammals has decreased drastically within the last 26. MY. Indeed, only three L1 insertions with intact ORF1 sequences were readily identifiable and no intact ORF2 sequences were identified. The last L1 and SINE insertions date to ~. 5.3. MYA and 4. MYA, respectively. Based on our inability to computationally identify recently inserted L1 elements we suggest that S. tridecemlineatus is experiencing a quiescence or extinction of non-LTR retrotransposon activity. Such a finding represents only the fourth instance of a loss of non-LTR retrotransposon activity identified in mammals and, as such, represents an important additional data point to guide our understanding of LINE dynamics in eutherians.
AB - The typical mammalian genome is dominated by two types of transposable elements (TEs), the autonomous and non-autonomous non-LTR retrotransposons, i.e. LINEs and SINEs, and with few exceptions there is a sole active LINE family (L1). During an ongoing investigation of TEs in rodents we determined that overall transposon activity has been steadily declining in Spermophilus tridecemlineatus. More specifically, the typically ubiquitous L1 activity of mammals has decreased drastically within the last 26. MY. Indeed, only three L1 insertions with intact ORF1 sequences were readily identifiable and no intact ORF2 sequences were identified. The last L1 and SINE insertions date to ~. 5.3. MYA and 4. MYA, respectively. Based on our inability to computationally identify recently inserted L1 elements we suggest that S. tridecemlineatus is experiencing a quiescence or extinction of non-LTR retrotransposon activity. Such a finding represents only the fourth instance of a loss of non-LTR retrotransposon activity identified in mammals and, as such, represents an important additional data point to guide our understanding of LINE dynamics in eutherians.
KW - Ground squirrel
KW - LINE
KW - Retrotransposon
KW - Transposable element
UR - http://www.scopus.com/inward/record.url?scp=84860335554&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2012.03.051
DO - 10.1016/j.gene.2012.03.051
M3 - Article
C2 - 22465530
AN - SCOPUS:84860335554
SN - 0378-1119
VL - 500
SP - 47
EP - 53
JO - Gene
JF - Gene
IS - 1
ER -