Article
Biotechnology & Applied Microbiology
Yu Bin, Qi Zhang, Yue Su, Chunqing Wang, Qiqi Jiang, Zhen Song, Changyong Zhou
Summary: This study used RNA-seq to analyze the gene expression patterns of lemon plants in response to CYVCV infection. There were 3691 differentially expressed genes (DEGs) identified, which were components of different pathways involved in phenylpropanoid biosynthesis, brassinosteroid biosynthesis, flavonoid biosynthesis, and photosynthesis. The DEGs related to phytohormone metabolism and photosynthesis pathways were further enriched and analyzed. It was found that different phytohormone-related genes had different responses toward CYVCV infection, while almost all of the photosynthesis-related DEGs were down-regulated in the infected plants.
Article
Oncology
Quang Ong, Shingo Sakashita, Emi Hanawa, Naomi Kaneko, Masayuki Noguchi, Masafumi Muratani
Summary: The study conducted RNA-Seq and ChIP-Seq integrative analysis of clinical lung tissue samples to capture transcriptomic profiles and identify somatically altered regions marked by H3K4me3 in lung cancer. Differential expressions of cancer-related genes and enhancer activity annotations of cancer regulatory genes were observed near the altered H3K4me3 regions. The study demonstrated a practical workflow of using LMD on clinical samples for integrative analyses, improving the understanding of genetic and epigenetic dysregulation in malignancy.
Article
Biochemistry & Molecular Biology
Rita Costa Pires, Ana Ferro, Tiago Capote, Ana Usie, Barbara Correia, Gloria Pinto, Esther Menendez, Liliana Marum
Summary: This article introduces a technique of tissue isolation using laser microdissection, which is used to isolate specific plant cell types from woody tissues of cork oak and conduct RNA-Seq analysis. Through the optimized method, the molecular pathways associated with different developmental processes of xylem and phellem in oaks can be better understood.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Urology & Nephrology
Lihe Chen, Chun-Lin Chou, Mark A. Knepper
Summary: This study used a full-length, small-sample RNA-seq protocol to profile transcriptomes for all 14 renal tubule segments microdissected from mouse kidneys, identifying over 34,000 transcripts and 3709 segment-specific transcripts. Gene-expression patterns of solute carriers, transcription factors, and G protein-coupled receptors along the renal tubule were found to be important for segment-specific function.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2021)
Article
Plant Sciences
Pudong Li, Xiaoe Xiao, Jingrui Wang, Fan Niu, Jiangnan Huang, Bianyue Xie, Lu Ye, Chaofan Zhang, Dengliang Wang, Qun Wu, Xueliang Zheng, Yunpeng Gai, Hongye Li, Chen Jiao
Summary: This study investigated the gene expression pattern of citrus leaves in response to Diaporthe citri infection at early and late infection stages using RNA-Seq. The results showed differences in transcriptional regulation associated with defense responses. Plant cell wall biogenesis was induced at early infection stage, while callose deposition response was more active at late infection stage. Some genes played important roles in defense responses. This study provides insights into the defense mechanism of citrus against Diaporthe citri infection.
Article
Horticulture
Melina C. da Silva, Patricia I. S. Pinto, Rui Guerra, Amilcar Duarte, Deborah M. Power, Natalia T. Marques
Summary: This study investigated the transcriptome changes in Citrus macrophylla in response to drought stress and identified thousands of differentially expressed transcripts. The results showed that drought stress can induce the up- and down-regulation of various genes in the stem tissue of Citrus macrophylla, some of which may be associated with drought tolerance in this species.
