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Liu G, Liu F, Pan L, Wang H, Lu Y, Liu C, Yu S, Hu X. Agronomic, physiological and transcriptional characteristics provide insights into fatty acid biosynthesis in yellowhorn ( Xanthoceras sorbifolium Bunge) during fruit ripening. Front Genet 2024; 15:1325484. [PMID: 38356698 PMCID: PMC10864670 DOI: 10.3389/fgene.2024.1325484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Yellowhorn (Xanthoceras sorbifolium Bunge) is an oil-bearing tree species in northern China. In this study, we used yellowhorn from Heilongjiang to analyze the morphological and physiological changes of fruit development and conducted transcriptome sequencing. The results showed that the fruit experienced relatively slow growth from fertilization to DAF20 (20 days after flowering). From DAF40 to DAF60, the fruit entered an accelerated development stage, with a rapid increase in both transverse and longitudinal diameters, and the kernel contour developed completely at DAF40. From DAF60 to DAF80, the transverse and vertical diameters of the fruit developed slowly, and the overall measures remained stable until maturity. The soluble sugar, starch, and anthocyanin content gradually accumulated until reaching a peak at DAF80 and then rapidly decreased. RNA-seq analysis revealed differentially expressed genes (DEGs) in the seed coat and kernel, implying that seed components have different metabolite accumulation mechanisms. During the stages of seed kernel development, k-means clustering separated the DEGs into eight sub-classes, indicating gene expression shifts during the fruit ripening process. In subclass 8, the fatty acid biosynthesis pathway was enriched, suggesting that this class was responsible for lipid accumulation in the kernel. WGCNA revealed ten tissue-specific modules for the 12 samples among 20 modules. We identified 54 fatty acid biosynthesis pathway genes across the genome, of which 14 was quantified and confirmed by RT-qPCR. Most genes in the plastid synthesis stage showed high expression during the DAF40-DAF60 period, while genes in the endoplasmic reticulum synthesis stage showed diverse expression patterns. EVM0012847 (KCS) and EVM0002968 (HCD) showed similar high expression in the early stages and low expression in the late stages. EVM0022385 (HCD) exhibited decreased expression from DAF40 to DAF60 and then increased from DAF60 to DAF100. EVM0000575 (KCS) was increasingly expressed from DAF40 to DAF60 and then decreased from DAF60 to DAF100. Finally, we identified transcription factors (TFs) (HB-other, bHLH and ARF) that were predicted to bind to fatty acid biosynthesis pathway genes with significant correlations. These results are conducive to promoting the transcriptional regulation of lipid metabolism and the genetic improvement in terms of high lipid content of yellowhorn.
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Affiliation(s)
- Guan Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Fengjiao Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Lin Pan
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Hanhui Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Yanan Lu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Changhua Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Song Yu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Xiaohang Hu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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Wang W, Hu C, Chang Y, Wang L, Bi Q, Lu X, Zheng Z, Zheng X, Wu D, Niu B. Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China. FRONTIERS IN PLANT SCIENCE 2023; 14:1265362. [PMID: 37954985 PMCID: PMC10634255 DOI: 10.3389/fpls.2023.1265362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Introduction As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood. Methods Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China. Results and Discussion We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.
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Affiliation(s)
- Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Congcong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Chang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Lu
- Chifeng Research Institute of Forestry Science, Chifeng, China
- National Forestry and Grassland Shiny-Leaved Yellowhorn Engineering and Technology Research Center, Chifeng, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Yu D, Wang W, Huo J, Zhuang Y, Chen Y, Du X. Study on molecular mechanism of volatiles variation during Bupleurum scorzonerifolium root development based on metabolome and transcriptome analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1159511. [PMID: 37035038 PMCID: PMC10079991 DOI: 10.3389/fpls.2023.1159511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Bupleurum scorzonerifolium Willd. is a medicinal herb. Its root has a high content of volatile oil (BSVO), which shows a variety of biological activities. Currently, BSVO in the injectable form is used for treating fever in humans and livestock. The yield and quality of volatile oils depends on the developmental stages of plants. However, the changes in BSVO yield and quality during root development in Bupleurum scorzonerifolium and the underlying molecular regulatory mechanisms remain unclear. This knowledge gap is limiting the improvement in the quality of BSVO. In the present study, B. scorzonerifolium root was collected at germinative, vegetative, florescence, fruiting and defoliating stages. The yield of BSVO, metabolic profile of volatile components and transcriptome of root samples at various developmental stages were comprehensively determined and compared. BSVO continuously accumulated from the germinative to fruiting stages, and its level slightly decreased from the fruiting to defoliating stages. A total of 82 volatile components were detected from B. scorzonerifolium root, of which 22 volatiles were identified as differentially accumulated metabolites (DAMs) during the root development. Of these volatiles, fatty acids and their derivatives accounted for the largest proportion. The contents of most major volatiles were highest at the fruiting stage. A large number of differentially expressed genes (DEGs) were detected during B. scorzonerifolium root development, of which 65 DEGs encoded various enzymes and transcription factors regulating the biosynthesis of fatty acids and their derivatives. In further analysis, 42 DEGs were identified to be significantly correlated with DAMs, and these DEGs may be the key genes for the biosynthesis of volatiles. To the best of our knowledge, this is the first study to comprehensively report the changes in the composition and content of volatiles and underlying mechanism during B. scorzonerifolium root development. This study provided important reference for future studies to determine the harvest time of B. scorzonerifolium roots and improve the quality of BSVO.
