Repeat library for Bombyx silkworm moth

We present a database of DNA repeats generated for Bombyx silkworms. This repeat library was generated de novo for Bombyx by combining results from a few separate data sources and methods for repeat discovery. First, we analyzed three Bombyx genome assemblies (p50ma: GCA_030269925.2, p50T: GCA_027366755.1, and Sakado: GCA_030267445.2) with the Earl Grey repeat discovery pipeline (v6.3.2, with default parameters). Second, to better capture tandem repeats with monomers 50-2000 bp long, we also analyzed these genomes using Tandem Repeats Finder (TRF; v4.09) and Tandem Repeats Analysis Program (TRAP; v1.1). Third, to complement these assembly-based approaches, we directly analyzed Illumina resequencing data from two B. mori Dazao strain females (Genbank accessions: SRR5828088, SRR5828090) using RepeatExplorer2 (Galaxy Version 2.3.12.1). To prepare the Illumina reads for the RepeatExplorer2 workflow, we removed the adaptors, quality-filtered, and trimmed reads to a uniform size of 95 bp using trimmomatic (v0.39), followed by removing overlapping read pairs and down-sampling to 9x105 read pairs. RepeatExplorer2 was run with default parameters using the Metazoan v3 library for repeat classification. Repeats found by TRF or RepeatExplorer2 estimated to comprise <0.01% of the genome were discarded from further analysis. Results from these distinct approaches to repeat discovery were consolidated into a single non-redundant repeat database “library” using CD-HIT (v4.8.1) following the 80-80-80 rule to define distinct repeat families. Manual inspection of the results revealed the combined library contained a single very large contig comprised of several tandem repeats of the same sequence, which we reduced to a single monomer.