Article
Biotechnology & Applied Microbiology
Xiaojie Liu, Xiaoshuang Li, Xuejing Wen, Yan Zhang, Yu Ding, Yiheng Zhang, Bei Gao, Daoyuan Zhang
Summary: This study elucidated the dynamic response mechanism of Malus sieversii to Valsa mali infection using phytohormone metabolite analysis and transcriptome analysis. Full-length transcriptomic analysis identified differentially expressed transcripts, revealing the crucial role of phytohormone signal pathway regulation and the contribution of enriched disease resistance pathways and differentially expressed transcription factors in the immune response.
Article
Biochemical Research Methods
Sebastien Guizard, Katarzyna Miedzinska, Jacqueline Smith, Jonathan Smith, Richard Kuo, Megan Davey, Alan Archibald, Mick Watson
Summary: nf-core/isoseq is a pipeline for automatic read processing and genome annotation. It follows nf-core guidelines and can be run on any platform.
Article
Biotechnology & Applied Microbiology
Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun, Jianxiong Jiang
Summary: This study identified a large number of non-redundant transcripts in Miscanthus sinensis through analyzing its full-length transcriptome data, providing important support for further research and genetic improvement of the species.
Article
Plant Sciences
Richard John Tiika, Jia Wei, Guangxin Cui, Yanjun Ma, Hongshan Yang, Huirong Duan
Summary: The study identified traits of the SeXTH gene family in S. europaea that are potential stress resistance regulators, providing a basis for future research on functional diversity.
Article
Plant Sciences
Neha Samir Roy, Ik-Young Choi, Taeyoung Um, Mi Jin Jeon, Bo-Yun Kim, Young-Dong Kim, Ju-Kyung Yu, Soonok Kim, Nam-Soo Kim
Summary: Berberis koreana is a medicinal plant that produces berberine, a bioactive compound widely used for its health benefits in the food and drug industry. Gene expression analysis and full-length cDNA sequencing were used to investigate the berberine biosynthesis pathway, revealing multiple gene isoforms and gene duplication contributing to the specificity of alkaloid synthesis. The study also showed how B. koreana streamlines berberine biosynthesis by blocking pathways leading to other benzylisoquinoline alkaloids, emphasizing the presence of specific enzymes only for berberine synthesis.
Article
Entomology
Min Liu, Feng Xiao, Jiayun Zhu, Di Fu, Zonglin Wang, Rong Xiao
Summary: This study obtained full-length transcriptome and comparative transcriptome data for T. absoluta using combined sequencing technology, and identified 21 P450 genes related to abamectin and chlorantraniliprole metabolism. The upregulation of 8 P450 genes in response to abamectin and chlorantraniliprole complex was validated by qRT-PCR.
Article
Plant Sciences
Grayson C. R. Proulex, Marcus J. Meade, Kalina M. Manoylov, A. Bruce Cahoon
Summary: Our study analyzed transcript termini in two green algae, providing insights into the differences in mitochondrial mRNA processing between chlorophytic and streptophytic algae. The findings suggest a conservation of mRNA processing among the chlorophyceae, while some processing events diverged with the split between chlorophytic and streptophytic algae.
Article
Fisheries
Kianann Tan, Peng Xu, Leong-Seng Lim, Chunhong Nie, Karsoon Tan, Ya Peng, Xiaohui Cai, Xueyu Yan, Youhou Xu, Kit Yue Kwan
Summary: This study employed various methods and technologies to investigate the molecular mechanisms of ovarian development in Fenneropenaeus penicillatus. The outcomes unveiled key pathways and expression patterns, providing a comprehensive genomic reference for future research and contributing to the development of artificial breeding techniques and sustainable aquaculture practices.
AQUACULTURE REPORTS
(2023)
Article
Plant Sciences
Lara Garcia-Campa, Luis Valledor, Jesus Pascual
Summary: To improve the quality of reference databases and their annotations, researchers combined full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics. By including Oxford Nanopore Technologies Direct RNA Sequencing (ONT-DRS) data, they enhanced the identification and discovery of proteoforms in Arabidopsis MS proteomics data. This approach offers unprecedented opportunities for investigating biological systems, but also presents challenges for existing protein searching algorithms.
