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1Dept. of Biological Sciences. Texas Tech University, Lubbock, TX 79402
Sarah F. Mangum1 , Roy N. Platt II1 , and David A. Ray1
Introduction▪ Spermophilus (Ictidomys) tridecemlineatus▪ Transposable elements (TEs)▪ LINE (L1) “Extinction”
Materials and methods▪ Preliminary bioinformatic analysis▪ Bench work▪ Bioinformatic analysis
Results and Discussion▪ Numbers/passed quality control▪ Preliminary findings
13-lined ground squirrel Ranges over central North America
Recent findings about very low L1 activity
• Class I • Mobilization via an RNA intermediate
Pol III transcription
Reverse transcription and insertion
L1 elements
T0 T 1 T2
T0 T3 T100
Number of mutations = 0Avg. genetic distance = 0
Number of mutations = 14Avg. genetic distance = 2.3
Number of mutations = 53Avg. genetic distance = 8.9
Young Old Oldest
Platt et al. 2012
S. tridecemlineatus
250 most similar (most recently active) L1 ORF2 fragments from human, mouse, rat, and 13-lined ground squirrel.
19-26 MYA
Platt et al. 2012
Spermophilus tridecemlineatus
Based on the presence of L1 in Primates, Mouse, Rat, and many other species it has generally been assumed that L1 is present and active in all mammals.
Identified L1 extinction events Megabats (Cantrell et al. 2008) Sigmodontine rodents (Grahn et al. 2005) Spider monkey (Boissinot et al. 2004) Tasmanian devil (Gallus et al. 2015)
35 mya
12 myaWhat happened to L1s in neighboring taxa?
Look at taxa diverged prior and after extinction event occurred.
Herron et al 2004
Used well-annotated L1s from other mammals Degenerate primer for region of ORF2 <500bp This allows for amplification of 100s of 1000s of
different LINE L1 elementsCantrell et al. 2000
Identify ORF2 fragment Develop primers Isolate DNA from liver tissue PCR Sanger sequencing to verify
diversity of amplicons Illumina paired end
sequencing
Spermophilus tridecemlineatus
Spermophilus parvidens
Spermophilus mexicanus
Cynomys ludovicianus
Spermophilus spilosoma
Marmota flavivientris
Spermophilus variegatus
Ammospermophilus harrissi
Tamias dorsalis
Glaucomys volans
Tamiasciurus hudsonicus
Sciurus niger
300bp reads from each end of amplified L1 ORF2 fragment
Overlap of ~100bp allows whole fragment to be sequenced
Read 1 (≤300bp)Read 2 (≤300bp)
This methodology allows for generation of huge data sets
Preliminary analyses
Raw CollapsedStri 64,344 42,697Spar 62,546 43,202Smex 388,986 181,563Clud 71,824 49,717Sspi 14,317 7,603Sric 120,142 75,874Mfla 41,203 29,631Svar 64,659 38,644Ahar 30,836 24,161Tdor 1,202 36,347Gvol 5,330 156Thud 45,135 970Snig 16,808 359Total Paired Reads 927,332 530,924Total Base Pairs <600,000,000 320,000,000
Ammospermophilus harrisii
Cynomys ludovicianus
Spermophilus parvidens
Most similar L1 fragments from each taxon
Use most similar in order to obtain the most recent active L1 elements
Long branches L1s highly diverged over
all taxa
L1 elements in sciurids have had very little recent activity.
Hypothesis based on preliminary data:
Suggests a group-wise shutdown of these LINE elements
Single extinction event ~25 mya (affecting all in-group taxa)
Use all available data
Did extinction event occur in neighboring taxa at the same time?
How wide-spread is the extinction?
Natural Science Research Laboratory(Museum of Texas Tech University)
Dr. Roy N. Platt, IIDr. David RayDr. Robert BradleyLaura Blanco-BerdugoKevin Sullivan Wesli Kay Stubbs
Texas Tech University Research and Testing
Texas Tech University High Performance Computer Center
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