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The insect is widespread in Africa, and has recently disseminated to Southwestern Europe. This study aimed at generating reference mitogenome sequences for<jats:italic>T. erytreae<\/jats:italic>, as a background for future genetic diversity surveys. Complete mitochondrial sequences of three specimens collected in Ethiopia, Uganda and South Africa were recovered using Ion Torrent technology. The mitogenomes of<jats:italic>T. erytreae<\/jats:italic>from Uganda and Ethiopia were highly similar, and distinct from that found in South Africa. The phylogeographic structure of<jats:italic>T. erytreae<\/jats:italic>was assessed using genetic clustering and pairwise distances, based on a dataset of public<jats:italic>COI<\/jats:italic>sequences recorded as<jats:italic>T. erytreae<\/jats:italic>. The dataset revealed ten haplotypes with strong phylogeographic structure in Africa and Europe. Three haplotypes found in Kenya on<jats:italic>Clausena anisata<\/jats:italic>belonged to pairs separated by distances as high as 11.2%, and were basal to all other sequences. These results indicate that not all sequences identified as<jats:italic>T. erytreae<\/jats:italic>belong to the same species, and that some degree of specificity with different plant hosts is likely to exist. This study provides new baseline information on the diversity of<jats:italic>T. erytreae<\/jats:italic>, with potential implications for the epidemiology of African Citrus Greening disease.<\/jats:p>","DOI":"10.1038\/s41598-020-65880-7","type":"journal-article","created":{"date-parts":[[2020,6,1]],"date-time":"2020-06-01T10:03:14Z","timestamp":1591005794000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Mitochondrial genetic variation reveals phylogeographic structure and cryptic diversity in Trioza erytreae"],"prefix":"10.1038","volume":"10","author":[{"given":"Inusa","family":"Ajene","sequence":"first","affiliation":[]},{"given":"Fathiya M.","family":"Khamis","sequence":"additional","affiliation":[]},{"given":"Gerhard","family":"Pietersen","sequence":"additional","affiliation":[]},{"given":"Barbara","family":"van Asch","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,1]]},"reference":[{"key":"65880_CR1","unstructured":"Food and Agriculture Organization of the United Nations. 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