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Affiliation(s)
- Dan Yu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wenxue Wang
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jinhai Huo
- Institute of Chinese Materia Medica, Heilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Yan Zhuang
- Institute of Chinese Materia Medica, Heilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Yiyang Chen
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiaowei Du
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, Harbin, China
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Liu Z, Zhao J, Huo J, Ma H, Chen Z. Influence of planting yellowhorn ( Xanthoceras sorbifolium Bunge) on the bacterial and fungal diversity of fly ash. PeerJ 2022; 10:e14015. [PMID: 36172497 PMCID: PMC9512002 DOI: 10.7717/peerj.14015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/15/2022] [Indexed: 01/19/2023] Open
Abstract
Phytoremediation is a low-cost solution to fly ash pollution and the rhizosphere interactions between plant roots and the fly ash microbiome were important for the phytoremediation. To analyze the dynamic changes of the rhizosphere microbiome during yellowhorn cultivation in fly ash, the bacterial 16S rRNA gene V3-V4 region and the fungal ITS region of the rhizosphere microbiome were sequenced using Illumina MiSeq technology. The changes in fly ash physicochemical properties and the heavy metal content of different yellowhorn tissues were also analyzed. The results showed that both the bacterial and fungal communities were noticeably different after yellowhorn cultivation compared with the control sample. Proteobacteria and Acidobacteria levels increased (p < 0.05) and Firmicutes and Actinobacteria decreased (p < 0.05) in the bacterial community after yellowhorn cultivation. In the fungal community, Ascomycota and Mortierellomycota decreased (p < 0.05), while Chytridiomycota increased (p < 0.05). The levels of four heavy metals (Cr, Cd, Hg, Pb and As) decreased in the fly ash after yellowhorn cultivation. These metals were absorbed by the yellowhorn plants and accumulated in the fibrous root, taproot, stem and leaf tissues of these plants. Accordingly, the abundance of bacteria that could solubilize heavy metals increased (p < 0.05). In summary, the cultivation of yellowhorn affected the composition of the rhizosphere microbial communities in fly ash, which is of great significance for the biological remediation of fly ash.
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Affiliation(s)
- Zehui Liu
- Institute of Carbon Materials Science, School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, China
| | - Jianguo Zhao
- Institute of Carbon Materials Science, School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, China
| | - Jinxian Huo
- Institute of Carbon Materials Science, School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, China
| | - Hongfang Ma
- Institute of Carbon Materials Science, School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, China
| | - Zhiwen Chen
- Institute of Carbon Materials Science, School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, China,Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
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Wang L, Ruan C, Bao A, Li H. Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn. BMC PLANT BIOLOGY 2021; 21:464. [PMID: 34641783 PMCID: PMC8513341 DOI: 10.1186/s12870-021-03239-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium), an endemic woody oil-bearing tree, has become economically important and is widely cultivated in northern China for bioactive oil production. However, the regulatory mechanisms of seed development and lipid biosynthesis affecting oil production in yellowhorn are still elusive. MicroRNAs (miRNAs) play crucial roles in diverse aspects of biological and metabolic processes in seeds, especially in seed development and lipid metabolism. It is still unknown how the miRNAs regulate the seed development and lipid biosynthesis in yellowhorn. RESULTS Here, based on investigations of differences in the seed growth tendency and embryo oil content between high-oil-content and low-oil-content lines, we constructed small RNA libraries from yellowhorn embryos at four seed development stages of the two lines and then profiled small RNA expression using high-throughput sequencing. A total of 249 known miRNAs from 46 families and 88 novel miRNAs were identified. Furthermore, by pairwise comparisons among the four seed development stages in each line, we found that 64 miRNAs (53 known and 11 novel miRNAs) were differentially expressed in the two lines. Across the two lines, 15, 11, 10, and 7 differentially expressed miRNAs were detected at 40, 54, 68, and 81 days after anthesis, respectively. Bioinformatic analysis was used to predict a total of 2654 target genes for 141 differentially expressed miRNAs (120 known and 21 novel miRNAs). Most of these genes were involved in the fatty acid biosynthetic process, regulation of transcription, nucleus, and response to auxin. Using quantitative real-time PCR and an integrated analysis of miRNA and mRNA expression, miRNA-target regulatory modules that may be involved in yellowhorn seed size, weight, and lipid biosynthesis were identified, such as miR172b-ARF2 (auxin response factor 2), miR7760-p3_1-AGL61 (AGAMOUS-LIKE 61), miR319p_1-FAD2-2 (omega-6 fatty acid desaturase 2-2), miR5647-p3_1-DGAT1 (diacylglycerol acyltransferase 1), and miR7760-p5_1-MED15A (Mediator subunit 15a). CONCLUSIONS This study provides new insights into the important regulatory roles of miRNAs in the seed development and lipid biosynthesis in yellowhorn. Our results will be valuable for dissecting the post-transcriptional and transcriptional regulation of seed development and lipid biosynthesis, as well as improving yellowhorn in northern China.
