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transcriptome analysis reveals the common and specific pathways of citric acid accumulation in different citrus species

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Horticultural Plant Journal 2025年第2期11卷 520-534页

作者： He, Jiaxian Sun, Juan Huang, Yue Wang, Lun Liu, Shengjun Jiang, Zhenghua Wang, Xia Xu, Qiang National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops Huazhong Agricultural University Hubei Wuhan 430070 China Hubei Hongshan Laboratory Hubei Wuhan 430070 China

Citric acid is an important contributor to fruit flavor. The extremely significant differences in citric acid levels are observed among citrus species and varieties. The molecular basis of citric acid accumulation remains largely unknown on the inter-species level. Here, we performed transcriptome analysis of five pairs of acidic and acidless variety fruits from kumquat (Citrus crassifolia), lemon (C. limon), pummelo (C. maxima), mandarin (C. reticulata), and sweet orange (C. sinensis) to investigate the common and specific genes related to citric acid accumulation in these citrus species. Transcript profiles of the citrate metabolism genes revealed that the mechanism of citric acid accumulation in kumquat differed from that in the other four species. The comparative analysis and weighted gene co-expression network analysis identified 61 candidate genes from lemon, pummelo, mandarin, and sweet orange. Vacuolar acidification regulated by CitPH4-CitAN1-CitPH5 was a common mechanism underlying citric acid accumulation in these four species. In addition, gene network analysis indicated that CitPH4 was a central regulator, exhibiting a strong correlation with the genes involved in vacuolar trafficking and potassium (K+) transport. The co-expression and functional enrichment analyses showed that active sugar metabolism and increased citrate synthesis were mainly responsible for the accumulation of citric acid in kumquat. Twenty-four transcription factors were identified as candidate regulators, of which CitbHLH28 was found to regulate acidity level via transactivating CWINV2 and PK3 expressions. Overall, this study provides an insight into the mechanism of citric acid accumulation in citrus fruit and provides useful references for fruit quality improvement through acidity control in different citrus species. © 2024 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).

关键词： Citrate synthesis Citric acid Citrus Regulatory network transcriptome Vacuolar acidification

Integration of transcriptome and metabolome reveals regulatory mechanisms of volatile flavor formation during tomato fruit ripening

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Horticultural Plant Journal 2025年第2期11卷 680-692页

作者： Liu, Zhiqiang Wu, Jianxin Wang, Licai Lu, Xiaonan Ahammed, Golam Jalal Zhang, Xiaolan Cui, Xia Wang, Haijing State Key Laboratory of Vegetable Biobreeding Sino-Dutch Joint Laboratory of Horticultural Genomics Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Beijing 100081 China Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable Ministry of Agriculture and Rural Affairs Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province College of Horticulture Science Zhejiang A & F University Zhejiang Hangzhou 311300 China Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops Department of Vegetable Sciences China Agricultural University Beijing 100193 China College of Horticulture and Plant Protection Henan University of Science and Technology Henan Luoyang 471023 China

Tomato is an important economic crop all over the world. Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality. However, the regulatory mechanism controlling the volatile flavors of tomatoes is still not clear. Here, we integrated the metabolome and transcriptome of the volatile flavors in tomato fruit to explore the regulatory mechanism of volatile flavor formation, using wild and cultivated tomatoes with significant differences in flavors. A total of 35 volatile flavor compounds were identified, based on the solid phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS). The content of the volatiles, affecting fruit flavor, significantly increased in the transition from breaker to red ripe fruit stage. Moreover, the total content of the volatiles in wild tomatoes was much higher than that in the cultivated tomatoes. The content variations of all volatile flavors were clustered into 10 groups by hierarchical cluster and Pearson coefficient correlation (PCC) analysis. The fruit transcriptome was also patterned into 10 groups, with significant variations both from the mature green to breaker fruit stage and from the breaker to red ripe fruit stage. Combining the metabolome and the transcriptome of the same developmental stage of fruits by co-expression analysis, we found that the expression level of 1 182 genes was highly correlated with the content of volatile flavor compounds, thereby constructing two regulatory pathways of important volatile flavors. One pathway is tetrahydrothiazolidine N-hydroxylase (SlTNH1)-dependent, which is regulated by two transcription factors (TFs) from the bHLH and AP2/ERF families, controlling the synthesis of 2-isobutylthiazole in amino acid metabolism. The other is lipoxygenase (SlLOX)-dependent, which is regulated by one TF from the HD-Zip family, controlling the synthesis of hexanal and (Z)-2-heptenal in fatty acid metabolism. Dual-luciferase assay confirmed the binding of