SCIENTIA HORTICULTURAE
(2023)
Article
Multidisciplinary Sciences
Nan Wang, Xietian Song, Junli Ye, Siqi Zhang, Zhen Cao, Chenqiao Zhu, Jianbing Hu, Yin Zhou, Yue Huang, Shuo Cao, Zhongjie Liu, Xiaomeng Wu, Lijun Chai, Wenwu Guo, Qiang Xu, Brandon S. Gaut, Anna M. G. Koltunow, Yongfeng Zhou, Xiuxin Deng
Summary: The study reveals the mechanism and evolution of apomixis in Citrinae. Multiple embryos of a maternal genotype form directly from nucellar cells, utilizing endosperm for growth, enabling asexual reproduction of the maternal genetic constitution. This mechanism poses a significant barrier to breeding in Citrinae. Genetic and molecular analyses suggest that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae, and introgression may be involved in apomixis in some varieties of Fortunella. The FhRWP gene, associated with apomixis, contains heterozygous structural variants that facilitate nucellar embryogenesis.
NATIONAL SCIENCE REVIEW
(2022)
Article
Plant Sciences
Oliver Berkowitz, Yue Xu, Lim Chee Liew, Yan Wang, Yanqiao Zhu, Bhavna Hurgobin, Mathew G. Lewsey, James Whelan
Summary: The research investigated the transcriptomes of different leaf tissues in Arabidopsis under various stress pathways, revealing a decrease in the overall number of expressed genes in response to stress stimuli. While no common stress response was identified, there was overlap of differentially expressed genes between tissues for individual treatments. Specific analysis indicated an interaction between auxin and ethylene in mediating retrograde signaling during mitochondrial dysfunction in the epidermis.
Article
Chemistry, Applied
Wenjun Wang, Ting Li, Qi Chen, Shixiang Yao, Kaifang Zeng
Summary: As the most productive fruit in the world, there is a lack of research on disease resistance mechanisms in citrus. This study identified CsWRKY23 as a mediator of disease resistance in citrus, enhancing resistance to Penicillium digitatum. Through DNA affinity purification sequencing and RNA sequencing, 48 direct target genes of CsWRKY23 were identified. CsWRKY23 contributed to SA synthesis pathway, ROS accumulation, and cell wall strengthening, forming a possible regulatory network for disease resistance.
Article
Horticulture
Ariana Silva Santos, Edson Mario de Andrade, Andressa Rodrigues de Oliveira Sousa, Marcos Mota do Carmo Costa, Roberto Togawa, Priscila Grynberg, Carlos Priminho Pirovani, Saulo Alves Santos Oliveira, Walter dos Santos Soares Filho, Mauricio Antonio Coelho Filho, Abelmon da Silva Gesteira, Claudia Fortes Ferreira
Summary: This study analyzed the transcriptomes of citrus rootstocks 'Sunki Maravilha' and 'Sunki Tropical' under water deficit conditions, revealing significant gene expression variations and providing candidate genes for engineering or breeding citrus plants with drought tolerance. The differentially expressed genes identified are involved in various biological processes and molecular functions, with a focus on oxidoreductase, protein phosphorylation, transcriptional regulation, ligation processes, and response to oxidative stress.
SCIENTIA HORTICULTURAE
(2021)
Article
Plant Sciences
Qihang Jiang, Junli Ye, Kaijie Zhu, Fangfang Wu, Lijun Chai, Qiang Xu, Xiuxin Deng
Summary: Bagging treatment enhances the accumulation of carotenoids, especially lycopene, in the pulp of pomelo fruit. Upregulation of PSY and downregulation of CCD1 gene expression directly contribute to the increase in carotenoid content. Thirteen candidate genes closely associated with lycopene accumulation were identified through RNA-seq and WGCNA analysis, and their regulatory mechanism on carotenoid pathway genes was discussed. Additionally, these candidate genes may indirectly influence carotenoid enhancement in the pulp through the regulation of phytohormones, primary metabolism, and stress responses.
HORTICULTURAL PLANT JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Chiara M. A. Cefalo, Teresa Mezza, Andrea Giaccari, Rohit N. Kulkarni
Summary: This study compared four methods for RNA extraction and found that the RNeasy MicroKit + Carrier (Qiagen) method provided the highest yield and purity.