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Affiliation(s)
- Li Wang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266100, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China.
| | - Aomin Bao
- Institute of Economic Forest, Tongliao Academy of Forestry Science and Technology, Tongliao, 028000, China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
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Yuan Y, Liu C, Zhao G, Gong X, Dang K, Yang Q, Feng B. Transcriptome analysis reveals the mechanism associated with dynamic changes in fatty acid and phytosterol content in foxtail millet (Setaria italica) during seed development. Food Res Int 2021; 145:110429. [PMID: 34112429 DOI: 10.1016/j.foodres.2021.110429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/18/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Foxtail millet (Setaria italica) is an excellent source of beneficial natural fatty acids and phytosterols. However, the mechanisms underlying the dynamic changes of fatty acids and phytosterols during seed development are unknown. In this study, a comprehensive dynamic change analysis of the bioactive compounds during seed development was conducted in two cultivars with different crude fat content (high-fat, JG 35 [5.40%]; and low-fat, JG 39 [2.90%]). GC-FID/MS analysis showed that the proportion of unsaturated fatty acids (UFAs) were higher than the saturated fatty acids (SFAs). UFA content first increased, then decreased during seed development, while SFA content showed the opposite trend. Oil contents continuously increased with seed development, especially at the S2 stage. Phytosterol contents initially increased, then decreased with seed development. Transcriptome analysis revealed that 152 genes were associated with fatty acid metabolism and phytosterol biosynthesis, of which 46 and 62 were related to UFA and phytosterol biosynthesis, respectively. Furthermore, the key genes involved in fatty acid synthesis (ACCase and FATA/B), triacylglycerol biosynthesis (LACS, GPAT, and DGAT), and phytosterols synthesis (CAS1, STM1, EGR6, and DWF1) were overexpressed. This led to maximum UFA, oil, and phytosterol accumulation in JG 35 at the S2 stage. This study reveals the mechanism behind the dynamic changes of fatty acid and phytosterol contents in foxtail millet during seed development.
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Affiliation(s)
- Yuhao Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Chunjuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Guan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Xiangwei Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Ke Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China.
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Transcriptome analysis of genes involved in starch biosynthesis in developing Chinese chestnut (Castanea mollissima Blume) seed kernels. Sci Rep 2021; 11:3570. [PMID: 33574357 PMCID: PMC7878784 DOI: 10.1038/s41598-021-82130-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Chinese chestnut (Castanea mollissima Blume) seed kernels (CCSK) with high quality and quantity of starch has emerged as a potential raw material for food industry, but the molecular regulatory mechanism of starch accumulation in developing CCSK is still unclear. In this study, we firstly analyzed the fruit development, starch accumulation, and microscopic observation of dynamic accumulation of starch granules of developing CCSK from 10 days after flowering (DAF) to 100 DAF, of which six representative CCSK samples (50–100 DAF) were selected for transcriptome sequencing analysis. Approximately 40 million valid reads were obtained, with an average length of 124.95 bp, which were searched against a reference genome, returning 38,146 unigenes (mean size = 1164.19 bp). Using the DESeq method, 1968, 1573, 1187, 1274, and 1494 differentially expressed unigenes were identified at 60:50, 70:60, 80:70, 90:80 and 100:90 DAF, respectively. The relationship between the unigene transcriptional profiles and starch dynamic patterns in developing CCSK was comparatively analyzed, and the specific unigenes encoding for metabolic enzymes (SUSY2, PGM, PGI, GPT, NTT, AGP3, AGP2, GBSS1, SS1, SBE1, SBE2.1, SBE2.2, ISA1, ISA2, ISA3, and PHO) were characterized to be involved potentially in the biosynthesis of G-1-P, ADPG, and starch. Finally, the temporal transcript profiles of genes encoding key enzymes (susy2, pgi2, gpt1, agp2, agp3, gbss1, ss1, sbe1, sbe2.1, sbe2.2, isa1, isa2, isa3, and pho) were validated by quantitative real-time PCR (qRT-PCR). Our findings could help to reveal the molecular regulatory mechanism of starch accumulation in developing CCSK and may also provide potential candidate genes for increasing starch content in Chinese chestnut or other starchy crops.
