Riwa Mahai¹, Rongpeng Liu¹, Xiaolang Du¹, Zejing Mu¹, Xiaoyun Wang^1,*, Jun Yuan^2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.6, pp. 1203-1219, 2024, DOI:10.32604/phyton.2024.051559

Abstract Rosaceae represents a vast and complex group of species, with its classification being intricate and contentious. The taxonomic placement of many species within this family has been a subject of ongoing debate. The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae. The cp genomes, varying in size from 153,366 to 159,895 bp, followed the typical quadripartite organization consisting of a large single-copy (LSC) region (84,545 to 87,883 bp), a small single-copy (SSC) region (18,174 to 19,259 bp), and a pair of inverted repeat (IR) regions (25,310 to… 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

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 >

Jing Wang^1,#, Wenqing Xiao^1,#, Qingnan Wang¹, Xu Wang¹, Bin Jiang¹, Yangchun Han², Yang Sun^1,*

Phyton-International Journal of Experimental Botany, Vol.93, No.5, pp. 859-873, 2024, DOI:10.32604/phyton.2024.048151

Abstract The basic leucine zipper (bZIP) is an important class of transcription factors in plants, playing a critical role in plant growth and development and responses to biotic and abiotic stress. Due to gene presence/absence variations, it is limited to identify bZIP genes based on the reference genome. Therefore, we performed the bZIP gene family analysis in the rice pan-genome. By employing a rice pan-genome, ninety-four OsbZIPs (72 core genes and 22 variable genes) were identified and divided into 11 groups in a phylogenetic tree. Based upon Ka/Ks values in 33 accessions, OsbZIPs were subjected to different selection… More >

Honghui Sun^1,2,#, Ruichao Liu^1,2,#, Yueting Qi¹, Hongsheng Gao¹, Xueting Wang¹, Ning Jiang^1,2, Xiaotong Guo^1,2, Hongxia Zhang¹, Chunyan Yu^1,2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.3, pp. 533-549, 2024, DOI:10.32604/phyton.2024.049417

Abstract Grapes, one of the oldest tree species globally, are rich in vitamins. However, environmental conditions such as low temperature and soil salinization significantly affect grape yield and quality. The glutamate receptor (GLR) family, comprising highly conserved ligand-gated ion channels, regulates plant growth and development in response to stress. In this study, 11 members of the VvGLR gene family in grapes were identified using whole-genome sequence analysis. Bioinformatic methods were employed to analyze the basic physical and chemical properties, phylogenetic trees, conserved domains, motifs, expression patterns, and evolutionary relationships. Phylogenetic and collinear analyses revealed that the VvGLRs… More >

ZHENHUA LI¹, HUILAI LV¹, FAN ZHANG¹, ZIMING ZHU², QIANG GUO³, MINGBO WANG¹, CHAO HUANG¹, LIJUAN CHEN⁴, WENPAN ZHANG⁴, YUN LI^5,*, ZIQIANG TIAN^1,*

BIOCELL, Vol.48, No.1, pp. 123-138, 2024, DOI:10.32604/biocell.2023.031568

Abstract Introduction: DNA polymerases are crucial for maintaining genome stability and influencing tumorigenesis. However, the clinical implications of DNA polymerases in tumorigenesis and their potential as anti-cancer therapy targets are not well understood. Methods: We conducted a systematic analysis using TCGA Pan-Cancer Atlas data and Gene Set Cancer Analysis results to examine the expression profiles of 15 DNA polymerases (POLYs) and their clinical correlations. We also evaluated the prognostic value of POLYs by analyzing their expression levels in relation to overall survival time (OS) using Kaplan-Meier survival curves. Additionally, we investigated the correlations between POLY expression… More >

Yajun Liang^1,2,#, Juyun Zheng^1,#, Junduo Wang^1,#, Zhaolong Gong¹, Zhiqiang Li³, Ling Min⁴, Zeliang Zhang², Zhiwei Sang², Yanying Qu², Xueyuan Li^1,*, Quanjia Chen^2,*

