Qunlu Liu^1,#, Fiza Liaquat^1,2,#, Qiqi Tang¹, Jun Yang^3,4, Shuai Qiu⁵, Amber Malik², Kang Ye^3,4, Kai Gao⁵, Jun Qin^3,4,*

Phyton-International Journal of Experimental Botany, Vol.94, No.11, pp. 3539-3562, 2025, DOI:10.32604/phyton.2025.071989 - 01 December 2025

Abstract Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value. It is known for its different flower shapes (lacecap and mophead) and the way its flowers change color depending on the pH of the soil. Even though it is important for gardening, we still don’t know much about the molecular processes that lead to flower growth. The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H. macrophylla flowers. Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors… More >

Mingxin Zhong^1,#, Yuanyuan Zhang^1,#, Xinlei Guo¹, Bainian Zhang², Chengjia Tan¹, Zhuo Xu¹, Xin Hu¹, Daren Feng³, Zhenpeng Xi⁴, Qian Wang^1,*, Hui Tian^1,*

Phyton-International Journal of Experimental Botany, Vol.94, No.10, pp. 3061-3084, 2025, DOI:10.32604/phyton.2025.070560 - 29 October 2025

Abstract Magnolia officinalis is a perennial deciduous tree that has medicinal properties. The AP2/ERF gene family has a number of roles in long-term growth and metabolism. The expression of this function varies with the growth period. In this work, based on the transcriptome data of Magnolia officinalis, the complete coding gene of Magnolia officinalis was obtained, and the corresponding protein sequence was retrieved from NCBI and compared with the model plant Arabidopsis thaliana. After screening, 75 protein sequences from the AP2/ERF gene family were identified and called MoAP2/ERF1–MoAP2/ERF75, followed by bioinformatics analysis. 75 AP2/ERF gene families were found and classified into four… More >

Zhong Ren^1,2,3,#, Shuiming Zhang^1,#, Yuzhi Fei¹, Zhu Chen³, Yue Zhao³, Xin Meng³, Hongfei Zhao^2,*, Jie Ren^3,*

Phyton-International Journal of Experimental Botany, Vol.94, No.9, pp. 2927-2947, 2025, DOI:10.32604/phyton.2025.067310 - 30 September 2025

Abstract Acer paxii belongs to the evergreen species of Acer, but it exhibits a unique feature of reddish leaves in fall in subtropical regions. Although the association of AP2/ERF transcription factors with color change has been well-documented in prior research, molecular investigations focusing on AP2/ERF remain notably lacking in Acer paxii. This research focuses on performing an extensive genome-wide investigation to identify and characterize the AP2/ERF gene family in Acer paxii. As a result, 123 ApAP2/ERFs were obtained. Phylogenetic analyses categorized the ApAP2/ERF family members into 15 subfamilies. The evolutionary traits of the ApAP2/ERFs were investigated by analyzing their… More >

Yuxin Zhao, Zhanxiang Tan, Yuying Li, Kaiyue Zhang, Lili Guo^*, Xiaogai Hou^*

Phyton-International Journal of Experimental Botany, Vol.94, No.4, pp. 1159-1176, 2025, DOI:10.32604/phyton.2025.063737 - 30 April 2025

Abstract Receptor-like cytoplasmic kinases (RLCKs) play a crucial role in the physiological processes of plant growth and development and stress response. To elucidate the characteristics and functions of the PBL gene family in tree peonies, the whole genome identification of PBL family members in tree peonies was conducted using a bioinformatics approach based on the published Arabidopsis thaliana PBL protein sequence. A total of 51 PoPBL members were identified, which were distributed unevenly on five chromosomes in the tree peony. PoPBL proteins were localized in the nucleus, cytoplasm, chloroplasts, and mitochondria, with most members of the same clade… More >

Mengjie Xu, Anbin Wang, Tonghong Zuo, Hecui Zhang, Zhihao Hu, Liquan Zhu^*

Phyton-International Journal of Experimental Botany, Vol.94, No.1, pp. 157-179, 2025, DOI:10.32604/phyton.2025.060566 - 24 January 2025

Abstract Calmodulin-like (CMLs) proteins are critical in calcium signaling and essential for plant growth, development, and stress responses. In many species, the CMLs families have been identified and described. However, the characterization and expression profiling of CMLs genes in tobacco is retrievable. In this study, a comprehensive whole-genome identification and analysis, and 75 NtCML genes were identified in tobacco, each containing two to four EF-hand domains. Most NtCML proteins exhibited conserved gene structures and motifs. Notably, most NtCML proteins were intron-less and distributed across 18 chromosomes. Two pairs of tandemly duplicated genes and seven pairs of segmentally More >

