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  • Open Access

    ARTICLE

    Comparative Non Participating Transcriptome Analysis Response to Low Phosphorus by CmPht1;2 in Chrysanthemum

    Chen Liu1,2 , Xiaowei Tang1,2, Xiaohui Qu1,2 , Fadi Chen1, Jiafu Jiang1 and Sumei Chen1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1391-1404, 2023, DOI:10.32604/phyton.2023.027231

    Abstract Chrysanthemum morifolium Ramat is one of the four major cut flowers in the world. Pht1 family is focus on the uptake and transport of phosphate in plants. In our previous studies, CmPht1;2 overexpression line (Oe1) had higher phosphate contents both in roots and shoots, and its root development was significantly enhanced than wild type (WT) at low phosphorus conditions in chrysanthemum. Metabolomics analysis showed that several metabolites had a change in pyruvate metabolism and tricarboxylic acid (TCA) cycle pathway. To explore the gene difference expression and the change of metabolic pathway between CmPht1;2-Oe1 and WT, we conducted the transcriptome analysis.… More >

  • Open Access

    ARTICLE

    Comparative Transcriptome Analyses Reveal Genes Related to Spine Development in Cucumber (Cucumis sativus)

    Yue Chen1,2,#, Huan Wang1,#, Taibai Xu1, Peng Zhou1, Junsong Pan2, Weiwei She1,*, Weiwei Zhang1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1059-1070, 2023, DOI:10.32604/phyton.2023.026486

    Abstract Fruit spine is an important quality trait of cucumber. To better understand the molecular basis of cucumber spine development and function, RNA-Seq was performed to identify differentially expressed genes (DEGs) in fruit spines of different development stages, namely, 8 days before anthesis (SpBA8), anthesis (SpA) and 8 days after anthesis (SpAA8). Stage-wise comparisons obtained 2,259 (SpBA8 vs. SpA), 4,551 (SpA vs. SpAA8), and 5,290 (SpBA8 vs. SpAA8) DEGs. All the DEGs were classified into eight expression clusters by trend analysis. Among these DEGs, in addition to the Mict, Tril, CsTTG1, CsMYB6, NS, and Tu genes that have been reported to… More >

  • Open Access

    ARTICLE

    Transcriptome analysis reveals potential genes associated with plant height in rice

    CAN CHEN#, RUI FENG#, ZONGQIONG ZHANG#, XIUZHONG XIA, BAOXUAN NONG, YU ZENG, HUI GUO, XINGHAI YANG*, DANTING LI*

    BIOCELL, Vol.47, No.2, pp. 409-421, 2023, DOI:10.32604/biocell.2023.023543

    Abstract Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs,… More >

  • Open Access

    ARTICLE

    De Novo Transcriptome Analysis in Hevea brasiliensis to Unveil Genes Involved in Low Temperature Stress Response

    Bingsong Yang1,2,#, Xiaomeng Shi2,#, Tingting Guo1,2, Meixia Liang1,2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 559-575, 2023, DOI:10.32604/phyton.2022.024266

    Abstract Low temperature is one of the adversities threatening the growth and development and reduces the yield of rubber trees. However, molecular mechanisms toward rubber trees in response to low temperature are largely unclear. In this study, 7,159 and 7,600 differentially expressed genes (DEGs) were identified in ‘Reyan 73397’ rubber trees. Through GO analysis, the catalytic activity was the representative of the GO term in the only DEGs at the two studied temperatures (room temperature and 4°C, respectively), while KEGG analysis showed that carbon metabolism was the most important grouping under the comparison of these two temperatures. In addition, expression of… More >

  • Open Access

    ARTICLE

    Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

    Liyan Wu1, Jie Cheng1,2, Yaju Gong1, Rui Bao1, Zhibin Li1, Min Gui1,*, Guanghui Du2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 591-609, 2023, DOI:10.32604/phyton.2022.023481

    Abstract In this study, wild eggplant germplasm No. M239, which is highly susceptible to Verticillium wilt, was used as the experimental material. The physiological and biochemical indices (SOD, PAL, MDA and soluble protein) of M239 roots were measured at different times (0, 12, 24, 36, 48, 60 and 72 h) post inoculation with Verticillium dahliae, and the key time points for the M239 response to Verticillium wilt infection were screened. Then, RNA-Seq technology was used to screen the differentially expressed genes (DEGs) in M239 roots at 0, 12 and 48 h post-inoculation (hpi). The transcriptional results of M239 were also compared… More >

  • Open Access

    ARTICLE

    Full-Length Transcriptome Analysis of Cultivated and Wild Tetraploid Peanut

    Danlei Song#, Xiaona Yu#, Yaoyao Li, Xianheng Wang, Xinyuan Cui, Tong Si, Xiaoxia Zou, Yuefu Wang, Minglun Wang, Xiaojun Zhang*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 439-453, 2023, DOI:10.32604/phyton.2022.023165