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Wang J, Zhang Y, Yan X, Guo J. Physiological and transcriptomic analyses of yellow horn (Xanthoceras sorbifolia) provide important insights into salt and saline-alkali stress tolerance. PLoS One 2020; 15:e0244365. [PMID: 33351842 PMCID: PMC7755187 DOI: 10.1371/journal.pone.0244365] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022] Open
Abstract
Yellow horn (Xanthoceras sorbifolia) is an oil-rich woody plant cultivated for bio-energy production in China. Soil saline-alkalization is a prominent agricultural-related environmental problem limiting plant growth and productivity. In this study, we performed comparative physiological and transcriptomic analyses to examine the mechanisms of X. sorbifolia seedling responding to salt and alkaline-salt stress. With the exception of chlorophyll content, physiological experiments revealed significant increases in all assessed indices in response to salt and saline-alkali treatments. Notably, compared with salt stress, we observed more pronounced changes in electrolyte leakage (EL) and malondialdehyde (MDA) levels in response to saline-alkali stress, which may contribute to the greater toxicity of saline-alkali soils. In total, 3,087 and 2,715 genes were differentially expressed in response to salt and saline-alkali treatments, respectively, among which carbon metabolism, biosynthesis of amino acids, starch and sucrose metabolism, and reactive oxygen species signaling networks were extensively enriched, and transcription factor families of bHLH, C2H2, bZIP, NAC, and ERF were transcriptionally activated. Moreover, relative to salt stress, saline-alkali stress activated more significant upregulation of genes related to H+ transport, indicating that regulation of intracellular pH may play an important role in coping with saline-alkali stress. These findings provide new insights for investigating the physiological changes and molecular mechanisms underlying the responses of X. sorbifolia to salt and saline-alkali stress.
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Affiliation(s)
- Juan Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Xingrong Yan
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
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Wang J, Guo J, Zhang Y, Yan X. Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress. PLoS One 2020; 15:e0236588. [PMID: 32706804 PMCID: PMC7380624 DOI: 10.1371/journal.pone.0236588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/08/2020] [Indexed: 01/10/2023] Open
Abstract
Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.
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Affiliation(s)
- Juan Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Xingrong Yan
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
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Lang Y, Liu Z, Zheng Z. Retracted Article: Investigation of yellow horn ( Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study. RSC Adv 2020; 10:6512-6519. [PMID: 35496033 PMCID: PMC9049705 DOI: 10.1039/c9ra09535g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/05/2020] [Indexed: 01/23/2023] Open
Abstract
Yellow horn (Xanthoceras sorbifolia Bunge) is a well-known oil-rich seed shrub which can grow well in barren and arid environments in the northern part of China. Yellow horn has received worldwide attention because of its excellent economic and environmental value. However, because of its limited genetic data, little information can be found regarding the molecular defense mechanisms of yellow horn exposed to various abiotic stresses. In view of this, the current study aims to investigate the impact of different abiotic stresses (i.e. NaCl, ABA and low temperature) on the transcriptome of yellow horn using RNA-Seq. Based on the transcriptome sequencing data, approximately 27% to 45% of stress-responsive genes were found highly expressed after stress treatment for 24 h. In addition, these genes were found to be still expressed after stress treatment for 48 h. However, many additional genes were stress-regulated after 48 h treatment compared with the 24 h treatment. GO enrichment analysis revealed that the expression patterns of the stress-responsive, type-specific terms were generally down-regulated. Most shared GO terms were primarily involved in protein folding, unfolding protein binding, protein transport and protein modification. Further, transcription factors (TFs), such as ERFs, bHLH, GRAS and NAC, were found to be enriched only in the low temperature treatment group, particularly the ERF TFs families. These combined results suggested that yellow horn may have developed specific molecular defense systems against diverse abiotic stresses.
