DOI: 10.5061/dryad.931zcrjtm
title: Data from: Transposable element diversity and activity patterns in neotropical salamanders

description: Transposable elements (TEs) compose a substantial proportion of the
 largest eukaryotic genomes. TE diversity has been hypothesized to be
 negatively correlated with genome size, yet empirical demonstrations of
 such a relationship in a phylogenetic context are largely lacking.
 Furthermore, the most abundant type of TEs in genomes varies across
 groups, and it is not clear if there are patterns of TE activity
 consistent with genome size among different taxa with large genome sizes.
 We use low-coverage sequencing of 16 species of Neotropical salamanders,
 which vary approximately seven-fold in genome size, to estimate TE
 relative abundance and diversity for each species. We also compare
 divergence of copies of each TE superfamily to estimate patterns of TE
 activity in each species. We find a negative relationship between TE
 diversity and genome size, which is consistent with the hypothesis that
 either competition among TEs or reduced selection against ectopic
 recombination may result in lower diversity in the largest genomes. We
 also find divergent activity patterns in the largest vs. the smallest
 genomes, suggesting that the history of TE activity may explain
 differences in genome size. Our results suggest that both TE diversity and
 relative abundance may be predictable, at least within taxonomic groups.
description: Low coverage sequencing genomic libraries were prepared and
 sequenced at the Vincent J. Coates Sequencing facility, QB3, at the
 University of California, Berkley, using the NovaSeq S4 seqquencing
 platform. Four samples were selected to asse,ble draft contigs using
 dipSPADES (Safanova et al. 2015). Transposable elements were retrieved and
 annotated using PiRATE (Pipeline to Retrieve and Annotate Transposable
 Elements). 
description: # Transposable element diversity and activity patterns in neotropical
 salamanders
 [https://doi.org/10.5061/dryad.931zcrjtm](https://doi.org/10.5061/dryad.931zcrjtm) ## Description of the data and file structure The data deposited in this repository corresponds to the Transposable Element libraries (sequences), and associated scripts used to describe the relative abundance and diversity of TEs in Neotropical salamanders. ### Files and variables ### On Zenodo #### File: te\_landscape\_sh.txt **Description:** Bash scripts for low coverage sampling and repeat masker. #### **File: batch\_te2.R** **Description:** R script containing all the code used for analysis and figures used in the present study. #### **File: te\_landscape\_experiment.R** **Description**: R code with a function to generate relative abudances of ransposable elements by species.  ### On Dryad #### File: salamander\_telib-v1.0.fasta **Description:** Consensus sequences of TEs generated by low coverage assembly of four species of neotropical salamanders, used as a library to determine TE abundance and diversity of other neotropical salamander species. CSV files containing the transposable element landscapes by species (repeat masker output) #### File: tnaris\_teland\_final.csv **Description:** *Thorius narisovalis* #### File: tluna\_teland\_final.csv **Description:** *Thorius lunaris* #### File: ttlax\_teland\_final.csv **Description:** *Thorius tlaxiacus* #### File: tspil\_teland\_final.csv **Description:** *Thorius spilogaster* #### File: cpris\_teland\_final.csv **Description:** *Chiropterotriton priscus* #### File: cdimi\_teland\_final.csv **Description:** *Chiropterotriton dimidiatus* #### File: byuca\_teland\_final.csv **Description:** *Bolitoglossa yucatana* #### File: bvera\_teland\_final.csv **Description:** *Bolitoglossa veracruscis* #### File: bstuar\_teland\_final.csv **Description:** *Bolitoglossa stuarti* #### File: bruf\_teland\_final.csv **Description:** *Bolitoglossa rufescens* #### File: bocci\_teland\_final.csv **Description:** *Bolitoglossa occidentalis* #### File: bmex\_teland\_final.csv **Description:** *Bolitoglossa mexicana* #### File: bmacri\_teland\_final.csv **Description:** *Bolitoglossa macrinii* #### File: bplaty\_teland\_final.csv **Description:** *Bolitoglossa platydactyla* #### File: bflavi\_teland\_final.csv **Description:** *Bolitoglossa flaviventris* #### File: bchin\_teland\_final.csv **Description:** *Bolitoglossa chinanteca* All CSV files have the same variables ##### Variables * X1: Smith-Waterman alignment score * X2: K2P percentage divergence * X3: Percentage of deletions * X4: Percentage of insertions * X5: Query start position * X6: Query end position * X7: Strand \ +: positive strand\ C: complementary strand * X8: Reference Consensus sequence id * X9: Reference Consensus sequence species of origin  * X10: TE class * X11: TE Order  * X12: TE Superfamily * NA: Not applicable * Bel-Pao: Bel-Pao superfamily (LTR retrotransposons) * CACTA: CACTA superfamily (Class II DNA transposons) * Copia: Copia superfamily (LTR retrotransposons) * Crypton: Crypton superfamily (Class II DNA transposons) * DIRS: DIRS superfamily (LTR retrotransposons) * ERV: Endogenous retrovirus superfamily (integrated retroviral sequences) * Gypsy: Gypsy superfamily (LTR retrotransposons) * hAT: hAT superfamily (Class II DNA transposons) * Helitron: Helitron superfamily (Class II DNA transposons) * I: I superfamily (non-LTR retrotransposons, LINE-like) * Jockey: Jockey superfamily (non-LTR retrotransposons, LINE-like) * Kolobok: Kolobok superfamily (Class II DNA transposons) * L1: L1 superfamily (LINE-1, non-LTR retrotransposons) * Maverick: Maverick superfamily (Class II DNA transposons) * MITE: Miniature Inverted-repeat Transposable Elements (Class II DNA transposons) * MuDR: MuDR superfamily (Class II DNA transposons) * Novosib: Novosib superfamily (Class II transposons) * Penelope: Penelope-like elements (PLEs; non-LTR retrotransposons) * PIF-Harbinger: PIF/Harbinger superfamily (Class II DNA transposons) * PiggyBac: PiggyBac superfamily (Class II DNA transposons) * R2: R2 superfamily (non-LTR retrotransposons) * Retrovirus: Retrovirus (exogenous retroviral elements) * RTE: RTE superfamily (non-LTR retrotransposons) * SINE: Short Interspersed Nuclear Elements (non-autonomous non-LTR retrotransposons) * Sola: Sola superfamily (Class II DNA transposons) * Tc1-Mariner: Tc1-Mariner superfamily (Class II DNA transposons) * termLTR: TE with terminal Long Terminal Repeat structure (unclassified or incomplete LTR retrotransposon) * termTIR: TE with terminal Tandem Inverted Repeat structure (unclassified or incomplete DNA transposon) * " ": Empty fields indicate no super-family could be assigned