Shixiang Duan^1,#, Yaomiao Guo^1,#, Yinping Wang¹, Muhammad Jawad Umer², Dongming Liu¹, Sen Yang¹, Huanhuan Niu¹, Shouru Sun¹, Luming Yang¹, Junling Dou^1,*, Huayu Zhu^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1311-1328, 2023, DOI:10.32604/phyton.2023.026928

Abstract Leaf is a vital organ of plants that plays an essential role in photosynthesis and respiration. As an important agronomic trait in leaf development, leaf shape is classified into lobed, entire (no-lobed), and serrated in most crops. In this study, two-lobed leaf watermelon inbred lines WT2 and WCZ, and a no-lobed leaf watermelon inbred line WT20 were used to create two F₂ populations. Segregation analysis suggested that lobed leaves were dominant over the no-lobed leaves, and it was controlled by a signal gene. A locus on watermelon chromosome 4 controlling watermelon lobed/no-lobed leaves was identified through BSA-seq strategy combined with… More >

Mortaza Hajyzadeh^*

Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1649-1664, 2023, DOI:10.32604/phyton.2023.028028

Abstract Abiotic stresses at different growth stages in the life of plants negatively affect yield productivity. Therefore, plants, including Amaranthus hypochondriacus, develop adaptive strategies to face the stresses and expand functional diversification. In plants, the mitochondrial transcription termination factors (mTERF) are essential functions in regulation, and organelles (mitochondria and chloroplasts) control gene expression (OGE) under several stress conditions. Based on the in-silico-wide genome and transcriptome analysis, twenty-four mTERF genes were detected in the main targeted mitochondria organelles clustered into three different main groups. The chromosomal location and gene duplication analysis indicated one segmental and one tandem duplication in the genome. The… More >

Jiayou Liu, Lian Ding, Xue Zhang, Song Li, Yunxiao Guan, Diwen Jia, Aiping Song, Jiafu Jiang, Fadi Chen^*

Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 311-331, 2023, DOI:10.32604/phyton.2022.023896

Abstract Chrysanthemum morifolium, an ornamental crop with diverse forms of inflorescence, is a good model for studying flower development in Asteraceae. However, the genetic background is complex and the mechanisms of regulating flower development are still unclear. Here, we identified two natural mutant lines of chrysanthemum and named them M1 and M2 according to the severity of the phenotype. Both lines showed defects in petal identity, and the petals of the M1 line had a mild phenotype: partially loss of petal identity and conversion of petals into green, leaf-like organs. The M2 line had severe phenotypes: in addition to severe petal… 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 >

Yinglong Song^1,#, Wenqian Shang^1,#, Zheng Wang^1,*, Songlin He^1,2,*, 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 >

Ting Zhang^1,2, Ping Li^3,*, Jiali Wei^3,*

Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2403-2417, 2022, DOI:10.32604/phyton.2022.022421

Abstract Hedera helix is an evergreen ornamental plant that is resistant to cool but not high temperature and deserves to be further researched for improving its adaptability to heat stress. Two Hedera helix cultivars, heat-tolerant (HT) ‘Jessica’ and heat-sensitive (HS) ‘Shamrock’, were used for differences analyses of transcriptome. We detected 6179 differentially expressed genes (DEGs) and 5992 DEGs in ‘Jessica’ and ‘Shamrock’ to heat stress, respectively. Among these, 1983 upregulated DEGs and 1400 downregulated DEGs were shared between both varieties, resulting in enhancement of various pathways such as biosynthesis of secondary metabolites, glyoxylate dicarboxylate metabolism, and protein processing in endoplasmic reticulum… More >

TIEJUN ZHAO, RIQIANG DENG^*, MENGQIU CHEN, XUNZHANG WANG

BIOCELL, Vol.46, No.7, pp. 1675-1686, 2022, DOI:10.32604/biocell.2022.018166

Abstract Sf9Sf9 are the ovarian cells of Spodoptera frugiperda that is the host of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), and hence can serve as an effective test vehicle to understand the AcMNPV infection mechanism. In this study, through high-throughput sequencing technology using samples collected from Sf9 cells at different time points after AcMNPV infection, 3463 pieces of time-series differentially expressed RNA (1,200 mRNA and 2,263 lncRNA) are identified and justified by experimental verification of randomly selected samples from them, proving the validity of the bioinformatical analysis on this topic. Functional enrichment analysis and target prediction are performed on those differentially expressed… More >

LIMIN CHEN^1,2, XIAOWEI LI¹, TIANJUN HE², QUANCONG WU², TINGTING CHEN³, JUN HUANG^1,*, YAOBIN LU^1,*

BIOCELL, Vol.46, No.3, pp. 821-828, 2022, DOI:10.32604/biocell.2021.016450

Abstract Venom plays several important roles in the life of the fire ant, Solenopsis invicta Buren. Laboratory rearing significantly affected the toxin component of S. invicta. However, the molecular mechanism of the change of venomous components when kept in the laboratory is unclear. In this study, RNA sequencing technique (RNA-Seq) was performed to explore differentially expressed genes in the venom gland of S. invicta at 0, 10, and 60 days after laboratory rearing. The RNA-Seq results showed that the expression of a large number of genes changed. The DEGs were involved in multiple pathways, including proteolysis, serine-type endopeptidase, and allergen. Furthermore,… More >

SAMUELE GRECO^1,#, ELISA D’AGOSTINO^2,#, CHIARA MANFRIN¹, ANASTASIA SERENA GAETANO¹, GAEL FURLANIS¹, FRANCESCA CAPANNI¹, GIANFRANCO SANTOVITO², PAOLO EDOMI¹, PIERO GIULIO GIULIANINI¹, MARCO GERDOL^1,*

BIOCELL, Vol.45, No.6, pp. 1611-1619, 2021, DOI:10.32604/biocell.2021.016121

Abstract We here report the de novo transcriptome assembly and functional annotation of Eusirus cf. giganteus clade g3, providing the first database of expressed sequences from this giant Antarctic amphipod. RNA-sequencing, carried out on the whole body of a single juvenile individual likely undergoing molting, revealed the dominant expression of hemocyanins. The mRNAs encoding these oxygen-binding proteins cumulatively accounted for about 40% of the total transcriptional effort, highlighting the key biological importance of high hemocyanin production in this Antarctic amphipod species. We speculate that this observation may mirror a strategy previously described in Antarctic cephalopods, which compensates for the decreased ability… More >

JOE R. DELANEY^*

BIOCELL, Vol.45, No.5, pp. 1167-1170, 2021, DOI:10.32604/biocell.2021.017296

Abstract Single-cell sequencing data has transformed the understanding of biological heterogeneity. While many flavors of single-cell sequencing have been developed, single-cell RNA sequencing (scRNA-seq) is currently the most prolific form in published literature. Bioinformatic analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scRNA-seq gene counts. One biologically relevant variable is readily inferred from scRNA-seq gene count tables regardless of individual gene representation within single cells: aneuploidy. Since hundreds of genes are present on chromosome arms, high-quality inferences of aneuploidy can be made… More >