Article
Plant Sciences
Liqing Lu, Haijian Yang, Yanhui Xu, Li Zhang, Juxun Wu, Hualin Yi
Summary: This study used RNA-seq and Pacbio-seq technologies to analyze the transcriptome and plant hormone signals in citrus seed development, revealing the important roles of hormone signaling, cell division, and nutrient metabolism processes. Additionally, several genes, including CrWRKY74, were found to play critical roles in seed abortion.
Article
Biochemistry & Molecular Biology
Fenglin Wu, Huiyu Huang, Mingyi Peng, Yinhua Lai, Qianqian Ren, Jiang Zhang, Zengrong Huang, Lintong Yang, Christopher Rensing, Lisong Chen
Summary: Copper toxicity affects the growth and gene expression of Citrus grandis, leading to reduced photosynthesis. However, it also triggers adaptive responses in the plant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Carles Borreda, Estela Perez-Roman, Manuel Talon, Javier Terol
Summary: This study provides broad evidence that genome introgressions during citrus domestication have largely shaped gene expression in their fruits.
Article
Biochemistry & Molecular Biology
Muhammad Junaid Rao, Yuantao Xu, Xiaomei Tang, Yue Huang, Jihong Liu, Xiuxin Deng, Qiang Xu
Article
Plant Sciences
Suwen Lu, Junli Ye, Kaijie Zhu, Yin Zhang, Mengwei Zhang, Qiang Xu, Xiuxin Deng
Summary: The study revealed that a MADS gene CsMADS5 in citrus positively regulates carotenoid biosynthesis by directly activating carotenogenic genes, leading to enhanced fruit coloration and carotenoid concentrations. Additionally, CsMADS5 physically interacts with another positive regulator CsMADS6, suggesting a collaborative role in promoting carotenoid accumulation. These findings expand our knowledge of the complex transcriptional regulatory network governing carotenoid biosynthesis during fruit ripening.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Kaijie Zhu, Quan Sun, Hongyan Chen, Xuehan Mei, Suwen Lu, Junli Ye, Lijun Chai, Qiang Xu, Xiuxin Deng
Summary: The study reveals that ethylene-induced CsERF061 in citrus enhances carotenoid accumulation by activating the expression of key carotenoid pathway genes, leading to changes in chromoplast numbers and concentrations of abscisic acid and gibberellin.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Qingjiang Wu, Jialing Fu, Juan Sun, Xia Wang, Xiaomei Tang, Wenjia Lu, Chen Tan, Li Li, Xiuxin Deng, Qiang Xu
Summary: Genetic manipulation of plant genes in prokaryotes has led to the discovery of a plant protein-coding gene that can act as a promoter in bacteria. This study identified a key 64-bp sequence, key64, crucial for prokaryotic promoter activity and explored its presence in various species across different kingdoms. The research also shed light on the importance of specific nucleotide positions in key64-like sequences for transcriptional activity.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Xiaomei Tang, Shulin Chen, Huiwen Yu, Xiongjie Zheng, Fei Zhang, Xiuxin Deng, Qiang Xu
Summary: A reliable protocol for fast and efficient gene-edited Anliu sweet orange plants production was developed, with in vitro shoot grafting technology and short-term heat stress treatments significantly reducing growth cycle and improving mutation efficiency, providing a reference for fast and efficient multiplex gene editing.
PLANT CELL REPORTS
(2021)
Review
Microbiology
Bin Hu, Muhammad Junaid Rao, Xiuxin Deng, Sheo Shankar Pandey, Connor Hendrich, Fang Ding, Nian Wang, Qiang Xu
Summary: Citrus Huanglongbing (HLB), also known as citrus greening, is a devastating citrus disease with no commercial citrus cultivars resistant to it. The most prevalent strain associated with HLB, Candidatus Liberibacter asiaticus (CLas), has yet to be cultured in vitro. Research has focused on the complex pathosystem of Ca. Liberibacter, including the interaction of host and CLas, and the impact of CLas infection on host transcripts, proteins, and metabolism. Identifying candidate genes for CLas pathogenicity and improving HLB tolerance in citrus are key research areas for the future.