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Affiliation(s)
- Yanhe Lang
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
| | - Zhi Liu
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
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11
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Liang Q, Li H, Li S, Yuan F, Sun J, Duan Q, Li Q, Zhang R, Sang YL, Wang N, Hou X, Yang KQ, Liu JN, Yang L. The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge). Gigascience 2019; 8:giz071. [PMID: 31241155 PMCID: PMC6593362 DOI: 10.1093/gigascience/giz071] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/06/2019] [Accepted: 05/22/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium Bunge), a deciduous shrub or small tree native to north China, is of great economic value. Seeds of yellowhorn are rich in oil containing unsaturated long-chain fatty acids that have been used for producing edible oil and nervonic acid capsules. However, the lack of a high-quality genome sequence hampers the understanding of its evolution and gene functions. FINDINGS In this study, a whole genome of yellowhorn was sequenced and assembled by integration of Illumina sequencing, Pacific Biosciences single-molecule real-time sequencing, 10X Genomics linked reads, Bionano optical maps, and Hi-C. The yellowhorn genome assembly was 439.97 Mb, which comprised 15 pseudo-chromosomes covering 95.42% (419.84 Mb) of the assembled genome. The repetitive fractions accounted for 56.39% of the yellowhorn genome. The genome contained 21,059 protein-coding genes. Of them, 18,503 (87.86%) genes were found to be functionally annotated with ≥1 "annotation" term by searching against other databases. Transcriptomic analysis showed that 341, 135, 125, 113, and 100 genes were specifically expressed in hermaphrodite flower, staminate flower, young fruit, leaf, and shoot, respectively. Phylogenetic analysis suggested that yellowhorn and Dimocarpus longan diverged from their most recent common ancestor ∼46 million years ago. CONCLUSIONS The availability and subsequent annotation of the yellowhorn genome, as well as the identification of tissue-specific functional genes, provides a valuable reference for plant comparative genomics, evolutionary studies, and molecular design breeding.
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Affiliation(s)
- Qiang Liang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Huayang Li
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
| | - Shouke Li
- Worth Agricultural Development Co. Ltd.,Taishanxi Road No. 17, Anqiu city, Weifang 262100, China
| | - Fuling Yuan
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Jingfeng Sun
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Qicheng Duan
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Qingyun Li
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
| | - Rui Zhang
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
| | - Ya Lin Sang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Nian Wang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Xiangwen Hou
- KeGene Science & Technology Co. Ltd., Nantianmen Middle Road, Tai'an 271018, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Jian Ning Liu
- KeGene Science & Technology Co. Ltd., Nantianmen Middle Road, Tai'an 271018, China
| | - Long Yang
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
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12
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Xiang Q, He J, Wang X, Sun K, Xu J, Zhang D, Guan W. Two complete plastid genome sequences of Sapindales: Zanthoxylum nitidum and Xanthoceras sorbifolium, and phylogenetic analyses in Sapindales. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1607586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Qiuhong Xiang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xinrui Wang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kuo Sun
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jiuheng Xu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dongxu Zhang
- College of Life Sciences, Shanxi Datong University, Datong, China
| | - Wenbin Guan
- School of Nature Conservation, Beijing Forestry University, Beijing, China
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13
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Wang X, Liang H, Guo D, Guo L, Duan X, Jia Q, Hou X. Integrated analysis of transcriptomic and proteomic data from tree peony ( P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism. HORTICULTURE RESEARCH 2019; 6:111. [PMID: 31645965 PMCID: PMC6804530 DOI: 10.1038/s41438-019-0194-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/10/2019] [Accepted: 08/15/2019] [Indexed: 05/04/2023]
Abstract
Tree peony (Paeonia section Moutan DC.) seeds are an excellent source of beneficial natural compounds that promote health, and they contain high levels of alpha-linolenic acid (ALA). In recent years, tree peony has been emerging as an oil crop. Therefore, combined analysis of the transcriptome and proteome of tree peony (P. ostii) seeds at 25, 32, 39, 53, 67, 81, 88, 95, and 109 days after pollination (DAP) was conducted to better understand the transcriptional and translational regulation of seed development and oil biosynthesis. A total of 38,482 unigenes and 2841 proteins were identified. A total of 26,912 differentially expressed genes (DEGs) and 592 differentially expressed proteins (DEPs) were clustered into three groups corresponding to the rapid growth, seed inclusion enrichment and conversion, and late dehydration and mature stages of seed development. Fifteen lipid metabolism pathways were identified at both the transcriptome and proteome levels. Pathway enrichment analysis revealed that a period of rapid fatty acid biosynthesis occurred at 53-88 DAP. Furthermore, 211 genes and 35 proteins associated with the fatty acid metabolism pathway, 63 genes and 11 proteins associated with the biosynthesis of unsaturated fatty acids (UFAs), and 115 genes and 24 proteins associated with ALA metabolism were identified. Phylogenetic analysis revealed that 16 putative fatty acid desaturase (FAD)-encoding genes clustered into four FAD groups, eight of which exhibited the highest expression at 53 DAP, suggesting that they play an important role in ALA accumulation. RT-qPCR analysis indicated that the temporal expression patterns of oil biosynthesis genes were largely similar to the RNA-seq results. The expression patterns of fatty acid metabolism- and seed development-related proteins determined by MRM were also highly consistent with the results obtained in the proteomic analysis. Correlation analysis indicated significant differences in the number and abundance of DEGs and DEPs but a high level of consistency in expression patterns and metabolic pathways. The results of the present study represent the first combined transcriptomic and proteomic analysis of tree peony seeds and provide insight into tree peony seed development and oil accumulation.