关键词： Co-expression Tomato Transcription factor transcriptome Volatile flavor

Integration of transcriptome and DNA methylome analysis reveals the molecular mechanism of taproot yield heterosis in radish

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Horticultural Plant Journal 2025年第2期11卷 645-660页

作者： Zhang, Xiaoli Xu, Liang Wang, Yan Zhang, Wei Zhang, Xinyu Dong, Junhui Ying, Jiali Wang, Lun Ma, Yinbo Liu, Liwang National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utlization Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR College of Horticulture Nanjing Agricultural University Jiangsu Nanjing 210095 China College of Horticulture and Landscape Architecture Yangzhou University Jiangsu Yangzhou 225009 China

Heterosis, a crucial biological phenomenon, plays a vital role in determining the yield and quality of plants. Radish, an important root vegetable crop, exhibits notable heterosis in terms of root yield and quality. Nevertheless, the molecular mechanism underlying the formation of heterosis in radish remains unclear. Herein, both the transcriptome and DNA methylome analyses were performed on the F1 hybrids and parental lines. Expression level dominance (ELD) genes and allele-specific expression (ASE) genes together significantly contribute to heterosis, primarily through energy metabolism and plant hormone signal transduction pathway. An increase in average methylation level in the F1 hybrids was observed compared to the parental lines. Interestingly, a negative correlation was found between the methylation level of differentially expressed genes (DEGs) in gene body regions and their expression levels in NAU-LB and the F1 hybrids. Moreover, the hybrids were more sensitive to the 5-azacytidine than their parents, and the root weight and total sugar content in the F1 hybrids were dramatically decreased compared to the control. Immunolocalization results indicated that the auxin content of the F1 hybrids were reduced under 5-azacytidine treatment. Proliferating cell nuclear antigen immunolocalization revealed significant inhibition of vascular cambium activity in both the hybrids and parental lines. Notably, the expression profiles of a few differentially methylated DEGs including RsSUS1, RsSUC2a, RsIAA7, and RsIAA18, were significantly increased in the root of hybrids compared to their parents, suggesting a potential role of DNA methylation in yield heterosis. Collectively, these findings would provide valuable insight into the molecular mechanism underlying taproot yield heterosis and facilitate the genetic improvement of taproot yield and quality in radish breeding programs. © 2023 Chinese Society for Horticultu

关键词： Allele-specific expression DNA methylation Heterosis Parental expression level dominance Raphanus sativus L. transcriptome

The transcriptome of MHV-infected RAW264.7 cells offers an alternative model for macrophage innate immunity research

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Animal Models and Experimental Medicine 2025年第1期8卷 57-66页

作者： Yun Liu Ting-Ting Feng Wei Tong Zhi Guo Xia Li Qi Kong Zhi-Guang Xiang Institute of Laboratory Animal Sciences Chinese Academy of Medical Sciences(CAMS)and Comparative Medicine CenterPeking Union Medical College(PUMC)BeijingP.R.China

Background:Macrophages are the primary innate immune cells encountered by the invading coronaviruses,and their abilities to initiate inflammatory reactions,to main-tain the immunity homeostasis by differential polarization,to train the innate immune system by epigenic modification have been reported in laboratory animal ***:In the current in vitro research,murine macrophage RAW 264.7 cell were infected by mouse hepatitis virus,a coronavirus existed in *** 3-,6-,12-,24-,and 48-h post infection(hpi.),the attached cells were washed with PBS and harvested in Trizol *** The harvest is subjected to transcriptome ***:The transcriptome analysis showed the immediate(3 hpi.)up regulation of DEGs related to inflammation,like Il1b and *** related to M2 differential po-larization,like Irf4 showed up regulation at 24 hpi.,the late term after viral *** addition,DEGs related to metabolism and histone modification,like Ezh2 were de-tected,which might correlate with the trained immunity of ***:The current in vitro viral infection study showed the key innated im-munity character of macrophages,which suggested the replacement value of viral infection cells model,to reduce the animal usage in preclinical research.