Article
Biochemistry & Molecular Biology
Dongna Ma, Jingping Fang, Qiansu Ding, Liufeng Wei, Yiying Li, Liwen Zhang, Xingtan Zhang
Summary: In this study, we sequenced the transcriptome of tea leaves using PacBio sequencing technology and found that the post-transcriptional regulatory mechanism affecting the synthesis of catechins in tea is still not well understood. We identified a large number of alternative splicing and alternative polyadenylation events, which play a crucial role in regulating the catechins content.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Biology
Wirulda Pootakham, Thippawan Yoocha, Nukoon Jomchai, Wasitthee Kongkachana, Chaiwat Naktang, Chutima Sonthirod, Srimek Chowpongpang, Panyavut Aumpuchin, Sithichoke Tangphatsornruang
Summary: This study sequenced the genome of Mitragyna speciosa (Kratom) and identified important bioactive alkaloids. The high-quality genome assembly provided valuable resources for studying the alkaloid biosynthesis pathway and assessing genetic diversity.
Article
Multidisciplinary Sciences
Dandan Liu, Yidong Chen, Yixin Ren, Peng Yuan, Nan Wang, Qiang Liu, Cen Yang, Zhiqiang Yan, Ming Yang, Jing Wang, Ying Lian, Jie Yan, Fan Zhai, Yanli Nie, Xiaohui Zhu, Yuan Chen, Rong Li, Hsun-Ming Chang, Peter C. K. Leung, Jie Qiao, Liying Yan
Summary: This study used single-cell RNA sequencing to explore the gene expression characteristics of trophectoderm (TE) development during the peri-implantation period in humans and mice. The findings revealed that polar and mural TE diverged after hatching, with polar TE being more mature. The implantation poles showed similarities in cell cycle activities and gene expression related to implantation and placentation. Embryos that failed to attach or implant exhibited abnormalities in pathways related to energy production, protein metabolism, and RNA methylation.
Article
Cell Biology
Sitong Liu, Rui Wei, Hongyang Liu, Ruiqi Liu, Pengxiao Li, Xiaoyu Zhang, Wei Wei, Xiaodong Zhao, Xiaomeng Li, Yang Yang, Xueqi Fu, Kang Zou
Summary: This study demonstrates the connection between p53 and pluripotency-associated factors in the transformation of SSCs, with SMAD3 identified as a key factor. However, an unknown event is required to activate SMAD3, serving as a prerequisite for SSCs reprogramming in long-term culture.
CELL PROLIFERATION
(2022)
Article
Medicine, Research & Experimental
Yingdong Deng, Simin Tang, Jiurong Cheng, Xiangsheng Zhang, Danqin Jing, Ziqiang Lin, Jun Zhou
Summary: The dorsal root ganglion (DRG) plays an active role in the development of neuropathic pain (NP), but its mechanism in NP regulation is not fully understood. The immune system has been increasingly recognized as important in the pathogenesis of NP, particularly through immune-related genes (IRGs) and specific immune cells. However, the involvement of IRGs in DRG and their regulation of NP action has not been fully elucidated.
Article
Genetics & Heredity
Alissa M. Williams, Michael W. Itgen, Amanda K. Broz, Olivia G. Carter, Daniel B. Sloan
Summary: The angiosperm genus Silene is a model system for studying ecological and evolutionary traits in plants. This study provides genomic and transcriptomic resources for a hermaphroditic species of Silene, offering valuable insights for further research and development in plant ecology and evolution. The resources include high-quality full-length cDNA sequences and a draft assembly of the large genome size of the species, which is confirmed to be diploid.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Zhaoxu Gao, Jun Li, Li Li, Yanzhi Yang, Jian Li, Chunxiang Fu, Danmeng Zhu, Hang He, Huaqing Cai, Lei Li
Summary: This study reconstructed an integrated miRNA network in Arabidopsis, which includes core transcription factors, miRNAs, and downstream genes. The study found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops in gene regulatory networks. Further analyses revealed how miRNA-containing feed-forward loops coordinate transcription factors in different hierarchical layers and their association with miRNA hubs.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Plant Sciences
Kunlong Su, Zhenying Wu, Yuchen Liu, Shanshan Jiang, Dongmei Ma, Yan Wang, Chunxiang Fu
Summary: The study successfully increased the detoxification efficiency of switchgrass to 2,4-DNT using the synthetic NfsI gene, alleviating root growth inhibition and excessive ROS production. The transgenic switchgrass plants showed a 1.7-fold increase in 2,4-DNT removal efficiency compared to control plants, and may participate in 2,4-DNT detoxification through pathways mediated by NfsI.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Huapeng Zhou, Fei Xiao, Yuan Zheng, Guoyong Liu, Yufen Zhuang, Zhiyue Wang, Yiyi Zhang, Jiaxian He, Chunxiang Fu, Honghui Lin
Summary: PIP3 and RLK7 form a module that regulates plant salt tolerance in Arabidopsis by activating MPK3/MPK6 cascades. This study provides new insights into how plants respond to salt stress.
