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Here, we report the first Boraginales species de novo genome (i.e. <jats:italic>Echium plantagineum<\/jats:italic> genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin\/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales\/Gentianales clade than the Lamiales clade, at least based on the single\u2010copy orthologous genes from genome\/transcriptome data; (ii) after the gamma (\u03b3) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin\/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and <jats:italic>O<\/jats:italic>\u2010acyl transferase.<\/jats:p>","DOI":"10.1111\/1755-0998.13104","type":"journal-article","created":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T09:59:55Z","timestamp":1571392795000},"page":"228-241","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Comparative genome\/transcriptome analysis probes Boraginales' phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin\/shikonin core pathway"],"prefix":"10.1111","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5672-695X","authenticated-orcid":false,"given":"Cheng\u2010Yi","family":"Tang","sequence":"first","affiliation":[{"name":"School of the Environment Nanjing University Nanjing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song","family":"Li","sequence":"additional","affiliation":[{"name":"School of the Environment Nanjing University Nanjing China"},{"name":"Biomarker Technologies Corporation Beijing 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