Article
Forestry
Yapeng Li, Ruiyang Hu, Yuhan Sun, Jinliang Xu, Yongbin Qiu, Yousry A. A. El-Kassaby, Huahong Huang, Huiquan Zheng, Yun Li
Summary: By conducting phenotypic observations, physiological and biochemical measurements, and transcriptome analysis, we found significant differences between embryonic callus (EC) and non-embryogenic callus (NEC) in Chinese fir. The comparison of transcriptomes also revealed specific gene expression patterns in callus, which could contribute to the rapid propagation of Chinese fir.
Article
Fisheries
Rongkang Tang, Yefei Zhu, Wu Gan, Yu Zhang, Ziliang Yao, Jianfeng Ren, Mingyou Li
Summary: This study performed transcriptome sequencing on the adult testis and ovary of Opsariichthys bidens to identify sex-related genes. A total of 50,321 unigenes were obtained and analyzed for differential gene expression. The expression levels of nine sex-related genes were confirmed by qRT-PCR. The results provide basic support for further research on the function of sex-related genes and the molecular mechanisms of sex determination in O. bidens.
AQUACULTURE REPORTS
(2022)
Article
Plant Sciences
Xiaoyue Cui, Pingying Zhang, Chengcheng Chen, Jianxia Zhang
Summary: In this study, it was found that the VyUSPA3 gene can enhance drought tolerance in grapevines by interacting with hormone signaling, ubiquitination system, ethylene-responsive element binding factor, and nuclear factors.
PLANT CELL REPORTS
(2023)
Article
Entomology
Ran Rosen, Galina Lebedev, Svetlana Kontsedalov, David Ben-Yakir, Murad Ghanim
Summary: The study explored the molecular and biological basis of resistance to spinosad in onion thrips populations, highlighting metabolic resistance mechanisms and increased fecundity in resistant populations. The research provides valuable genetic resources and insights for future studies on insect pest resistance in agriculture.
Article
Agriculture, Multidisciplinary
Suwen Lu, Jiayang Wang, Yaxian Zhuge, Mengwei Zhang, Chang Liu, Haifeng Jia, Jinggui Fang
Summary: This study integrated multi-omics data to explore global metabolic and transcriptional profiles in grape skins and pulps, revealing large-scale differences in the flavonoid metabolic pathway. The identified flavonoids, including flavone and flavone C-glycosides, showed a positive correlation with anthocyanins in grapes. The study also identified novel transcription factors and ubiquitin proteins as promising regulatory candidates for flavonoid biosynthesis in grapes, providing valuable information for the development of grape health products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Plant Sciences
Yafan Hu, Hongjuan Zhang, Bao Gu, Jianxia Zhang
Summary: Expression of VaMYC2 enhances cold tolerance of transgenic grapes by increasing accumulation of osmotic regulatory substances, improving cell membrane stability, enhancing antioxidant enzyme activity, and activating expression of cold tolerance-related genes. VaMYC2 interacts with VaJAZ1 and VaJAZ7 and activates the expression of VaCBF1 and VaP5CS to mediate cold tolerance in grapes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Matin Miryeganeh, Hidetoshi Saze
Summary: Mangrove trees, with their high adaptability to difficult coastal conditions, serve as an interesting model system for understanding stress tolerance in plants. This study utilized RNA-Seq to characterize the leaf transcriptome of the Bruguiera gymnorhiza species and compared gene expression profiles between populations growing under different levels of stress, providing valuable insights into plant adaptations. Genes related to salt and osmotic stress showed elevated expression levels in trees growing in high salinity conditions, suggesting potential targets for future research on salt resistance in mangroves and other woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