关键词： coronavirus innate immunity macrophage transcriptome

Establishment of somatic embryogenesis regeneration system and transcriptome analysis of early somatic embryogenesis in litchi

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Horticultural Plant Journal 2025年第2期11卷 535-547页

作者： Qin, Yaqi Zhang, Bo Wang, Shiqian Guo, Wuyan Zhang, Zhike Qin, Yonghua Zhao, Jietang Hu, Guibing State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China) Ministry of Agriculture and Rural Affairs/Guangdong Litchi Engineering Research Center College of Horticulture South China Agricultural University Guangdong Guangzhou 510642 China

Litchi chinensis Sonn. is an important economic fruit tree in tropical and subtropical regions. Regrettably, the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants. The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in ‘Heiye’ cultivar of litchi. Our results demonstrated that MS medium supplemented with 2.0 mg L−1 2,4-D was optimal for callus induction. For somatic embryo (SE) induction, MS medium containing 0.5 g L−1 activated charcoal (AC) was the most effective, while the use of zeatin (ZT) and thidiazuron (TDZ) resulted in abnormal somatic embryos. The rooting and regeneration rate of 2.15% and 17.5%, respectively, were achieved using MS medium supplemented with 0.5 g L−1 AC. Furthermore, transcriptome analysis was performed on embryogenic callus (EC), globular embryo (GE), and heart embryo (HE) to explore the molecular mechanisms of early somatic embryogenesis. 2,587 common differentially expressed genes (DEGs) between EC_vs_GE and EC_vs_HE were identified, and the expression patterns of these common DEGs were separated into twelve major clusters. GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction, auxin-activated signaling pathway, and other biological processes. Additionally, differentially expressed transcription factors were identified, and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified. Overexpression of LcBBM2 in tomato promotes callus and shoot formation. Therefore, this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi. © 2025 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).

关键词： LcBBM2 Litchi chinensis Somatic embryogenesis transcriptome

A genome-wide association study and transcriptome analysis reveal the genetic basis for the Southern corn rust resistance in maize

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Journal of Integrative Agriculture 2025年第2期24卷 453-466页

作者： Yang Wang Chunhua Mu Xiangdong Li Canxing Duan Jianjun Wang Xin Lu Wangshu Li Zhennan Xu Shufeng Sun Ao Zhang Zhiqiang Zhou Shenghui Wen Zhuanfang Hao Jienan Han Jianzhou Qu Wanli Du Fenghai Li Jianfeng Weng College of Agronomy Shenyang Agricultural University Institute of Crop Sciences Chinese Academy of Agricultural Sciences Institute of Maize Research Shandong Academy of Agricultural Sciences College of Plant Protection Shandong Agricultural University Institute of Maize Shanxi Agricultural University

Southern corn rust(SCR) is an airborne fungal disease caused by Puccinia polysora Underw.(P. polysora) that adversely impacts maize quality and yields worldwide. Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen. Using phenotypic SCR resistance-related data collected over two years and three geographical environments, a genome-wide association study was carried out in this work, which eventually identified 91 loci that were substantially correlated with SCR susceptibility. These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73＿RefGen＿v4). Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection, with 2,586 and 797 differentially expressed genes(DEGs) ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P. polysora infection, respectively, including 306 genes common to both lines. Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes. One of these genes is ZmHCT9, which encodes the protein hydroxycinnamoyl transferase 9. This gene was up-regulated in susceptible inbred lines and linked to greater P. polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS) system-mediated gene silencing. These data provide important insights into the genetic basis of the maize SCR response. They will be useful for for future research on potential genes related to SCR resistance in maize.

关键词： maize southern corn rust genome-wide association study transcriptome

transcriptome reveals overview of Ca^(2+) dose-dependent metabolism disorders in zebrafish larvae after Cd^(2+) exposure

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Journal of Environmental Sciences 2023年第3期125卷 480-491页

作者： Biran Zhu Ziniu Wang Lei Lei Yongyong Guo Jian Han Bingsheng Zhou State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China School of Basic Medical Sciences Hubei University of Chinese MedicineWuhan 430065China State Key Laboratory of Environmental Chemistry and Ecotoxicology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China

Cadmium (Cd),a ubiquitous environmental hazardous heavy metal,poses a significant threat to the health of aquatic organisms,including *** the toxic profile of Cd is well recognized,little is known regarding the overall view of toxic responses to varying aquatic environmental parameters (e.g.,water hardness) at an individual ***,differences in water hardness were partially mimicked by adjusting Ca^(2+)levels in E3 *** an in vivo model,zebrafish embryos were exposed to variable Ca^(2+)levels (NV,normal Ca^(2+);LV,low Ca^(2+);HV,high Ca^(2+)) alone or combined with 30.7μg/L Cd^(2+)(NC,LC,and HC,respectively) until 144 hr *** genome-wide transcriptome revealed differentially expressed genes between *** enrichment analysis found that biological processes related to metabolism,particularly lipid metabolism,were significantly disrupted in NC and LC treatments,while a remission was observed in the HC *** assays confirmed that the decrease in Ca^(2+)enhanced synthesis,inhibited mobilization and increased the storage of lipids in Cd^(2+)*** study suggests that the toxic effect of Cd on biological pathways will be influenced by Ca^(2+),which will improve the toxicological understanding and facilitate accurate assessment of Cd.

