high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

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 assembli..., , , # 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 est...