Transcriptome profile analysis reveals the regulation mechanism of floral sex differentiation in Jatropha curcas L

Hui, Wenkai; Yang, Yuanmu; Wu, Guojiang; Peng, Chang-Cao; Chen, Xiaoyang; Zayed, Mohamed Zaky

doi:10.1038/s41598-017-16545-5

Cited by 33 publications

(31 citation statements)

References 62 publications

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“…In a previous study, the lower fruit yield was limited by poor female flowers in J. curcas, and the female floral differentiation could be initiated by inhibiting the expression of TS2, a gene for carpel abortion in J. curcas [26]. Additionally, our previous study also found that the DEGs were mainly down-regulated in the female floral differentiation process [27]. Thus, we suggested that some genes might inhibit the female floral differentiation, which resulted in the lower fruit yield in J. curcas.…”

Section: Differential Expressed Gene Analysismentioning

confidence: 85%

Differential gene expression analyses related to fruit yield of Jatropha curcas L. using RNA-seq

Hui

Yang

et al. 2018

Biotechnology & Biotechnological Equipment

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Jatropha curcas L. seeds possess high oil content. However, the low fruit yield is a bottleneck for its utilisation in biodiesel production. To date, the genes related to fruit yield of J. curcas are still poorly studied. Therefore, this study was conducted to compare the transcriptome profiles of two J. curcas clones with high and low fruit yield. The results showed that 52 381 unigenes were obtained and annotated to 55 orthologous terms. More than 9 653 single nucleotide polymorphisms (SNPs)/Indels and 15 971 SSR loci were identified. In addition, 76 differential expression genes (DEGs) were obtained and mainly down-regulated in a high fruit yield sample. Moreover, the DEGs were significantly enriched in phytohormone signalling pathways, including gibberellin, brassinolide and jasmonic acid. Furthermore, we suggested that some genes might inhibit the initiation of female floral differentiation to decrease the fruit yield in J. curcas. These data will create a reference transcriptome for the genomics database of J. curcas for future studies. We expect that the dataset will serve as a foundation to study the genes function, which help in engineering high-yielding varieties in J. curcas.

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Section: Differential Expressed Gene Analysismentioning

confidence: 85%

Differential gene expression analyses related to fruit yield of Jatropha curcas L. using RNA-seq

Hui

Yang

et al. 2018

Biotechnology & Biotechnological Equipment

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“…Despite the expression of all JcRbohs, the transcript of JcRbohH was only detected in late stages of ovule and stamen development as well as a mixed sample of root, mature leaf, flower, developing seed, and embryo (Natarajan & Parani, 2011;Hui et al, 2017), and the transcript level was shown to be extremely low. Manuscript to be reviewed PID2 for JcRbohB, JcRbohC, and JcRbohD, respectively.…”

Section: Expression Profiles Of Jcrboh Genesmentioning

confidence: 97%

Peer Review #1 of "Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean (v0.1)"

Rosa¹

2019

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Respiratory burst oxidase homologs (RBOHs), which catalyze the production of superoxide from oxygen and NADPH, play key roles in plant growth and development, hormone signaling, and stress responses. Compared with extensive studies in model plants arabidopsis and rice, little is known about RBOHs in other species. This study presents a genome-wide analysis of Rboh family genes in jatropha (Jatropha curcas) as well as the comparison with castor bean (Ricinus communis), another economically important nonfood oilseed crop of the Euphorbiaceae family. The family number of seven members identified from the jatropha genome is equal to that present in castor bean, and further phylogenetic analysis assigned these genes into seven groups named RBOHD,-C,-B,-E,-F,-N, and-H. In contrast to a high number of paralogs present in arabidopsis and rice that experienced several rounds of recent whole-genome duplications, no duplicate was identified in both jatropha and castor bean. Conserved synteny and one-to-one orthologous relationship were observed between jatropha and castor bean Rboh genes. Although exon-intron structures are usually highly conserved between orthologs, loss of certain introns was observed for JcRbohB, JcRbohD, and RcRbohN, supporting their divergence. Global gene expression profiling revealed diverse patterns of JcRbohs over various tissues. Moreover, expression patterns of JcRbohs during flower development as well as various stresses were also investigated. These findings will not only improve our knowledge on species-specific evolution of the Rboh gene family, but also provide valuable information for further functional analysis of Rboh genes in jatropha.

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“…ZaUBQ was selected as an internal control according to a previous study [2]. The 2 -ΔΔCt method was used to calculate the relative expression levels of the genes in different samples [63]. Fr1 (Fruit 1) was used as a control sample to estimate the relative expression of the DEGs associated with terpenoid compounds and fatty acid metabolism during the fruit development and maturation process in this study.…”

Section: Quantitative Real-time Pcr Analysismentioning

confidence: 99%

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

et al. 2020

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De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism Abstract Background: Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.Results: Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions: The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.

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Transcriptome profile analysis reveals the regulation mechanism of floral sex differentiation in Jatropha curcas L

Cited by 33 publications

References 62 publications

Differential gene expression analyses related to fruit yield of Jatropha curcas L. using RNA-seq

Differential gene expression analyses related to fruit yield of Jatropha curcas L. using RNA-seq

Peer Review #1 of "Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean (v0.1)"

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

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