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As an intracellular microbe,<jats:italic>Toxoplasma<\/jats:italic>establishes an intimate relationship with its host cell from the outset of infection. Macrophages are targets of infection and they are important in early innate immunity and possibly parasite dissemination throughout the host. Here, we employ an RNA-sequencing approach to identify host and parasite transcriptional responses during infection of mouse bone marrow-derived macrophages (BMDM). We incorporated into our analysis infection with the high virulence Type I RH strain and the low virulence Type II strain PTG. Because the well-known TLR-MyD88 signaling axis is likely of less importance in humans, we examined transcriptional responses in both MyD88<jats:sup>+\/+<\/jats:sup>and MyD88<jats:sup>\u2212\/\u2212<\/jats:sup>BMDM. Long noncoding (lnc) RNA molecules are emerging as key regulators in infection and immunity, and were, therefore, included in our analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We found significantly more host genes were differentially expressed in response to the highly virulent RH strain rather than with the less virulent PTG strain (335 versus 74 protein coding genes for RH and PTG, respectively). Enriched in these protein coding genes were subsets associated with the immune response as well as cell adhesion and migration. We identified 249 and 83 non-coding RNAs as differentially expressed during infection with RH and PTG strains, respectively. Although the majority of these are of unknown function, one conserved lncRNA termed mir17hg encodes the mir17 microRNA gene cluster that has been implicated in down-regulating host cell apoptosis during<jats:italic>T. gondii<\/jats:italic>infection. Only a minimal number of transcripts were differentially expressed between MyD88 knockout and wild type cells. However, several immune genes were among the differences. While transcripts for parasite secretory proteins were amongst the most highly expressed<jats:italic>T. gondii<\/jats:italic>genes during infection, no differentially expressed parasite genes were identified when comparing infection in MyD88 knockout and wild type host BMDM.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The large dataset presented here lays the groundwork for continued studies on both the MyD88-independent immune response and the function of lncRNAs during<jats:italic>Toxoplasma gondii<\/jats:italic>infection.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12864-021-07437-0","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T13:03:23Z","timestamp":1614085403000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Transcriptomics analysis of Toxoplasma gondii-infected mouse macrophages reveals coding and noncoding signatures in the presence and absence of MyD88"],"prefix":"10.1186","volume":"22","author":[{"given":"Kayla L.","family":"Menard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijing","family":"Bu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9020-3327","authenticated-orcid":false,"given":"Eric Y.","family":"Denkers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,2,23]]},"reference":[{"issue":"2","key":"7437_CR1","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1128\/CMR.05013-11","volume":"25","author":"F Robert-Gangneux","year":"2012","unstructured":"Robert-Gangneux F, Darde ML. 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