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We report ~339\u00a0Mbp draft whole genome sequence of <jats:italic>J.\u00a0curcas<\/jats:italic> var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (<jats:styled-content style=\"fixed-case\">TAG<\/jats:styled-content>), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of <jats:styled-content style=\"fixed-case\">TAG<\/jats:styled-content>. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up\u2010regulation of a dozen family of <jats:styled-content style=\"fixed-case\">TF<\/jats:styled-content>s in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine <jats:italic>Jatropha<\/jats:italic> species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.<\/jats:p>","DOI":"10.1111\/pbi.12995","type":"journal-article","created":{"date-parts":[[2018,7,30]],"date-time":"2018-07-30T16:23:59Z","timestamp":1532967839000},"page":"517-530","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":71,"title":["Genome sequence of <i>Jatropha curcas<\/i> L., a non\u2010edible biodiesel plant, provides a resource to improve seed\u2010related traits"],"prefix":"10.1111","volume":"17","author":[{"given":"Jungmin","family":"Ha","sequence":"first","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"},{"name":"Plant Genomics and Breeding Institute Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sangrea","family":"Shim","sequence":"additional","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taeyoung","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang J.","family":"Kang","sequence":"additional","affiliation":[{"name":"Division of Applied Life Science (BK21 plus program) Department Gyeongsang National University PMBBRC Jinju\u2010si Korea"},{"name":"Division of Life Science Department Gyeongsang National University Jinju\u2010si Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Won J.","family":"Hwang","sequence":"additional","affiliation":[{"name":"CJ Food R&amp;D Suwon Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haneul","family":"Jeong","sequence":"additional","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kularb","family":"Laosatit","sequence":"additional","affiliation":[{"name":"Department of Agronomy Faculty of Agriculture at Kamphaeng Saen Kasetsart University Nakhon Pathom Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayern","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sue K.","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Chemistry College of Natural Science Dankook University Cheonan South Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dani","family":"Satyawan","sequence":"additional","affiliation":[{"name":"Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD\u2010IAARD) Bogor Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Puji","family":"Lestari","sequence":"additional","affiliation":[{"name":"Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD\u2010IAARD) Bogor Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min Y.","family":"Yoon","sequence":"additional","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moon Y.","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Plant Science and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea"},{"name":"Plant Genomics and Breeding Institute Seoul National University Seoul Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annapurna","family":"Chitikineni","sequence":"additional","affiliation":[{"name":"Center of Excellence in Genomics &amp; 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