    Abstract The high-quality genomes and large-scale full-length cDNA sequences of allotetraploid peanuts have been sequenced and released, which has accelerated the functional genomics and molecular breeding research of peanut. In order to understand the difference in the transcriptional levels of wild and cultivated peanuts. In this study, we integrated of second- and third-generation sequencing technologies to sequence full-length transcriptomes in peanut cv. Pingdu9616 and its putative ancestor Arachis monticola. The RNA extracted from six different tissues (i.e., roots, stems, leaves, flowers, needles and pods) were sampled at 20 days after flowering. A total of 31,764 and 33,981 high-quality transcripts were obtained… More >

  • Open Access

    ARTICLE

    The transcriptome analysis of cleft lip/palate-related PTCH1 variants in GMSM-K cells show carcinogenic potential

    MINGZHAO LI1, QIAN ZHANG2, WENBIN HUANG1, SHIYING ZHANG1, NAN JIANG2, XIAOSHUAI HUANG3,*, FENG CHEN2,*

    BIOCELL, Vol.47, No.1, pp. 205-214, 2023, DOI:10.32604/biocell.2022.022572

    Abstract Cancer progression involves the sonic hedgehog (SHH) pathway, in which the receptor PTCH1 actives the downstream pathways. Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome (NBCCs) including neoplastic disease and congenital disorder. To evaluate the relationship between PTCH1 and cancer, we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells (GMSM-K). Then we screened six PTCH1 variants associated with cleft lip/palate (CL/P), one of the congenital disorders in NBCCs, and generated PTCH1 variant and wild-type recombinant PTCH1−/− GMSM-K cell lines. Transcriptome sequencing was conducted in these cell lines. The results revealed that differentially… More >

  • Open Access

    ARTICLE

    Transcriptome Analysis and Physiological Responses of Economic Macroalga Gracilariopsis lemaneiformis under Sulfate Deficiency

    Haojie Jia1,2, Hong Du1,2,*, Muhmmad Aslam1,2, Tangcheng Li1,2, Canqi Zheng1,2, Xihui Xie1,2, Nan Huang1,2, Honghao Liang1,2, Pengbing Pei1,2, Ping Li1,2, Weizhou Chen1,2, Xiaojuan Liu1,2

    Phyton-International Journal of Experimental Botany, Vol.92, No.1, pp. 91-110, 2023, DOI:10.32604/phyton.2022.022663

    Abstract Sulfur is an essential macronutrient for the growth of all photosynthetic organisms and plays important roles in different metabolic pathways. However, sulfur metabolism and its related research on macroalgae with important ecological value is rather limited. In this study, marine ecological valued macroalga Gracilariopsis lemaneiformis was used to study the general physiological responses and transcriptome profiling under the sulfate deficiency. The relative growth rate of algae under sulfate deficiency was statistically significantly lower than that of control after 6 days. However, no significant differences were observed in the pigments content and Fv/Fm value, indicating that the photosynthesis was not obviously… More >

  • Open Access

    ARTICLE

    Comparative Transcriptome Analysis of Salt-Stress-Responsive Genes in Rice Roots

    Rui Song1, Yan Huang2, Xin Ji3, Yunfei Wei3, Qiuyuan Liu3, Shumei Li3, Juan Liu3,*, Pengfei Dong1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.1, pp. 237-250, 2023, DOI:10.32604/phyton.2022.023081

    Abstract Soil salinity greatly impairs plant growth and crop productivity. Rice (Oryza sativa L.) is a salt-sensitive crop. To better understand the molecular mechanisms of salt tolerance in roots, the BGISEQ-500 sequencing platform was employed to elucidate transcriptome changes in rice roots after 0, 3, 24, and 72 h of salt stress. The results showed that root K+ content decreased and Na+ content increased rapidly after the initial stage of salt stress, but that fresh and dry weight in root did not significantly reduce. Compared to the control (no salt stress), 1,292, 453, and 486 differentially expressed genes (DEGs) were upregulated,… More >

  • Open Access

    ARTICLE

    Transcriptome Analysis and Genes Function Verification of Root Development of Paeonia suffruticosa under Sandy Loam Cultivation

    Yinglong Song1,#, Wenqian Shang1,#, Zheng Wang1,*, Songlin He1,2,*, Xinya Meng3, Liyun Shi1, Yuxiao Shen1, Dan He1, Xueyuan Lou1, Yuke Sun1

    Phyton-International Journal of Experimental Botany, Vol.91, No.12, pp. 2791-2812, 2022, DOI:10.32604/phyton.2022.023572

    Abstract Relatively poor in vitro rooting has limited the large-scale commercial production of tree peony. In this study, on the basis of transcriptome sequencing, differentially expressed genes and the associated metabolic pathways were identified in tree peony roots at different stages of root formation under sandy loam cultivation. A total of 31.63 Gb raw data were generated and 120,188 unigenes (mean length of 911.98 bp) were annotated according to six databases (NR, NT, GO, KEGG, COG, and Swiss-Prot). Analyses of the ungerminated root primordium period, induced root primordium period, and root formation period detected 8,232, 6,907, and 10,687 differentially expressed genes related… More >

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