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The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea,\n                      <jats:italic>Ctenocephalides felis<\/jats:italic>\n                      , an insect with substantial human health and veterinary importance across the globe.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      By combining Illumina and PacBio sequencing of DNA derived from multiple inbred female fleas with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly for\n                      <jats:italic>C. felis<\/jats:italic>\n                      . Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ~\u200938% of protein-coding genes with two or more copies and over 4000 tRNA genes. A broad range of genome size determinations (433\u2013551\u2009Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) in\n                      <jats:italic>C. felis<\/jats:italic>\n                      . Similarly, broad genome sizes were also calculated for individuals of\n                      <jats:italic>Xenopsylla cheopis<\/jats:italic>\n                      (Oriental rat flea), indicating that this remarkable \u201cgenome-in-flux\u201d phenomenon could be a siphonapteran-wide trait. Finally, from the\n                      <jats:italic>C. felis<\/jats:italic>\n                      sequence reads, we also generated closed genomes for two novel strains of\n                      <jats:italic>Wolbachia<\/jats:italic>\n                      , one parasitic and one symbiotic, found to co-infect individual fleas.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Rampant CNV in\n                      <jats:italic>C. felis<\/jats:italic>\n                      has dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novel\n                      <jats:italic>Wolbachia<\/jats:italic>\n                      endosymbionts\u2014potential tools for blocking pathogen transmission\u2014these oddities highlight a unique and underappreciated disease vector.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12915-020-00802-7","type":"journal-article","created":{"date-parts":[[2020,6,19]],"date-time":"2020-06-19T13:03:59Z","timestamp":1592571839000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity"],"prefix":"10.1186","volume":"18","author":[{"given":"Timothy P.","family":"Driscoll","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria I.","family":"Verhoeve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5447-7264","authenticated-orcid":false,"given":"Joseph J.","family":"Gillespie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. 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