@article{01GW0FND4N67NFMKW105TBDMNP,
  abstract     = {{Free-living bacteria have evolved multiple times to become host-restricted
endosymbionts. The transition from a free-living to a host-restricted lifestyle comes with a
number of different genomic changes, including a massive loss of genes. In host-restricted
endosymbionts, gene inactivation and genome reduction are facilitated by mobile genetic
elements, mainly insertion sequences (ISs). ISs are small autonomous mobile elements, and
one of, if not the most, abundant transposable elements in bacteria. Proliferation of ISs is
common in some facultative endosymbionts, and is likely driven by the transmission bottlenecks,
which increase the level of genetic drift. In this study, we present a manually curated
genome annotation for a Cardinium endosymbiont of the dwarf spider Oedothorax gibbosus.
Cardinium species are host-restricted endosymbionts that, similarly to ColbachiaWolbachia
spp., include strains capable of manipulating host reproduction. Through the focus on mobile
elements, the annotation revealed a rampant spread of ISs, extending earlier observations in
other Cardinium genomes. We found that a large proportion of IS elements are pseudogenized,
with many displaying evidence of recent inactivation. Most notably, we describe the
lineage-specific emergence and spread of a novel IS-derived Miniature Inverted repeat
Transposable Element (MITE), likely being actively maintained by intact copies of its parental
IS982-family element. This study highlights the relevance of manual curation of these
repeat-rich endosymbiont genomes for the discovery of novel MITEs, as well as the possible
role these understudied elements might play in genome streamlining.
IMPORTANCE Cardinium bacteria, a widespread symbiont lineage found across insects and nematodes, have been linked to reproductive manipulation of their hosts. However, the study of Cardinium has been hampered by the lack of comprehensive genomic resources. The high content of mobile genetic elements, namely, insertion sequences (ISs), has long complicated the analyses and proper annotations of these genomes. In this study, we present a manually curated annotation of the Cardinium symbiont of the spider Oedothorax gibbosus. Most notably, we describe a novel IS-like element found exclusively in this strain. We show that this mobile element likely evolved from a defective copy of its parental IS and then spread throughout the genome, contributing to the pseudogenization of several other mobile elements. We propose this element is likely being maintained by the intact copies of its parental IS element and that other similar elements in the genome could potentially follow this route.}},
  articleno    = {{02627-22}},
  author       = {{Halter, Tamara and Hendrickx, Frederik and Horn, Matthias and Manzano-Marín, Alejandro}},
  editor       = {{Chen, Swaine L.}},
  issn         = {{2165-0497}},
  journal      = {{MICROBIOLOGY SPECTRUM}},
  keywords     = {{Infectious Diseases,Cell Biology,Microbiology (medical),Genetics,General Immunology and Microbiology,Ecology,Physiology,Cardinium,mobile element,insertion sequence,endosymbiont,Amoebophilaceae,BACTERIAL,EVOLUTION,REDUCTION,SYMBIONT,GENES}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{6}},
  title        = {{A novel widespread MITE element in the repeat-rich genome of the Cardinium endosymbiont of the spider Oedothorax gibbosus}},
  url          = {{http://doi.org/10.1128/spectrum.02627-22}},
  volume       = {{10}},
  year         = {{2022}},
}

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