DOI: 10.5061/dryad.76487
title: Data from: Genomic dynamics of transposable elements in the Western Clawed Frog (Silurana tropicalis)

description: Transposable elements (TEs) are repetitive DNA sequences that can make new
 copies of themselves that are inserted elsewhere in a host genome. The
 abundance and distributions of TEs vary considerably among
 phylogenetically diverse hosts. With the aim of exploring the basis of
 this variation, we evaluated correlations between several genomic
 variables and the presence of TEs and non-TE repeats in the complete
 genome sequence of the Western clawed frog (Silurana tropicalis). This
 analysis reveals patterns of TE insertion consistent with gene disruption
 but not with the insertional preference model. Analysis of non-TE repeats
 recovered unique features of their genome-wide distribution when compared
 with TE repeats, including no strong correlation with exons and a
 particularly strong negative correlation with GC content. We also
 collected polymorphism data from 25 TE insertion sites in 19 wild-caught
 S. tropicalis individuals. DNA transposon insertions were fixed at eight
 of nine sites and at a high frequency at one of nine, whereas insertions
 of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at
 only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood
 model failed to attribute these differences in insertion frequencies to
 variation in selection pressure on different classes of TE, opening the
 possibility that other phenomena such as variation in rates of replication
 or duration of residence in the genome could play a role. Taken together,
 these results identify factors that sculpt heterogeneity in TE
 distribution in S. tropicalis and illustrate that genomic dynamics differ
 markedly among TE classes and between TE and non-TE repeats.
description: Logistic regression
 input and related R script, description of TE familesSupplementary Material:
 Description of Supplementary Files. We include 22 files as supplementary
 material, including (a) all TE and non-TE repeat fragments in the Silurana
 tropicalis genome, as reported by RepeatMasker (b) input files to run
 logistic regression in R, for the models where TEs are not included in the
 GC calculations (c) input files to run logistic regression in R, for the
 model where TEs are included in the GC calculations (d) R script to run
 both logistic regression models (e) descriptions of TE and non-TE repeat
 classes (f) description of TE families. (a) 2012RepeatMasked: this is the
 standard output file from RepeatMasker. Columns include: SW score, percent
 div. (percent diverged), percent del. (percent deletion), percent ins.,
 begin position in query, end position in query, TE family of matching
 repeat, repeat class/family, begin and end position in repeat, and
 RepeatMasker assigned ID number. (b)Input files contain information on the
 various genomic features and the presence of TE or non-TE repeats in 2
 kilobase windows. All windows are ordered in the same manner across the
 different input files for the same model (model for GC calculated
 including TE and non-TE repeats or not). Because number of windows in the
 2 models are different (we have to exclude windows that are completely
 full of TE from the model of GC content calculated without including TEs),
 2 sets of input files are used. a. TENoTENotContam.csv. This file denotes
 the presence or absence of TE and non-TE repeats with a 1 or 0. The
 columns are of different TE or non-TE repeat classes and the rows of are
 of the presence or absence of these repeats in 2 kilobase windows. b. The
 fourth column of ConservedNoTE.txt, exonsNoTE.txt, intronsNoTE.txt and
 GCNoTE.txt lists the proportion of window that is conserved across
 species, is exon, is intron, and percent GC content respectively. The
 first 3 columns are “linkage group or not” (whether we concatenated
 different chromosomes into a linkage group “LG” or not “nonLG”), “linkage
 group number or chromosome number”, “genomic window number”. The total c.
 distancesNoTE.txt lists the distance, in basepairs, of the closest gene up
 or downstream in columns 4 and 5 respectively. expressionNoTE.txt lists
 the proportion of windows that is expressed in germline genes or soma
 genes in columns 4 and 5 respectively. The first 3 columns are again
 “linkage group or not” (whether we concatenated different chromosomes into
 a linkage group “LG” or not “nonLG”), “linkage group number or chromosome
 number”, “genomic window number”. (c) This pattern of input files is
 repeated for the model where percent GC content in a window is calculated
 including TE and non-TE repeats. The files are similarly named as
 TENotContam.csv, Conserved.txt, exons.txt, introns.txt, GC.txt,
 distances.txt and expression.txt. (d) For long TEs and short TEs, separate
 files are provided for the presence or absence of TE in genomic windows,
 where GC content is calculated either including or excluding TEs and
 non-TE repeats. These files are titled “TELong.csv”,”TELongNoTE.csv”,
 “TEshort.csv”, “TEShortNoTE.csv”. (e) modelTE.R is the script used to read
 the input files and run the logistic regressions. (f) Summary of
 classes.xlsx is the summary of total length and number of fragments of
 different classes of TEs and non-TE Repeat (g) Summary of Families.xlsx is
 the summary of total TE or non-TE repeat fragments in each TE family or
 non-TE RepeatsuppMat.zip