关键词： Cadmium Calcium Zebrafish larvae transcriptome Metabolism disorder

transcriptome Analysis of Crassostrea sikamea (♀) × Crassostrea gigas (♂) Hybrids Under and After Thermal Stress

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Journal of Ocean University of China 2022年第1期21卷 213-224页

作者： ZHANG Xuekai FAN Chao ZHANG Xingzhi LI Qiongzhen LI Yangchun MA Peizhen YUE Shaobo HUO Zhongming WANG Zhaoping Fisheries College Ocean University of ChinaQingdao 266003China Guangxi Academy of Fisheries Sciences Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy AquacultureNanning 530021China

Crossbreeding is an effective approach to manage the genetic decline in ***-way hybrids of Crassostrea sikamea(♀)and Crassostrea gigas(♂)have advantages in growth traits and adaptation to high ***,we used high-throughput sequencing to analyze the molecular processes in the hybrids under and after thermal *** hybrids were cultured in the seawater with an increasing temperature from 25℃to 40℃during 10 hours,which is regarded as the thermal stress *** the temperature decreased from 40℃to 25℃within 2 h,which is regarded as the recovery *** this study,1293 significant diffe-rentially expressed genes(DEGs)were obtained under thermal stress,of which 576 were upregulated and 717 were downregulated,and 740 significant differentially expressed genes(DEGs)were obtained in the recovery stage,of which the number of upregulated and downregulated genes was 409 and 331,*** antigen processing and presentation,NOD-like,and NF-kappa B path-ways were significantly enriched during the thermal stress *** MAPK and PPAR signaling pathways were significantly enrich-ed during the recovery *** HSP70,HSP90,and CANX genes were strongly and rapidly upregulated in the control/thermal stress groups but were slightly less upregulated in the thermal stress/recovery *** results indicate that the innate immune system or nonspecific immunity was deployed to protect interior tissues from thermal *** addition,85%of the mutual DEGs were involved in bidirectional regulation(up/down or down/up)when the oysters were removed from the thermal stress to *** study provides preliminary insight into the molecular response of ***(♀)and ***(♂)hybrids to thermal stress and provides a basis for future studies on temperature-adaptation and the possible expansion of hybrid breeding.

关键词： oyster hybrids gill thermal stress recovery transcriptome

transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

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Science China(Life Sciences) 2016年第2期59卷 164-171页

作者： Changsong Zou Qiaolian Wang Cairui Lu Wencui Yang Youping Zhang Hailiang Cheng Xiaoxu Feng Mtawa Andrew Prosper Guoli Song State Key Laboratory of Cotton Biology Institute of Cotton Research Chinese Academy of Agricultural Sciences

Long noncoding RNAs （lncRNAs） play important roles in various biological regulatory processes in yeast, mammals, and plants. However, no systematic identification of lncRNAs has been reported in Gossypium arboreum. In this study, the strand-specific RNA sequencing （ssRNA-seq） of samples from cotton fibers and leaves was performed, and lncRNAs involved in fiber initiation and elongation processes were systematically identified and analyzed. We identified 5,996 lncRNAs, of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs （lincRNAs） and natural antisense transcripts （IncNAT）, respectively. LincRNAs and lncNATs are similar in many aspects, but have some differences in exon number, exon length, and transcript length. Expression analysis revealed that 51.9% of lincRNAs and 54.5% of lncNATs transcripts were preferentially expressed at one stage of fiber development, and were significantly highly expressed than protein-coding tran- scripts （21.7%）. During the fiber and rapid elongation stages, rapid and dynamic changes in lncRNAs may contribute to fiber development in cotton. This work describes a set of lncRNAs that are involved in fiber development. The characterization and expression analysis of lncRNAs will facilitate future studies on their roles in fiber development in cotton.

关键词： long noncoding RNAs strand specific RNA sequencing fiber transcriptome expression