Phyton-International Journal of Experimental Botany, Vol.92, No.12, pp. 3345-3357, 2023, DOI:10.32604/phyton.2023.028755

Abstract Upland cotton (Gossypium hirsutum) is the most important plant producing natural fibers for the textile industry. In this study, we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018, which were from 18 geographical regions. We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution. We then genotyped the collection with 81,612 high quality SNPs. Phylogenetic tree and population structure revealed a diverse genetic structure of the core… More >

XIAO-JUN ZHOU^1,*, YU-WEI TIAN¹, RUI-HAN LI²

BIOCELL, Vol.47, No.8, pp. 1907-1913, 2023, DOI:10.32604/biocell.2023.030191

Abstract Background: Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value. However, the lack of information on its genome size and characteristics hinders further work at the genome level. Methods: This paper applied bioinformatics methods to predict the characteristics and patterns of the A. griseum genome, providing an important basis for formulating its whole-genome sequencing scheme. This study also characterized the simple sequence repeats (SSRs) of A. griseum, laying the foundation for the development and application of genome-wide SSR markers. In this study, PE150 sequencing was performed by the BGI MGISEQ platform,… More >

Xiaolan Guo^1,2, Jinbin Hu³, Shimei Yang⁴, Delu Wang^2,*, Jianbing Wang¹

Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2683-2697, 2023, DOI:10.32604/phyton.2023.029820

Abstract The F3′5′H gene family plays an important role in regulating anthocyanin biosynthesis, abiotic stress, and hormone signaling. In this study, 14 F3′5′H genes were identified from the blueberry genome. The chromosomal distribution, physicochemical properties, F3′5′H domain, conserved motifs, cis-acting elements, and intron/exon compositions were analyzed. The functional prediction analysis of these VcF3′5′Hs indicated that their biological functions included light response and other secondary metabolites. The results of qRT-PCR showed that VcF3′5′Hs (especially VcF3′5′H4) were highly expressed at the ripening stage. Subcellular localization revealed that VcF3′5′H4 may be located in the endoplasmic reticulum. Co-expression analysis showed that the VcF3′5′H More >

Minghui Niu^1,#, Heng Zhang^1,#, Xiangyang Li¹, Zhibao Hu¹, Hongjiao Zhang^2,3, Zhiru Xu^2,3, Chunpu Qu^1,4,*, Guanjun Liu^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2001-2015, 2023, DOI:10.32604/phyton.2023.029350

Abstract KANADI (KAN) is a plant-specific gene that controlled the polarity development of lateral organs. It mainly acted on the abaxial characteristics of plants to make the lateral organs asymmetrical. However, it had been less identified in woody plants. In this study, the members of the KAN gene family in Populus trichocarpa were identified and analyzed using the bioinformatics method. The results showed that a total of 8 KAN family members were screened out, and each member contained the unique GARP domain and conserved region of the family proteins. Phylogenetic analysis and their gene structures revealed that all KAN genes… More >

Cherith Somerville^1,2, Kelsey Kalbfleisch^1,2, Roozbeh Manshaei^1,2, Qiliang Ding^1,2, John B.A. Okello^1,2,3, Rachel Silver⁴, David Chitayat^2,4, Varsha Thakur⁵, Olivier Villemain^5,6,7, Rebekah Jobling^1,2,8,*

Congenital Heart Disease, Vol.18, No.2, pp. 213-218, 2023, DOI:10.32604/chd.2023.023042

Abstract We report a three-year-old male child who presented with congenital valvular defects, right ventricular malformation, and initial developmental delay. Genome sequencing showed rare deleterious biallelic missense variants in PLD1. In his parents’ second pregnancy, echocardiogram at 13 weeks gestation revealed right-sided cardiac malformations resembling the clinical presentation of the family’s first child. Targeted DNA analysis showed that the fetus carried the same biallelic PLD1 variants as their older sibling. This case helps to further delineate the clinical spectrum of PLD1-related defects and highlights the value of both genome sequencing in congenital heart disease and early fetal echocardiography More >