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Affiliation(s)
- Xiaojing Wang
- College of Agriculture / College of Tree Peony, Henan University of Science and Technology, Luoyang, 471023 China
| | - Haiying Liang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634-0318 USA
| | - Dalong Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 China
| | - Lili Guo
- College of Agriculture / College of Tree Peony, Henan University of Science and Technology, Luoyang, 471023 China
| | - Xiangguang Duan
- College of Agriculture / College of Tree Peony, Henan University of Science and Technology, Luoyang, 471023 China
| | - Qishi Jia
- College of Agriculture / College of Tree Peony, Henan University of Science and Technology, Luoyang, 471023 China
| | - Xiaogai Hou
- College of Agriculture / College of Tree Peony, Henan University of Science and Technology, Luoyang, 471023 China
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14
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Wang L, Ruan C, Liu L, Du W, Bao A. Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development. Int J Mol Sci 2018; 19:ijms19103071. [PMID: 30297676 PMCID: PMC6212864 DOI: 10.3390/ijms19103071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 11/16/2022] Open
Abstract
Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.
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Affiliation(s)
- Li Wang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China.
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China.
| | - Lingyue Liu
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China.
| | - Wei Du
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China.
| | - Aomin Bao
- Institute of economic forest, Tongliao Academy of Forestry Science and Technology, Tongliao 028000, China.
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15
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Comparative transcriptome analysis of lipid biosynthesis in seeds and non-seed tissues of sea buckthorn. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0564-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Chen SY, Zhang XZ. Characterization of the complete chloroplast genome of Xanthoceras sorbifolium, an endangered oil tree. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0732-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Lin Z, An J, Wang J, Niu J, Ma C, Wang L, Yuan G, Shi L, Liu L, Zhang J, Zhang Z, Qi J, Lin S. 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. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:134. [PMID: 28559925 PMCID: PMC5445305 DOI: 10.1186/s13068-017-0820-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/15/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation. RESULTS We first analyzed the dynamic patterns of growth tendency, oil content, FA compositions, biodiesel properties, and the contents of ATP and pyridine nucleotide of L. glauca fruits from seven different developing stages. Comprehensive characterization of transcriptome of the developing L. glauca fruit was performed using a combination of two different next-generation sequencing platforms, of which three representative fruit samples (50, 125, and 150 DAF) and one mixed sample from seven developing stages were selected for Illumina and 454 sequencing, respectively. The unigenes separately obtained from long and short reads (201, and 259, respectively, in total) were reconciled using TGICL software, resulting in a total of 60,031 unigenes (mean length = 1061.95 bp) to describe a transcriptome for developing L. glauca fruits. Notably, 198 genes were annotated for photosynthesis, sucrose cleavage, carbon allocation, metabolite transport, acetyl-CoA formation, oil synthesis, and energy metabolism, among which some specific transporters, transcription factors, and enzymes were identified to be implicated in carbon partitioning and energy source for oil synthesis by an integrated analysis of transcriptomic sequencing and qRT-PCR. Importantly, the carbon and energy metabolic model was well established for oil biosynthesis of developing L. glauca fruits, which could help to reveal the molecular regulatory mechanism of the increased oil production in developing fruits. CONCLUSIONS This study presents for the first time the application of an integrated two different sequencing analyses (Illumina and 454) and qRT-PCR detection to define a minimal reference transcriptome for developing L. glauca fruits, and to elucidate the molecular regulatory mechanism of carbon flux control and energy provision for oil synthesis. Our results will provide a valuable resource for future fundamental and applied research on the woody biodiesel plants.
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Affiliation(s)
- Zixin Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Jiyong An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Jun Niu
- College of Horticulture and Landscape Architecture, Key Laboratory of Protection and Development Utilization of Tropical Crop Germplasm Resources, Ministry of Education, Hainan University, Haikou, 570228 China
| | - Chao Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Libing Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Guanshen Yuan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Lingling Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Lili Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Jinsong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Zhixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Ji Qi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
| | - Shanzhi Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, 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
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Liu Q, Sun Y, Chen J, Li P, Li C, Niu G, Jiang L. Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit. BMC Genomics 2016; 17:929. [PMID: 27852215 PMCID: PMC5112726 DOI: 10.1186/s12864-016-3275-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 11/09/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages. RESULTS The transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data. CONCLUSIONS The transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata.