P. Vignesh, C. Mahadevaiah, R. Parimalan, R. Valarmathi, S. Dharshini, Singh Nisha, G. S. Suresha, S. Swathi, H. K. Mahadeva Swamy, V Sreenivasa, K. Mohanraj, G. Hemaprabha, Ram Bakshi, C. Appunu
Summary: A comparative study on salt-responsive genes and metabolic pathways between salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010 revealed that IND99-907 exhibited higher proline content, higher relative water content, intact root anatomical structures, and lower Na+/K+, Ca2+/K+, and Mg2+/K+ ratio compared to Co 97010. The differences in gene expression patterns and metabolic pathways between the two genotypes indicate unique characteristics of each in response to salt stress.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Gopal Peddinti, Hannu Hotti, Teemu H. Teeri, Heiko Rischer
Summary: In this study, the first-ever transcriptome sequencing of poison hemlock was conducted using next-generation RNA sequencing approach, resulting in a high-quality transcriptome assembly. The focus of the study was on describing the coniine pathway and identifying several enzymes related to coniine biosynthesis. Further in vitro testing will be necessary to confirm the functions of the selected candidates.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Chen Jiao, Xuepeng Sun, Xiaoxiao Yan, Xiaozhao Xu, Qin Yan, Min Gao, Zhangjun Fei, Xiping Wang
Summary: Comparative transcriptome profiling of two Chinese wild grape accessions with varying resistance levels to Erysiphe necator revealed a higher proportion of down-regulated genes in the susceptible variety, Hunan-1, at every infection stage. In contrast, the resistant variety, Shang-24, showed a greater number of up-regulated genes, suggesting a potential molecular basis for grape resistance to powdery mildew disease caused by E. necator.
Article
Plant Sciences
Carolina Enriquez-Gonzalez, Cristina Garciduenas-Pina, Osvaldo Adrian Castellanos-Hernandez, Sergio Enriquez-Aranda, Abraham Loera-Muro, Gilberto Ocampo, Eugenio Perez-Molphe Balch, Jose Francisco Morales-Dominguez
Summary: In this study, a de novo transcriptome of Mammillaria bombycina was obtained for the identification and expression analysis of genes related to abiotic stress. The study identified 13 isoforms of genes belonging to glyoxalase pathway and observed their expression under in vitro and ex vitro conditions.
Article
Genetics & Heredity
Liqiang Zhao, Shengxiang Zhang, Chunmiao Shan, Yuanyuan Shi, Huan Wu, Jiawen Wu, Daiyin Peng
Summary: This study revealed the transcriptome information of Angelica dahurica and identified key genes related to coumarin biosynthesis. The research laid the foundation for further exploration of this biosynthetic pathway.
Article
Genetics & Heredity
Rongfei Zhang, Yuanyuan Miao, Lingyun Chen, Shanyong Yi, Ninghua Tan
Summary: This study unveiled the genes involved in anthraquinone biosynthesis and their regulation in R. yunnanensis using high-throughput sequencing technology. Treatment with Methyl Jasmonate significantly increased the expression of specific genes and anthraquinone contents.
Article
Plant Sciences
Wei Long, Xiaohua Yao, Kailiang Wang, Yu Sheng, Leyan Lv
Summary: In this study, the gene expression and global gene expression profiles during Camellia oleifera seed germination were analyzed using transcriptome sequencing. Differentially expressed genes were identified, indicating the role of cotyledons in seed germination and seedling growth. This study will contribute to the breeding and cultivation of C. oleifera.
