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

BackgroundSiberian 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.ResultsWe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0213-3) contains supplementary material, which is available to authorized users.

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel

“…1; Table 1) revealed the oils from L. glauca fruits with a high quality and quantity as a novel potential source of woody biodiesel feedstock in China, which corresponded to the previous studies on traditional woody oil plants such as P. chinensis , P. sibirica and J. curcas [2–4, 32]. However, the complex regulatory mechanism of carbon flux and energy source required for oil synthesis in developing L. glauca fruits is poorly understood to date.…”

“…Of all the obtained unigenes, 34,916 (58.16%) homologous unigenes were annotated in at least one database, but those unmatched unigenes (25,115, 41.84%) might be present as the putative specific novel genes for L. glauca or probably resulting from the shorter sequences with a lack of characterized protein domain to get BLAST hits [32, 39]. …”

Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process

“…In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data (Additional file 11: Table S1), smaller than that in the previously reported woody plants: such as longan ( Dimocarpus longan L.), lilac ( Syringa oblata L.), and Siberian apricot ( Prunus sibirica L.) [25–27]. It is worth to mention that a total of 89,633 unigenes were obtained from the clean reads, which is similar to longan (68,905 unigenes), Siberian apricot (124,070 unigenes), and lilac (104,691 unigenes); additionally, the average length of unigenes in hickory (659 bp) was also on the same level to longan (448 bp), Siberian apricot (830 bp), and lilac (853 bp) [25–27].…”

“…It is worth to mention that a total of 89,633 unigenes were obtained from the clean reads, which is similar to longan (68,905 unigenes), Siberian apricot (124,070 unigenes), and lilac (104,691 unigenes); additionally, the average length of unigenes in hickory (659 bp) was also on the same level to longan (448 bp), Siberian apricot (830 bp), and lilac (853 bp) [25–27]. These results demonstrated that our sequencing data could be used for gene discovery in the non-model woody tree, hickory.…”

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

“…The potential of NGS in apricot science was reviewed by Martínez-Gómez et al (2011). NGS technologies have been applied in apricot species to facilitate the transcriptome analysis of several biological and agronomical aspects: seasonal bud dormancy (Zhong et al, 2013) and self-and crosspollinated pistils (Habu et al, 2014) in Japanese apricot, global gene profiling and the search for potential SSR markers (Dong et al, 2014), oil dynamic accumulation in developing seed kernels for the development of woody biodiesel (Niu et al, 2015) in Siberian apricot (Prunus sibirica L.), Plum Pox Virus (PPV) (Sharka) susceptibility/ resistance , single nucleotide polymorphism (SNP) discovery (Salazar et al, 2015), the study of the development of embryos (Bai et al, 2016), and SNP discovery and genetic characterization via genotyping by sequencing in common apricot (Gürcan et al, 2016).…”