Transcriptome Analysis of the Oil-Rich Tea Plant, Camellia oleifera, Reveals Candidate Genes Related to Lipid Metabolism

Xia, Enhua; Jiang, Jianjun; Huang, Hui; Zhang, Liping; Zhang, Haibin; Gao, Li‐Zhi

doi:10.1371/journal.pone.0104150

Cited by 69 publications

(74 citation statements)

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“…This tendency implies that the higher the degree of drought, the more obvious the effect on gene expression in plants. Similar results were also reported on other plants, such as Camellia oleifera (Dong et al 2017;Xia et al 2014) and Cicer arietinum L. (Mahdavi et al 2018). According to the GO analysis, most of the DEGs were involved in ''integral component of membrane'' ''oxidation-reduction process'', ''metal ion binding'' and ''DNA binding'' from the seven pairs mentioned earlier.…”

Section: Discussionsupporting

confidence: 85%

Transcriptome sequencing of okra (Abelmoschus esculentus L. Moench) uncovers differently expressed genes responding to drought stress

Shi

Wang

Bai

et al. 2019

J. Plant Biochem. Biotechnol.

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Drought affects the growth and development of plants and can cause crop failure. As an important edible and medicinal plant, okra (Abelmoschus esculentus L. Moench) is very popular in China and shows strong resistance to drought. In this study, gene expression profiles of okra leaves were investigated under water-limited conditions at the seedling stage. A total of 94,769 unigenes with an average length of 1921 bp and an N90 of 981 bp were obtained through next-generation sequencing. Furthermore, 38.18% of total unigenes were annotated in NT, NR, COG, KEGG, and SwissProt databases. A total of 2276, 5626, 11,719, 14,892, 855, 4593, and 5170 differentially expressed genes (DEGs) in seven pairwise comparisons (A5 vs. A0; A7 vs. A0; A15 vs. A0; A20 vs. A0; A7 vs. A5; A15 vs. A7, and A20 vs. A15) were identified. Among these, 22,751 DEGs were up-regulated, and the number was slightly more than that of the down-regulated DEGs. The number of up-regulated DEGs among different samples increased with increasing drought stress. We identified that the majority of DEGs were related to ''integral component of membrane'', ''oxidation-reduction process'', and ''metal ion binding'' categories. Pathway analysis revealed that most DEGs were enriched in ''Biosynthesis of secondary metabolites'', ''Carbon metabolism'', and ''Glycolysis/Gluconeogenesis pathways''. Additionally, a total of 17,456 simple sequence repeat motifs, 47,9831 single nucleotide polymorphisms, and 3746 transcription factors were identified in this study. RNA-Seq data were also verified by RT-qPCR. Our findings engender a further understanding of molecular mechanisms in response to drought stress. Keywords Okra (Abelmoschus esculentus L.) Á Transcriptome sequencing Á Drought stress Á Differential expression Abbreviations RNA-Seq Ribonucleic acid-sequencing NGS Next generation sequencing cDNA Complementary deoxyribonucleic acid PCR Polymerase chain reaction EB Ethambutol GO Gene ontology KEGG Kyoto encyclopedia of genes and genomes CDSs Coding sequences SSR Simple sequence repeat Jiyue Wang and Yu Bai: co-first author.

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Section: Discussionsupporting

confidence: 85%

Transcriptome sequencing of okra (Abelmoschus esculentus L. Moench) uncovers differently expressed genes responding to drought stress

Shi

Wang

Bai

et al. 2019

J. Plant Biochem. Biotechnol.

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“…Beside the transcriptomes of tea plant collected from different developmental stages or under different stresses or response to different hormones, we also literately gathered a total of nine transcriptomes from its close relatives, including C. azalea (Fan et al ., ), C. japonica (Li et al ., ), C. meiocarpa (Feng et al ., ), C. nitidissima (Zhou et al ., ), C. oleifera (Xia et al ., ), C. reticulate (Yao et al ., ), C. sasanqua (Huang et al ., ), C. chekiangoleosa (Wang et al ., ) and C. taliensis (Zhang et al ., ). The detail information of each transcriptome that comprises published journal, authors, study background, main conclusion, data accession numbers and investigated tissues was collected.…”

Section: Data Contentmentioning

confidence: 99%

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Xia

Tong

et al. 2019

Plant Biotechnology Journal

224

181

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Summary Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large‐scale omics‐data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web‐accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well‐organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well‐resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.

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“…Since the generated reads can assemble without a reference genome, it is also an ideal tool for transcriptome sequencing for those species without a sequenced genome [17]. Recently, RNA-Seq has been used to analyze the transcriptomic profiles of oil accumulation in oil plants such as Jatropha ( Jatropha curcas ) [18], oil tea ( Camellia oleifera ) [19], oil palm ( Elaeis guineensis ) [20], peanut ( Arachis hypogaea ) [21], rapeseed ( Brassica napus ) [22], and sesame ( Sesamum indicum ) [23]. However, the functional genes involved in the oil biosynthesis and metabolism of S. paniculata are not yet to be investigated.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

Liu

Sun²,

Chen

et al. 2016

BMC Genomics

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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.ResultsThe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3275-0) contains supplementary material, which is available to authorized users.

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Transcriptome Analysis of the Oil-Rich Tea Plant, Camellia oleifera, Reveals Candidate Genes Related to Lipid Metabolism

Cited by 69 publications

References 50 publications

Transcriptome sequencing of okra (Abelmoschus esculentus L. Moench) uncovers differently expressed genes responding to drought stress

Transcriptome sequencing of okra (Abelmoschus esculentus L. Moench) uncovers differently expressed genes responding to drought stress

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

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