Article
Plant Sciences
Ruijuan Yang, Wenwen Liu, Ying Sun, Zhichao Sun, Zhenying Wu, Yamei Wang, Mengqi Wang, Honglun Wang, Shiqie Bai, Chunxiang Fu
Summary: PvLBO functions as an important gene in regulating tillering through the SL biosynthetic pathway in switchgrass, and it is activated by PvSPL2, which is targeted by miR156.
Article
Plant Sciences
Xiao Xu, Wenwen Liu, Xiaoyan Liu, Yingping Cao, Xiaoning Li, Guangyang Wang, Chunxiang Fu, Jinmin Fu
Summary: In this study, a more efficient Agrobacterium-mediated transformation method was established for improving bermudagrass. The introduction of CdHEMA1 gene successfully enhanced photosynthetic capacity, providing a solid platform for further gene function study and molecular breeding of bermudagrass.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Biochemistry & Molecular Biology
Rui Li, Yan Zhao, Zhen Sun, Zhenying Wu, Honglun Wang, Chunxiang Fu, Hongbo Zhao, Feng He
Summary: This study conducted a genome-wide analysis of the laccase multigene family in switchgrass and identified 49 laccase genes, which can be divided into five subclades. Tandem and segmental duplication of laccase genes on Chr05 and Chr08 contributed to the expansion of the gene family. Switchgrass laccases exhibited distinct tissue/organ expression patterns and responded differently to heavy metals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Zhen Yan, Man-Yu Yang, Biligen-Gaowa Zhao, Guo Li, Qing Chao, Feng Tian, Ge Gao, Bai-Chen Wang
Summary: OsAPL positively regulates seedling growth and grain size in rice by controlling the number of transporters, the expression of plasma membrane H+ -ATPase, and H+-coupled secondary active transporter genes.
Article
Agricultural Engineering
Chen Bai, Yingping Cao, Siyi Zhao, Zhenying Wu, Shaojun Dai, Honglun Wang, Chunxiang Fu
Summary: This study successfully established a genome editing platform for Monochasma savatieri for the first time using the Agrobacterium rhizogenes-mediated co-transformation system. This will enable the development of novel M. savatieri germplasm/cultivars for facility cultivation and exploitation of its medicinal value in the future.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Plant Sciences
Zhi-Fang Gao, Xiu Yang, Yingchang Mei, Jiao Zhang, Qing Chao, Bai-Chen Wang
Summary: In this study, the researchers analyzed the proteome and phosphoproteome of maize leaf samples at multiple time points during a day/night cycle. They identified new phosphosites and found that heat stimulus and changing light conditions had significant effects on protein abundance and phosphorylation. The database they generated provides valuable resources for improving C4 crop plants.
Article
Green & Sustainable Science & Technology
Kunlong Su, Yan Wang, Yuchen Liu, Meifeng Liu, Xiao Men, Haibo Zhang, Mo Xian, Zhenying Wu, Chunxiang Fu
Summary: In this study, a novel bacterial strain, Bacillus altitudinis D47, with a high capacity to biodegrade dinitrotoluene sulfonates (DNTS) was isolated and identified from TNT red water-contaminated soil. The genome of B. altitudinis D47 was sequenced, and six nitroreductases (NRs) were retrieved. Transcriptomic analysis showed that the expression of five NRs was significantly upregulated in DNTS-treated B. altitudinis D47, and enzymatic activity assay validated their nitro reduction capability. The addition of B. altitudinis D47 alleviated the phytotoxicity of DNTS to alfalfa, suggesting its potential application in the bioremediation of TNT red water-contaminated soil.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Plant Sciences
Man-Yu Yang, Xiu Yang, Zhen Yan, Qing Chao, Jie Shen, Guang-Hou Shui, Peng-Mei Guo, Bai-Chen Wang
Summary: In this study, it was found that the sugar transport protein OsTST1 in rice affects yield and development by mediating the transportation of sugar from source to sink tissues, indirectly influencing the accumulation of intermediate metabolites from the tricarboxylic acid cycle.
