Yanyan Pu^1,#, Liwen Wang^2,#, Leilei Li³, Yujun Si⁴, Shubin Xie², Yunzhe Cong¹, Dong Wang¹, Yongchao Gong¹, Rumei Tian¹, Xue Chen³, Xiaoyan Zhang¹, Min Liu¹, Hanfeng Ding^1,3,*, Nana Li^1,3,*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1793-1812, 2023, DOI:10.32604/phyton.2023.026822

Abstract During the life cycle of a plant, seed germination is crucial. Upon ingestion of water, the dry seeds resumed energy metabolism and cellular repair. To dissect the complex mechanisms at the very beginning of seed germination, two approaches including transcriptome and small RNA sequencing were conducted during the water imbibition process of mung bean seeds compared with dry seed. The transcriptome sequencing analysis identified 10,108 differentially expressed genes (DEGs) between dry and imbibed mung bean seeds. KEGG enrichment analyses demonstrated numerous DEGs involved in hormone signaling pathways, carbohydrate, and energy metabolism. Out of the total DEGs, 129 genes were investigated… More >

Chen Liu^1,2 , Xiaowei Tang^1,2, Xiaohui Qu^1,2 , Fadi Chen¹, Jiafu Jiang¹ and Sumei Chen^1,*

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 >

Yue Chen^1,2,#, Huan Wang^1,#, Taibai Xu¹, Peng Zhou¹, Junsong Pan², Weiwei She^1,*, Weiwei Zhang^1,*

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 >

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 >

Bingsong Yang^1,2,#, Xiaomeng Shi^2,#, Tingting Guo^1,2, Meixia Liang^1,2,*

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 >

Liyan Wu¹, Jie Cheng^1,2, Yaju Gong¹, Rui Bao¹, Zhibin Li¹, Min Gui^1,*, Guanghui Du^2,*

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 >

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 >

MINGZHAO LI¹, QIAN ZHANG², WENBIN HUANG¹, SHIYING ZHANG¹, NAN JIANG², XIAOSHUAI HUANG^3,*, FENG CHEN^2,*

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 >

Haojie Jia^1,2, Hong Du^1,2,*, Muhmmad Aslam^1,2, Tangcheng Li^1,2, Canqi Zheng^1,2, Xihui Xie^1,2, Nan Huang^1,2, Honghao Liang^1,2, Pengbing Pei^1,2, Ping Li^1,2, Weizhou Chen^1,2, Xiaojuan Liu^1,2

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 >

Rui Song¹, Yan Huang², Xin Ji³, Yunfei Wei³, Qiuyuan Liu³, Shumei Li³, Juan Liu^3,*, Pengfei Dong^1,*

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 >