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After processing from imperfect fold\u2010back structures, mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s are incorporated into <jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>\u2010induced silencing complexes (<jats:styled-content style=\"fixed-case\">RISC<\/jats:styled-content>s) before targeting transcripts with varying degrees of complementarity. Some mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s are evolutionarily deep\u2010rooted, and sequence complementarity with their targets is maintained through purifying selection. Both <jats:italic>Arabidopsis<\/jats:italic> and <jats:italic>Capsella<\/jats:italic> belong to the tribe Camelineae in the Brassicaceae, with <jats:italic>Capsella rubella<\/jats:italic> serving as an outgroup to the genus <jats:italic>Arabidopsis<\/jats:italic>. The genome sequence of <jats:italic>C.\u00a0rubella<\/jats:italic> has recently been released, which allows characterization of its mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> complement in comparison with <jats:italic>Arabidopsis thaliana<\/jats:italic> and <jats:italic>Arabidopsis lyrata<\/jats:italic>. Through next\u2010generation sequencing, we identify high\u2010confidence mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> candidates specific to the <jats:italic>C.\u00a0rubella<\/jats:italic> lineage. Only a few lineage\u2010specific mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s have been studied for evolutionary constraints, and there have been no systematic studies of mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s and their targets within <jats:italic>A.\u00a0thaliana<\/jats:italic>, and between <jats:italic>A.\u00a0thaliana<\/jats:italic>,<jats:italic> A.\u00a0lyrata<\/jats:italic> and <jats:italic>C.\u00a0rubella<\/jats:italic>. We document a surprising amount of small\u2010scale variation in mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>\u2013target pairs, where many mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s are predicted to have species\u2010specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>\u2013target pairs can be observed even on a relatively short evolutionary time\u2010scale, with non\u2010random occurrences of differences in mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s and their complements in the mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> precursors, the mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>* sequences.<\/jats:p>","DOI":"10.1111\/tpj.12754","type":"journal-article","created":{"date-parts":[[2014,12,31]],"date-time":"2014-12-31T12:47:20Z","timestamp":1420030040000},"page":"597-610","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae"],"prefix":"10.1111","volume":"81","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2364-8187","authenticated-orcid":false,"given":"Lisa M.","family":"Smith","sequence":"first","affiliation":[{"name":"Department of Animal and Plant Sciences University of Sheffield Western Bank Sheffield S10 2TN UK"},{"name":"Department of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 35 72076 T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hern\u00e1n A.","family":"Burbano","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 35 72076 T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 35 72076 T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joffrey","family":"Fitz","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 35 72076 T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 35 72076 T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonca","family":"Ural\u2010Blimke","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology Max Planck Institute for Developmental Biology Spemannstrasse 35 72076 T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Detlef","family":"Weigel","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology Max Planck Institute 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