DOI: 10.5061/dryad.cjsxksncs
title: Data from: high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

description: Transposable elements (TE) play critical roles in shaping genome
 evolution. However, the highly repetitive sequence content of TEs is a
 major source of assembly gaps. This makes it difficult to decipher the
 impact of these elements on the dynamics of genome evolution. The
 increased capacity of long-read sequencing technologies to span highly
 repetitive regions of the genome should provide novel insights into
 patterns of TE diversity. Here we report the generation of highly
 contiguous reference genomes using PacBio long read and Omni-C
 technologies for three species of sparrows in the family Passerellidae. To
 assess the influence of sequencing technology on TE annotation, we
 compared these assemblies to three chromosome-level sparrow assemblies
 recently generated by the Vertebrate Genomes Project and nine other
 sparrow species generated using a variety of short- and long-read
 technologies. All long-read based assemblies were longer in length (range:
 1.12-1.41 Gb) than short-read assemblies (0.91-1.08 Gb). Assembly length
 was strongly correlated with the amount of repeat content, with longer
 genomes showing much higher levels of repeat content than typically
 reported for the avian order Passeriformes. Repeat content for the
 Bell's sparrow (31.2% of genome) was the highest level reported to
 date for a songbird genome assembly and was more in line with woodpecker
 (order Piciformes) genomes. CR1 LINE elements retained from an expansion
 that occurred 25-30 million years ago were the most abundant TEs in the
 song sparrow genome. Although the other five sparrow species also exhibit
 evidence for a spike in CR1 LINE activity at 25-30 million years ago, LTR
 elements stemming from more recent expansions were the most abundant
 elements in these species. LTRs were uniquely abundant in the Bell's
 sparrow genome deriving from two recent peaks of activity. Higher levels
 of repeat content (79.2-93.7%) were found on the W chromosome relative to
 the Z (20.7-26.5) or autosomes (16.1-30.9%). These patterns support a
 dynamic model of transposable element expansion and contraction
 underpinning the seemingly constrained and small sized genomes of birds.
 Our work highlights how the resolution of difficult-to-assemble regions of
 the genome with new sequencing technologies promises to transform our
 understanding of avian genome evolution.
description: # README: Data from: high repeat content in the genomes of sparrows: the
 importance of genome assembly completeness for transposable element
 discovery https://doi.org/10.5061/dryad.cjsxksncs Supplementary datasets
 and code for the manuscript: High repeat content in the genomes of
 sparrows: the importance of genome assembly completeness for transposable
 element discovery. ## Description of the data and file structure Five
 folders containing data and code for the manuscript. (1)
 GenomeSizeVariation * GenomeAssemblySize.csv: Genome assembly length
 versus c-value genome size length. column names Species: Scientific name
 of Passerelidae sparrow corrCvalue: c-value estimate of genome length
 corrected using that 1pg = 0.978 Gb. assembly: genome size estimate based
 on assembly length. * GenomeSize_passerellidae.csv: Genome size dataset
 for members of the sparrow family Passerellidae. column names Species:
 Scientific name of Passerelidae sparrow C_value: Genome size estimate in
 picograms (pg) Adjusted_genome_size: c-value estimate of genome length in
 Gigabases (Gb) adjusted using 1pg = 0.978 Gb. CellType: cell type used for
 c-value measurements method: method used to generate c-value estimates
 source: publication from which data were obtained * TE_evolution_plot.py:
 Python code to make histogram of c-value genome size estimates for
 Passerellidae sparrows. (2) PhylogenyConstruction *
 MCMCtrees.sparrows.ctl: parameter file for MCMCtree analysis *
 Sparrow_UCE_Tree.txt: Newick format file for input to MCMCtree with
 calibrated node * RAxML_input_parameters_CIPRES.pdf: Input parameters for
 running RAxML on the CIPRES computing cluster *
 sparrow-cleaned-95p.phylip.txt: phylip formatted UCEs for all sparrows
 used to construct phylogenies. (3) RepeatAnnotation *
 Passerellidae.final_TElibrary.fa: Final library of consensus transposable
 element sequence. Generated from de novo annotation in RepeatModeler2,
 manual curation, and merger with other avian repeats. *
 RepeatContent_Sparrows.csv: summary data of RepeatMasker results for each
 sparrow species. column names (NA signifies missing data) Species: Species
 name using 4 letter alpha codes. (white-crowned sparrow: WCSP; California
 towhee: CALT; swamp sparrow: SWSP; Nelson's sparrow: NESP; saltmarsh
 sparrow short-read: SALS_SR; saltmarsh sparrow long-read: SALS_VG;
 Savannah sparrow: SAVS; Bell's sparrow: BESP; song sparrow: SOSP;
 white-throated sparrow: WTSP; dark-eyed junco: DEJU; chipping sparrow:
 CHSP; grasshopper sparrow: GRSP) LINE: percent LINE elements present in
 genome SINE: percent SINE elements present in genome LTR: percent LTR
 elements present in genome DNA: percent DNA elements present in genome RC:
 percent RC (rolling circle) elements present in genome Unclassified:
 percent Unclassified elements present in genome Total: Percent of entire
 genome spanned by transposable elements Genome_length_Gb: Length of genome
 assembly in Gigabases (Gb) contig_N50_Mb: The contig N50 of the assembly
 in Megabases (Mb) ContigLoHigh: Whether the contig N50 is above or below
 the 1Mb threshold corrCvalue: c-value estimate of genome length corrected
 using that 1pg = 0.978 Gb. Missing_length: Amount of missing data based on
 c-value minus assembly length Per_missing: percent of missing DNA from
 genome assembly. * Repeat_assemblyPlot.R: R code for generating scatter
 plots and regression analyses of genome assembly length versus repeat
 content or DNA missingness and % repeat content. * SOSP_genome_plot.R: R
 code for generating barplots comparing total number of TE elements and
 amount of genome spanned by TEs across different genome assemblies for
 song sparrow and saltmarsh sparrow. (4) RepeatMasker_results Folder with
 .tbl output files from RepeatMasker for each species and sex chromosomes
 for some species. (5) TE_landscapes Divergence landscapes for each species
 and R code for generating TE landscape figures. These landscapes show the
 distribution of divergence times from the consensus sequence for each TE
 element family. CSV files exist for each sparrow species and chromosome
 and serve as input to R code for generating the TE landscape figures. Each
 CSV file has estimates of percent divergence from consensus for each TE
 class in 1% bins from 0-70% divergence. We summed across different TE
 families within each of the 4 classes to get a total length of LTR
 sequence (for example) that is x% divergent from each LTR consensus
 sequence. Column names for csv (sex chromosome files do not have Myrs
 column) Div: The percent divergence from the consensus TE sequence.
 Estimated as Kimura-2-parameter distance with CpG sites excluded. Myrs:
 Estimate of divergence time form the consensus in millions of years
 (Myrs). length: length of genome spanned by TEs that are within each
 divergence from consensus bin element: element class, includes LINE, DNA,
 LTR, and SINE elements ## Sharing/Access information Please contact Phred
 Benham (phbenham@gmail.com) if there are any questions or issues about the
 code and data shared here.