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Affiliation(s)
- Qiang Liu
- Central South University of Forestry and Technology, 498 South Shaoshan Rd., Changsha, Hunan, 410004, China.,Texas A&M AgriLife Research Center at El Paso, 1380 A&M Circle, El Paso, TX, 79927, USA
| | - Youping Sun
- Texas A&M AgriLife Research Center at El Paso, 1380 A&M Circle, El Paso, TX, 79927, USA
| | - Jinzheng Chen
- Central South University of Forestry and Technology, 498 South Shaoshan Rd., Changsha, Hunan, 410004, China.,Hunan Academy of Forestry, 658 South Shaoshan Rd., Changsha, Hunan, 410004, China
| | - Peiwang Li
- Hunan Academy of Forestry, 658 South Shaoshan Rd., Changsha, Hunan, 410004, China
| | - Changzhu Li
- Hunan Academy of Forestry, 658 South Shaoshan Rd., Changsha, Hunan, 410004, China
| | - Genhua Niu
- Texas A&M AgriLife Research Center at El Paso, 1380 A&M Circle, El Paso, TX, 79927, USA
| | - Lijuan Jiang
- Central South University of Forestry and Technology, 498 South Shaoshan Rd., Changsha, Hunan, 410004, China.
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Ahmed S, Zhan C, Yang Y, Wang X, Yang T, Zhao Z, Zhang Q, Li X, Hu X. The Transcript Profile of a Traditional Chinese Medicine, Atractylodes lancea, Revealing Its Sesquiterpenoid Biosynthesis of the Major Active Components. PLoS One 2016; 11:e0151975. [PMID: 26990438 PMCID: PMC4798728 DOI: 10.1371/journal.pone.0151975] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
Atractylodes lancea (Thunb.) DC., named “Cangzhu” in China, which belongs to the Asteraceae family. In some countries of Southeast Asia (China, Thailand, Korea, Japan etc.) its rhizome, commonly called rhizoma atractylodis, is used to treat many diseases as it contains a variety of sesquiterpenoids and other components of medicinal importance. Despite its medicinal value, the information of the sesquiterpenoid biosynthesis is largely unknown. In this study, we investigated the transcriptome analysis of different tissues of non-model plant A. lancea by using short read sequencing technology (Illumina). We found 62,352 high quality unigenes with an average sequence length of 913 bp in the transcripts of A. Lancea. Among these, 43,049 (69.04%), 30,264 (48.53%), 26,233 (42.07%), 17,881 (28.67%) and 29,057(46.60%) unigenes showed significant similarity (E-value<1e-5) to known proteins in Nr, KEGG, SWISS-PROT, GO, and COG databases, respectively. Of the total 62,352 unigenes, 43,049 (Nr Database) open reading frames were predicted. On the basis of different bioinformatics tools we identify all the enzymes that take part in the terpenoid biosynthesis as well as five different known sesquiterpenoids via cytosolic mevalonic acid (MVA) pathway and plastidal methylerythritol phosphate (MEP) pathways. In our study, 6, 864 Simple Sequence Repeats (SSRs) were also found as great potential markers in A. lancea. This transcriptomic resource of A. lancea provides a great contribution in advancement of research for this specific medicinal plant and more specifically for the gene mining of different classes of terpenoids and other chemical compounds that have medicinal as well as economic importance.
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Affiliation(s)
- Shakeel Ahmed
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Chuansong Zhan
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yanyan Yang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xuekui Wang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Tewu Yang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zeying Zhao
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qiyun Zhang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaohua Li
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xuebo Hu
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- * E-mail:
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Chen SF, Li MW, Jing HJ, Zhou RC, Yang GL, Wu W, Fan Q, Liao WB. De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform. PLoS One 2015; 10:e0139373. [PMID: 26427005 PMCID: PMC4591120 DOI: 10.1371/journal.pone.0139373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/11/2015] [Indexed: 11/19/2022] Open
Abstract
Many Firmiana species are locally endemic, providing an interesting system for studying adaptation and speciation. Among these species, F. danxiaensis is a tree species endemic to Mount Danxia in Guangdong, China, which is an area known for presenting the Danxia landform. How F. danxiaensis could have adapted to the stressful environment of rocky cliffs covered with barren soils in the Danxia landform is still unknown. In this study, we performed de novo assembly of the transcriptome of F. danxiaensis, obtaining 47,221 unigenes with an N50 value of 987 bp. Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao. Gene Ontology (GO) annotation showed that hundreds of unigenes participated in responses to various stresses or nutritional starvation, which may help us to understand the adaptation of F. danxiaensis to Danxia landform. Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species. The EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed many genes playing roles in the biosynthesis of secondary metabolites and environmental adaptation, which may also contribute to the survivor and success of Firmiana species in extreme environments. Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.
