To quantify variation in repeat content within and between bdelloid species, we generated de novo whole-genome assemblies for 31 rotifer samples encompassing nine species. Three of these assemblies were generated using 10x Genomics linked-read data from clonal populations grown from single wild-caught individuals (for Adineta steineri, Rotaria sordida, and Rotaria sp. ‘Silwood-1’), while 26 are from Illumina libraries of DNA extracted directly from single wild-caught individuals. In order to capture as many potential repeats as possible, we generated two assemblies for each Illumina sample: a ‘reference’ assembly, with a focus on quality and contiguity, and a ‘maximum haplotype’ (maxhap) assembly that included small or highly similar contigs that might be derived from recent TE duplications or other sources of copy number variation, at the expense of contiguity.
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