title: Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel.
abstract: BACKGROUND
  Siberian apricot (Prunus sibirica L.) has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of oil accumulation in Siberian apricot seed kernels (SASK) is still unknown at present. To better develop SASK oil as woody biodiesel, it is essential to profile transcriptome and to identify the full repertoire of potential unigenes involved in the formation and accumulation of oil SASK during the different developing stages.
  
  
  RESULTS
  We firstly detected the temporal patterns for oil content and fatty acid (FA) compositions of SASK in 7 different developing stages. The best time for obtaining the high quality and quantity of SASK oil was characterized at 60 days after flowering (DAF), and the representative periods (10, 30, 50, 60, and 70 DAF) were selected for transcriptomic analysis. By Illumina/Solexa sequencings, approximately 65 million short reads (average length = 96 bp) were obtained, and then assembled into 124,070 unigenes by Trinity strategy (mean size = 829.62 bp). A total of 3,000, 2,781, 2,620, and 2,675 differentially expressed unigenes were identified at 30, 50, 60, and 70 DAF (10 DAF as the control) by DESeq method, respectively. The relationship between the unigene transcriptional profiles and the oil dynamic patterns in developing SASK was comparatively analyzed, and the specific unigenes encoding some known enzymes and transcription factors involved in acetyl-coenzyme A (acetyl-CoA) formation and oil accumulation were determined. Additionally, 5 key metabolic genes implicated in SASK oil accumulation were experimentally validated by quantitative real-time PCR (qRT-PCR). Our findings could help to construction of oil accumulated pathway and to elucidate the molecular regulatory mechanism of increased oil production in developing SASK.
  
  
  CONCLUSIONS
  This is the first study of oil temporal patterns, transcriptome sequencings, and differential profiles in developing SASK. All our results will serve as the important foundation to further deeply explore the regulatory mechanism of SASK high-quality oil accumulation, and may also provide some reference for researching the woody biodiesel plants.
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Jun
authors.initials: J
authors.lastname: Niu
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Jiyong
authors.initials: J
authors.lastname: An
authors.affiliation: Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China.
authors.forename: Libing
authors.initials: L
authors.lastname: Wang
authors.affiliation: Jigongshan National Nature Reserve, Xingyang, 464133 China.
authors.forename: Chengliang
authors.initials: C
authors.lastname: Fang
authors.affiliation: Jigongshan National Nature Reserve, Xingyang, 464133 China.
authors.forename: Denglong
authors.initials: D
authors.lastname: Ha
authors.affiliation: Liaocheng Food and Drug Administration, Liaocheng, 252000 Shandong China.
authors.forename: Chengyu
authors.initials: C
authors.lastname: Fu
authors.affiliation: Jigongshan National Nature Reserve, Xingyang, 464133 China.
authors.forename: Lin
authors.initials: L
authors.lastname: Qiu
authors.affiliation: Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Yu
authors.affiliation: Jigongshan National Nature Reserve, Xingyang, 464133 China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Zhao
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Hou
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Xiang
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Sufan
authors.initials: S
authors.lastname: Zhou
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Xinyi
authors.initials: X
authors.lastname: Feng
authors.affiliation: College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 10083 China.
authors.forename: Shanzhi
authors.initials: S
authors.lastname: Lin
keywords: Differential expression; Oil accumulation mechanism; Siberian apricot; Transcriptome sequencing; Woody biodiesel
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