Article
Biochemistry & Molecular Biology
Jingyin Yu, Shan Wu, Honghe Sun, Xin Wang, Xuemei Tang, Shaogui Guo, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Cecilia McGregor, Susanne S. Renner, Sandra Branham, Chandrasekar Kousik, W. Patrick Wechter, Amnon Levi, Rebecca Grumet, Yi Zheng, Zhangjun Fei
Summary: The Cucurbit Genomics Database is an important resource for studying cucurbit plants, providing large-scale genomic data and functionally annotated information. The database contains reference genomes, variome data, and gene expression profiles for multiple cucurbit species, facilitating efficient mining, analysis, and dissemination of these datasets. It plays a significant role in advancing cucurbit research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Chaofan Zhang, Chen Jiao, Xuepeng Sun, Xiaolong Li
Summary: This study conducted a comprehensive analysis of the MYB superfamily in 437 different plant species to explore its evolutionary contributions to species diversification, trait formation, and environmental adaptation. The research revealed major changes in gene copy number and genomic context within subclades and proposed the role of transposable element insertion in promoting sub-/neo-functionalization of MYB genes. It emphasizes the importance of lineage-/tissue-specific characterization to understand trait variability and environmental adaptation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Min Xu, Qiang Gao, Mengwei Jiang, Wenling Wang, Juan Hu, Xiaojun Chang, Dinggao Liu, Yuwei Liang, Yifan Jiang, Fei Chen, Chuhao Li, Haoran Huang, Feng Chen, Fan Li, Robert N. Trigiano, Jihua Wang, Chen Jiao, Xiaofan Zhou, Liangsheng Zhang
Summary: Jasminum sambac is a well-known plant known for its attractive fragrance and its flowers are used to produce scented tea. This study provides insights into the genetic basis of aromatic volatile production and salicylic acid and jasmonate accumulation in J. sambac under non-stress conditions through comprehensive comparative genomic, transcriptomic, and metabolomic analyses. The findings offer valuable genomic resources for further utilization of natural products.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Wenyong Shao, Kewei Sun, Tianling Ma, Huixian Jiang, Matthias Hahn, Zhonghua Ma, Chen Jiao, Yanni Yin
Summary: SUMOylation plays crucial roles in multiple biological processes in eukaryotic organisms. This study reveals the regulatory functions of SUMOylation in low-temperature survival and oxidative DNA damage tolerance during infection in B. cinerea. SUMOylated BcSsb affects the stability of microtubules and consequently mycelial growth at low temperature, while SUMOylated BcRad18 modulates the mono-ubiquitination of pcna involved in oxidative DNA damage response during infection.
Article
Agronomy
Bei Liu, Xingxing Liang, Jinchao Kong, Chen Jiao, Hongye Li, Yunpeng Gai
Summary: In this study, the genetic structure and diversity of Colletotrichum gloeosporioides, the dominant species causing citrus anthracnose, were analyzed using the Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. A total of 19 GAPDH haplotypes were identified, with the main haplotype (haplotype 5) distributed widely among isolates from different Citrus species and locations. The genetic differentiation index (Fst) revealed significant genetic differentiation between populations from different regions and host species. The results suggest that genetic differentiation in C. gloeosporioides is mainly influenced by gene mutation, recombination, or migration within native populations rather than natural selection caused by geography or host variety.
Article
Plant Sciences
Philippe Nicolas, Richard J. Pattison, Yi Zheng, Taly Lapidot-Cohen, Yariv Brotman, Sonia Osorio, Alisdair R. Fernie, Zhangjun Fei, Carmen Catala
Summary: Tomato fruits with disrupted starch biosynthesis undergo significant transcriptional and metabolic remodeling, affecting central carbohydrate and lipid metabolism and impacting stress responses. The lack of carbon flow into starch leads to increased levels of soluble sugars, readjustment of metabolism, and activation of growth and stress protection pathways. These findings provide insights into the effects of carbohydrate metabolism perturbations on tomato fruit development and potential implications for enhancing protective mechanisms against abiotic stress in fleshy fruit.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Mei Liu, Baoshan Kang, Huijie Wu, Miguel A. Aranda, Bin Peng, Liming Liu, Zhangjun Fei, Ni Hong, Qinsheng Gu
Summary: This study reveals that SA-induced flavonoid biosynthesis plays a critical role in watermelon development and resistance to CGMMV. Understanding the defense mechanism of watermelon against CGMMV infection is essential for managing viral diseases in agriculture.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Xiaofen Yu, Mengyun Qin, Minghao Qu, Quan Jiang, Sumin Guo, Zhenghai Chen, Yufang Shen, Guodong Fu, Zhangjun Fei, Hongwen Huang, Lei Gao, Xiaohong Yao
Summary: Despite a lack of documented homoploid hybridization events in plants, this study provides insights into the evolutionary consequence of homoploid hybridization in kiwifruit species. Through genome sequencing and population genomic analyses, the study reveals that A. zhejiangensis is mainly composed of F-1 hybrids of A. hemsleyana and A. eriantha, with gene flow initiating about 0.98 million years ago. The study also identifies five inversions containing genes related to pollen germination and pollen tube growth that may account for the fertility breakdown in hybrids. Despite distinct morphological traits, A. zhejiangensis does not initiate speciation.