Article
Plant Sciences
Guanghui Zheng, Shaoqiang Hu, Simin Cheng, Liyang Wang, Lijun Kan, Zhengming Wang, Qiang Xu, Zhongchi Liu, Chunying Kang
Summary: The study identifies the crucial role of FveFDM1 in the growth and development of horticultural crops, specifically strawberry. FveFDM1 modulates organ size by regulating cell division and is involved in the RdDM-mediated DNA methylation process.
Article
Multidisciplinary Sciences
Nan Wang, Chaochao Li, Lihua Kuang, Xiaomeng Wu, Kaidong Xie, Andan Zhu, Qiang Xu, Robert M. Larkin, Yongfeng Zhou, Xiuxin Deng, Wenwu Guo
Summary: This study investigates the evolutionary conflicts between cytoplasmic and nuclear genomes in citrus plants. The researchers constructed a pan-mitogenome and identified chimeric open reading frames generated by extensive structural variations. They also analyzed the variations in the nuclear, mitochondrial, and chloroplast genomes of 184 citrus accessions. The findings suggest discordant interactions between the cytoplasmic and nuclear genomes due to mutation rate and levels of heteroplasmy. The study provides important implications for genetics and breeding in citrus plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Letter
Plant Sciences
David J. Mabberley, Qiang Xu
Review
Agronomy
Prakash Babu Adhikari, Qiang Xu, Michitaka Notaguchi
Summary: Plant grafting is an ancient technique used for efficient propagation and modification of plant traits. Despite its wide application, the cause behind compatible graft establishment is not fully understood. This review discusses the factors involved in successful graft establishment and highlights the challenges in understanding graft incompatibility on fruit trees.
Article
Plant Sciences
Kaijie Zhu, Hongyan Chen, Xuehan Mei, Suwen Lu, Heping Xie, Junwei Liu, Lijun Chai, Qiang Xu, Eleanore T. Wurtzel, Junli Ye, Xiuxin Deng
Summary: The MADS-box transcription factor CsMADS3 plays a regulatory role in the development and coloration of citrus fruits by coordinating chlorophyll and carotenoid metabolism. Overexpression of CsMADS3 enhances carotenoid biosynthesis and accelerates chlorophyll degradation, while interference of CsMADS3 expression inhibits carotenoid biosynthesis and chlorophyll degradation. CsMADS3 regulates the synthesis of chlorophyll and carotenoid by directly regulating genes involved in these metabolic pathways.
Article
Plant Sciences
Yawei Li, Shuting Wang, Prakash Babu Adhikari, Bing Liu, Shengjun Liu, Yue Huang, Gang Hu, Michitaka Notaguchi, Qiang Xu
Summary: Phase transition and floral induction in citrus is hindered by a long period of juvenility. The miR156-SPL pathway plays a crucial role in regulating this process. This study analyzed SPLs in 15 citrus-related species and identified SPL5, SPL9, and SPL11 as differentially expressed genes in adult and young tissues.
MOLECULAR HORTICULTURE
(2023)
Article
Horticulture
Hongfei Li, Fang Song, Xiaoxiao Wu, Chongling Deng, Qiang Xu, Shu'ang Peng, Zhiyong Pan
Summary: The study identified significant changes in rhizosphere and root bacterial genera in response to CLas infection, with particular impacts on carbohydrate metabolism and phosphoinositide signaling pathways.
Review
Biochemistry & Molecular Biology
Muhammad Junaid Rao, Hao Zuo, Qiang Xu
Summary: Citrus, originating from Southeast Asia, is one of the most important fruit crops globally, with reduction in acidity being a critical trait for domestication. The genetic model associated with domestication changes may involve a regulatory complex known as WD-repeat-MYB-bHLH-WRKY (WMBW), impacting acidification and anthocyanin accumulation. This review also summarizes domestication traits and candidate genes for breeding purposes, laying a foundation for future research on citrus acidity, flavor, and disease resistance.
PLANT COMMUNICATIONS
(2021)