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Affiliation(s)
- Su-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming-Wan Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hui-Juan Jing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Gui-Li Yang
- National Engineering Resarch Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wu
- South China Botanical Garden, Chinese Academy of Science, Guangzhou 510650, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- * E-mail: (QF); (WL)
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- * E-mail: (QF); (WL)
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Chen J, Tan RK, Guo XJ, Fu ZL, Wang Z, Zhang ZY, Tan XL. Transcriptome Analysis Comparison of Lipid Biosynthesis in the Leaves and Developing Seeds of Brassica napus. PLoS One 2015; 10:e0126250. [PMID: 25965272 PMCID: PMC4429122 DOI: 10.1371/journal.pone.0126250] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/30/2015] [Indexed: 12/17/2022] Open
Abstract
Brassica napus seed is a lipid storage organ containing approximately 40% oil, while its leaves contain many kinds of lipids for many biological roles, but the overall amounts are less than in seeds. Thus, lipid biosynthesis in the developing seeds and the leaves is strictly regulated which results the final difference of lipids. However, there are few reports about the molecular mechanism controlling the difference in lipid biosynthesis between developing seeds and leaves. In this study, we tried to uncover this mechanism by analyzing the transcriptome data for lipid biosynthesis. The transcriptome data were de novo assembled and a total of 47,216 unigenes were obtained, which had an N50 length and median of 1271 and 755 bp, respectively. Among these unigenes, 36,368 (about 77.02%) were annotated and there were 109 up-regulated unigenes and 72 down-regulated unigenes in the developing seeds lipid synthetic pathway after comparing with leaves. In the oleic acid pathway, 23 unigenes were up-regulated and four unigenes were down-regulated. During triacylglycerol (TAG) synthesis, the key unigenes were all up-regulated, such as phosphatidate phosphatase and diacylglycerol O-acyltransferase. During palmitic acid, palmitoleic acid, stearic acid, linoleic acid and linolenic acid synthesis in leaves, the unigenes were nearly all up-regulated, which indicated that the biosynthesis of these particular fatty acids were more important in leaves. In the developing seeds, almost all the unigenes in the ABI3VP1, RKD, CPP, E2F-DP, GRF, JUMONJI, MYB-related, PHD and REM transcript factor families were up-regulated, which helped us to discern the regulation mechanism underlying lipid biosynthesis. The differential up/down-regulation of the genes and TFs involved in lipid biosynthesis in developing seeds and leaves provided direct evidence that allowed us to map the network that regulates lipid biosynthesis, and the identification of new TFs that are up-regulated in developing seeds will help us to further elucidate the lipids biosynthesis pathway in developing seeds and leaves.
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Affiliation(s)
- Jie Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
| | - Ren-Ke Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
| | - Xiao-Juan Guo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
| | - Zheng-Li Fu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
| | - Zheng Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
| | - Zhi-Yan Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, P. R. China
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Niu J, An J, Wang L, Fang C, Ha D, Fu C, Qiu L, Yu H, Zhao H, Hou X, Xiang Z, Zhou S, Zhang Z, Feng X, Lin S. Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:29. [PMID: 25834637 PMCID: PMC4381669 DOI: 10.1186/s13068-015-0213-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/27/2015] [Indexed: 05/11/2023]
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.
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Affiliation(s)
- Jun Niu
- />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
| | - Jiyong An
- />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
| | - Libing Wang
- />Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Chengliang Fang
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Denglong Ha
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Chengyu Fu
- />Liaocheng Food and Drug Administration, Liaocheng, 252000 Shandong China
| | - Lin Qiu
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Haiyan Yu
- />Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 10091 China
| | - Haiyan Zhao
- />Jigongshan National Nature Reserve, Xingyang, 464133 China
| | - Xinyu Hou
- />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
| | - Zheng Xiang
- />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
| | - Sufan Zhou
- />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
| | - Zhixiang Zhang
- />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
| | - Xinyi Feng
- />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
| | - Shanzhi Lin
- />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
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Bi Q, Guo B, Zhang D, Guan W. Identification and characterization of conserved and novel microRNAs in Xanthoceras sorbifolium via deep sequencing. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0248-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Efficiently developing a large set of polymorphic EST-SSR markers for Xanthoceras sorbifolium by mining raw reads from high-throughput sequencing. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0386-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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