Zhenbing Qiao^1,2, Mengyun Chen^1,2, Wenjun Ma^1,2, Juan Zhao^1,2, Jiaju Zhu^1,2, Kaikai Zhu^1,2, Pengpeng Tan^1,2, Fangren Peng^1,2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.9, pp. 2349-2365, 2024, DOI:10.32604/phyton.2024.056655 - 30 September 2024

Abstract Ammonium nitrogen (NH₄⁺-N) is one of the main forms of nitrogen absorbed and utilized by plants, and mastering the regulatory mechanism of plant ammonium assimilation is a key way to improve the efficiency of plant nitrogen utilization. Glutamine synthetase (GS) and glutamate synthase (GOGAT), two key enzymes for ammonium assimilation, have rarely been studied in pecan. In this study, GS and GOGAT family members of pecan were identified and analyzed using bioinformatics methods. The results indicated that 6 GS and 4 GOGAT genes were identified. The cis-acting elements can be broadly categorized into light-responsive, hormone-responsive, and stress-responsive elements.… More >

Xianwen Ji^#, Ziying Jiang^#, Jichao Wang, Lili Dong, Xinyi Deng^*

Phyton-International Journal of Experimental Botany, Vol.93, No.8, pp. 1839-1850, 2024, DOI:10.32604/phyton.2024.052809 - 30 August 2024

Abstract Genes in the glycogen synthase kinase 3 (GSK3) family are essential in regulating plant response to stressful conditions. This study employed bioinformatics to uncover the GSK3 gene family from the sunflower genome database. The expressions of GSK3 genes in different tissues and stress treatments, such as salt, drought, and cold, were assessed using transcriptome sequencing and quantitative real-time PCR (qRT-PCR). The study results revealed that the 12 GSK3 genes of sunflower, belonging to four classes (Classes I–IV), contained the GSK3 kinase domain and 11–13 exons. The majority of GSK3 genes were highly expressed in the leaf axil and… More >

Mingchuan Yang¹, Jia Zheng², Wenhui Yu¹, Yanghua Li², Yali Wang¹, Zilu Zhang¹, Zhenhui Kang^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.7, pp. 1503-1521, 2024, DOI:10.32604/phyton.2024.051718 - 30 July 2024

Abstract Sorghum is not only an important bio-energy crop but also a vital raw material for brewing. Exogenous copper affects the growth and metabolism of crops in specific ways. This study identified 8475 differentially expressed genes (DEGs) by high-throughput transcriptome sequencing in the sorghum cultivar ‘Jinnuoliang 2’ after 24 h of treatment with 10 mM CuSO. Using GO analysis, 476 genes were functionally annotated, which were mainly related to catabolism and biosynthetic processes. Additionally, 90 pathways were annotated by employing the KEGG analysis. Among them, glutathione metabolism and peroxisome were induced, while photosynthesis, photosynthesis-antenna protein, and… More >

Zhengfeng Lai, Dongmei Lian, Shaoping Zhang, Yudong Ju, Bizhen Lin, Yunfa Yao, Songhai Wu, Jianji Hong, Zhou Li^*

Phyton-International Journal of Experimental Botany, Vol.93, No.6, pp. 1143-1158, 2024, DOI:10.32604/phyton.2024.051207 - 27 June 2024

Abstract The cytokinin oxidase/dehydrogenase (CKX) enzyme is essential for controlling the fluctuating levels of endogenous cytokinin (CK) and has a significant impact on different aspects of plant growth and development. Nonetheless, there is limited knowledge about CKX genes in tomato (Solanum lycopersicum L.). Here we performed genome-wide identification and analysis of nine SlCKX family members in tomatoes using bioinformatics tools. The results revealed that nine SlCKX genes were unevenly distributed on five chromosomes (Chr.1, Chr.4, Chr.8, Chr.10, and Chr.12). The amino acid length, isoelectric points, and molecular weight of the nine SlCKX proteins ranged from 453 to 553, 5.77… More >

Cong Hou¹, Kang Ning¹, Xiuye Wei¹, Yufei Cheng¹, Huatao Yu¹, Haibin Yu², Xia Liu^1,*, Linlin Dong^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2087-2103, 2023, DOI:10.32604/phyton.2023.029041 - 29 May 2023

Abstract Abscisic acid (ABA) is involved in regulating diverse biological processes, but its signal transduction genes and roles in hemp seed germination are not well known. Here, the ABA signaling pathway members, PYL, PP2C and SnRK2 gene families, were identified from the hemp reference genome, including 7 CsPYL (pyrab-actin resistance1-like, ABA receptor), 8 CsPP2CA (group A protein phosphatase 2c), and 7 CsSnRK2 (sucrose nonfermenting1-related protein kinase 2). The content of ABA in hemp seeds in germination stage is lower than that in non-germination stage. Exogenous ABA (1 or 10 μM) treatment had a significant regulatory effect on the selected PYL,… More >