Zhaoli Chen, Ying Liu^*, Bingshan Zeng, Qingbin Jiang, Shengkun Wang, Xiangyang Li

Phyton-International Journal of Experimental Botany, Vol.92, No.10, pp. 2891-2906, 2023, DOI:10.32604/phyton.2023.030664

Abstract Michelia macclurei Dandy is a significant tree species that has extensive cultivation for forestry and horticulture purposes in southern China, owing to its economic and practical importance. Light quality influences plantlet growth and development during tissue culture. However, the growth characteristic and molecular regulation of M. macclurei under different light quality conditions are not well understood yet. In this study, we investigated the morphological, chlorophyll content, and transcriptomic responses of M. macclurei plantlets under different light-emitting diode (LED) qualities, including white, blue, and red light. The results showed that blue light significantly increased plant height (21.29%) and leaf number (18.65%),… More >

Jing Yang, Tianxiunan Pu, Ke Wan, Linqi Wang, Yuanshuai Shi, Xu Luo, Jie Tan, Dongmei Wang, Yang Liu^*

Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2555-2576, 2023, DOI:10.32604/phyton.2023.030301

Abstract Drought has severely affected the yield and quality of commercial crops. The BRI1 family plays an important role in plant response to drought stress, and BRL3 gene plays an important role in the study of drought in Arabidopsis thaliana. In this study, NtBRL3 was constructed as a vector and genetically transformed to obtain ‘N. Tobacco K326’ overexpression of NtBRL3. The enzyme activities of transgenic tobacco and wild-type tobacco were measured and transcriptome and metabolome analyses were performed. The results showed that the antioxidant enzymes of transgenic tobacco were more active under drought conditions, and 85 significantly differentially metabolites and 106… More >

Genhai Hu^1,*, Maoni Chao¹, Xiuren Zhou², Yuanzhi Fu²

Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2535-2554, 2023, DOI:10.32604/phyton.2023.030163

Abstract Gossypium hirsutum L. is an important cash crop native to the subtropics and is widely cultivated around the world. Low temperature is an important stress that seriously affects seed germination and emergence during planting. In this study, transcriptomic profiles of low-temperature- and normal-temperature-germinated seeds of Xinluzao 25, a variety with low-temperature tolerance and high germination rates, were analyzed and compared. The following results were obtained. (1) A total of 81.06 Gb of clean data were obtained after transcriptome sequencing and assembly, and 76,931 non-redundant Unigene sequences were obtained after data consolidation and concatenation; of these, 69,883 Unigene sequences were annotated.… More >

Jie Zhang¹, Yingwei Zhao², Hongying Li³, Jianwei Ni^4,*, Dongmei Wang^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2591-2610, 2023, DOI:10.32604/phyton.2023.028338

Abstract Paper mulberry is a high-quality woody feed resource plant with high crude protein content. It is widely distributed in China and has excellent characteristics of salt and alkali tolerance. Paper mulberry has ecological and economic importance. Salt stress has become a critical factor with the increasing degree of soil salinity that restricts plant growth. In the saline-alkali environments, transcriptome expression is altered leading to phenotypic defects in most plants. However, the regulatory mechanism related to paper mulberry’s salt-stress (SS) response is not clearly understood. In the present study de novo transcriptomic assembly was performed, and gene expression levels were measured… More >

WUYAO LIU, CHANGBAO QU, XIAOLU WANG^*

Oncology Research, Vol.31, No.4, pp. 543-567, 2023, DOI:10.32604/or.2023.029563

Abstract The high immune infiltration and heterogeneity of the microenvironment in clear cell renal cell carcinoma (ccRCC) result in the variability of prognosis and clinical response. While PANoptosis has strong immunogenicity and is worthy of further study. In this study, data from The Cancer Genome Atlas database was used to obtain immune-related PANoptosis lncRNAs with prognostic value. Subsequently, the role of these lncRNAs in cancer immunity, progression and the therapeutic response was analyzed, and a new prediction model was constructed. Additionally, we further explored the biological value of PANoptosis-related lncRNAs using single-cell data from the Gene Expression Omnibus database. PANoptosis-associated lncRNAs… More >

JIAHENG XIE^1,#, MENGMENG OU^1,#, PAN YU^1,#, DAN WU^2,#, QIKAI TANG³, YUAN CAO⁴, JING HANG⁵, LU YIN¹, TINGHONG XIANG¹, MING WANG^1,*, JINGPING SHI^1,*

Oncology Research, Vol.31, No.3, pp. 389-403, 2023, DOI:10.32604/or.2023.029274

Abstract Purpose: To screen potential tumor antigens for melanoma vaccine development and identify different immune subtypes. Methods: Transcriptional data (HTSEQ-FPKM) and clinical information of a 472 Melanoma cohort GDC TCGA Melanoma (SKCM) were downloaded from the UCSC XENA website (). Subsequently, transcriptome data and clinical information of 210 melanoma cohort GSE65904 were downloaded from Gene Expression Omnibus (GEO), a large global public database. All the transcriptome expression data matrices were log2 transformed for subsequent analysis. GEPIA, TIMER, and IMMPORT databases are also used for analysis. Cell function experiments were performed to validate the role of the IDO1 gene in melanoma cell… More >

Shunde Su^1,2,#, Huan Chang^3,#, Xiangyang Kang^1,*, Renhua Zheng^2,*

Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1713-1723, 2023, DOI:10.32604/phyton.2023.027586

Abstract As the reproductive organ of the endangered species Fokienia hodginsii, the size of the cones is a constraint on the reproductive renewal of the population. In this study, the molecular basis of the influence of cone size on F. hodginsii was elucidated by comparing the phenotype, biochemistry, and transcriptome of two cultivars of F. hodginsii (‘FJ431’ and ‘FJ415’). The two cultivars differed significantly in cone size, with FJ431 having a significantly larger cone size and weight than FJ415, 1.32 and 1.90 times that of FJ415, respectively. RNA-Seq analysis of both cultivars retrieved 75,940 genes whose approximate functions were classified as… More >

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 >