Abstract
House dust mites are common pests with an unusual evolutionary history, being descendants of a parasitic ancestor. Transition to parasitism is frequently accompanied by genome rearrangements, possibly to accommodate the genetic change needed to access new ecology. Transposable element (TE) activity is a source of genomic instability that can trigger large-scale genomic alterations. Eukaryotes have multiple transposon control mechanisms, one of which is RNA interference (RNAi). Investigation of the dust mite genome failed to identify a major RNAi pathway: the Piwi-associated RNA (piRNA) pathway, which has been replaced by a novel small-interfering RNA (siRNA)-like pathway. Co-opting of piRNA function by dust mite siRNAs is extensive, including establishment of TE control master loci that produce siRNAs. Interestingly, other members of the Acari have piRNAs indicating loss of this mechanism in dust mites is a recent event. Flux of RNAi-mediated control of TEs highlights the unusual arc of dust mite evolution.
Highlights
House dust mites are ubiquitous inhabitants of human dwellings, and are the primary cause of indoor allergy [1]
Apart from several nematode and platyhelminths lineages, Piwi-associated RNA (piRNA) are an essential component of animal genome surveillance, actively targeting and silencing transposable elements
The dramatic difference we find in dust mites is likely a consequence of their evolutionary history, which is marked by descent from a parasite to the current free-living form
Summary
The dust mite genome was assembled using reads produced by PacBio and Illumina platforms. The initial assembly was generated by PacBio HGAP. Illumina reads were preprocessed in three steps before using them for extending PacBio contigs: a) Using Trimmomatic [63], from both ends of reads, nucleotides with base quality lower than 15 were removed. Any initial genome sequence has bacterial contamination due, at least, to the presence of gut microbiota in DNA isolates. To remove bacterial DNA sequences from D. farinae genome sequence, 4,864,367 Bacterial genome sequences [66] were downloaded from RefSeq database at: ftp://ftp.ncbi.nih.gov/refseq/release/bacteria and a blast database was created using the sequences [66, 67]. All the contigs were blasted against the created
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