Article
Plant Sciences
Yuxin Shen, Zhengrui Qin, Gaojie Ren, Pingchuan Deng, Wanquan Ji, Chen Jiao, Liang Wu
Summary: Alternative splicing mediated by SCL33, SCL33L, and miR156 is involved in phase transitions in Brachypodium, regulating intron assembly and miR156 targets in growth transitions.
Article
Plant Sciences
Dong Meng, Hongyan Cao, Qing Yang, Mengxia Zhang, Ewa Borejsza-Wysocka, Huicong Wang, Abhaya M. Dandekar, Zhangjun Fei, Lailiang Cheng
Summary: Sorbitol, a major photosynthate in apple and other tree fruits, stimulates its own metabolism through the SnRK1-mediated phosphorylation of bZIP39. SnRK1 interacts with and phosphorylates bZIP39, a transcription factor that activates the expression of key enzymes in sorbitol metabolism. This study reveals the molecular mechanism of how sorbitol regulates its own metabolism and integrates sorbitol signaling into the sugar signaling network to modulate plant carbohydrate metabolism.
Article
Agronomy
Yunpeng Gai, Qichen Niu, Jinchao Kong, Lei Li, Xingxing Liang, Yuwei Cao, Xianqi Zhou, Xuepeng Sun, Haijie Ma, Mingshuang Wang, Neeraj Shrivastava, Hongye Li, Chen Jiao
Summary: A comparative transcriptome analysis was performed to study the gene expression patterns of Alternaria alternata during infection of citrus. Significant gene expression differences were found between the early and late stages of infection. Several novel genes related to plant-pathogen interaction were identified. RT-qPCR analysis confirmed the expression patterns of selected genes from the peroxisome pathway.
Article
Agronomy
Lei Li, Rongjie Wang, Xingxing Liang, Yunpeng Gai, Chen Jiao, Meiqin Wang
Summary: The present study provides a comprehensive overview of Bacillus velezensis strain Htq6 and its potential applications in plant disease control. The study conducted genomic analysis and transcriptome analysis to better understand the strain's biological control mechanism and response to pathogens. The results show promise for the development of an effective biocontrol agent for various plant diseases.
Article
Microbiology
Wen Wang, Tao Xiong, Yating Zeng, Wenwen Li, Chen Jiao, Jianping Xu, Hongye Li
Summary: This study conducted an extensive survey of Phyllosticta species across 11 citrus-producing provinces in southern China and identified five Phyllosticta species with pathogenicity on different citrus species. The findings have important implications for the control and management of Citrus Black Spot and related diseases.
Article
Agronomy
Xingxing Liang, Qichen Niu, Jinchao Kong, Xiaoyan Zhao, Bin Zhang, Lei Li, Chen Jiao, Yunpeng Gai
Summary: Antioxidant molecules play a crucial role in regulating redox homeostasis in fungi. This study identified a component called AaBemA involved in the regulation of the antioxidant system in Alternaria alternata. Loss-of-function analysis revealed the importance of AaBemA in response to oxidative stress. The study also revealed the interaction of multiple genes in the antioxidant system and their role in oxidative stress response.
Article
Genetics & Heredity
Anze Svara, Honghe Sun, Zhangjun Fei, Awais Khan
Summary: In this study, long-read sequencing and in silico gene sequence characterization were used to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Multiple highly homologous DNA sequences were identified on linkage groups 1 and 6, and two candidate genes located close to the scab-resistance marker Ch-Vf1 were found. This study provides novel genomic resources and identifies candidate genes for further resistance characterization.
G3-GENES GENOMES GENETICS
(2023)