Article
Biotechnology & Applied Microbiology
Xiangyan Han, Shanjie Tang, Xuan Ma, Wenwen Liu, Ruijuan Yang, Shuaibin Zhang, Ningning Wang, Xianwei Song, Chunxiang Fu, Rongxin Yang, Xiaofeng Cao
Summary: This study reported a new function of miR528 in controlling biomass traits in switchgrass. Blocking miR528 activity or editing its genome can improve tillering number and regrowth rate. The up-regulation of miR528 targets is responsible for the improved traits in mutant plants.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Sheng-Ying Zhang, Biligen-Gaowa Zhao, Zhuo Shen, Ying-Chang Mei, Guo Li, Feng-Qin Dong, Jiao Zhang, Qing Chao, Bai-Chen Wang
Summary: In this study, leaf development in Populus Nanlin895 was investigated using anatomical observations and RNA-seq analysis. The results showed that mesophyll cells exhibited distinct vascular, palisade, and spongy tissue with intercellular spaces after the third leaf. RNA-seq analysis revealed that genes highly expressed in the first and second leaf were related to cell division and differentiation, while those highly expressed in the third leaf were enriched in photosynthesis. Integration of ATAC-seq and RNA-seq identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility, including 87 transcription factors (TFs). Motif enrichment analysis suggested potential regulatory functions for the DEGs through upstream TFs such as TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, this research provides a potential molecular foundation for exploring the regulatory network of leaf development.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yayu Guo, Shufang Wang, Keji Yu, Hou-Ling Wang, Huimin Xu, Chengwei Song, Yuanyuan Zhao, Jialong Wen, Chunxiang Fu, Yu Li, Shuizhong Wang, Xi Zhang, Yan Zhang, Yuan Cao, Fenjuan Shao, Xiaohua Wang, Xin Deng, Tong Chen, Qiao Zhao, Lei Li, Guodong Wang, Paul Gruenhofer, Lukas Schreiber, Yue Li, Guoyong Song, Richard A. Dixon, Jinxing Lin
Summary: Modifying plant lignin pathway to enhance saccharification efficiency often results in growth penalty. However, overexpression of Pag-miR408 in poplar can improve saccharification efficiency and growth, and laccase genes are the targets of Pag-miR408.
NATURE COMMUNICATIONS
(2023)
Article
Horticulture
Yingping Cao, Yue Xu, Yue Zhang, Heng Zhang, Zhi Qin, Chen Bai, Hailing Zhang, Dongmei Ma, Quanhua Wang, Chunxiang Fu, Meihong Sun, Shaojun Dai
Summary: CRISPR/Cas9-based gene editing system was successfully used to edit two CSLD genes involved in root hair formation in spinach hairy roots. Different mutation types and mutation rates were observed, and the homozygous/bi-allelic mutants showed changes in the root hair characteristics. Transcriptomic analysis revealed disruption of multiple gene expressions related to cell-wall modulation and membrane trafficking in the mutants.
Article
Biotechnology & Applied Microbiology
Xue-Mei Yang, Jing-Hao Zhao, Xiao-Yu Xiong, Zhang-Wei Hu, Ji-Fen Sun, Hao Su, Yan-Jing Liu, Ling Xiang, Yong Zhu, Jin-Lu Li, Sadam Hussain Bhutto, Guo-Bang Li, Shi-Xin Zhou, Chi Li, Mei Pu, He Wang, Zhi-Xue Zhao, Ji-Wei Zhang, Yan-Yan Huang, Jing Fan, Wen-Ming Wang, Yan Li
Summary: The Arabidopsis RPW8.1 gene enhances disease resistance but compromises plant growth. It has been found that RPW8.1 constitutively enhances the expression of WRKY51 transcription factor and activates salicylic acid and ethylene signaling pathways. WRKY51, in turn, suppresses RPW8.1 expression, forming a feedback regulation loop.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Hannes Claeys, Eveline Neyrinck, Lies Dumoulin, Anne Pharazyn, Arne Verstichele, Laurens Pauwels, Michael L. Nuccio, Frederic Van Ex
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Melanie Ormancey, Bruno Guillotin, Camille Ribeyre, Clemence Medina, Nathanael Jariais, Helene San Clemente, Patrice Thuleau, Serge Plaza, Martina Beck, Jean-Philippe Combier
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Edgar Perez-Matas, Diego Hidalgo-Martinez, Elisabeth Moyano, Javier Palazon, Mercedes Bonfill
Summary: In this study, the production of paclitaxel was enhanced by overexpressing the bottleneck genes BAPT and DBTNBT in Taxus baccata cells. The transgenic cells showed significantly higher expression of these genes and improved taxane production compared to the wild type. Transcriptional profiling revealed that the GGPPS, TXS, and DBAT genes were most responsive to DBTNBT overexpression and the dual elicitation treatment.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Biying Dong, Dong Meng, Zhihua Song, Hongyan Cao, Tingting Du, Meng Qi, Shengjie Wang, Jingyi Xue, Qing Yang, Yujie Fu
Summary: This study identified the involvement of the citrate transporter CcMATE35 and the long noncoding RNA CcLTCS in aluminum stress response in pigeon pea. These findings suggest that the modules CcNFYB3-CcMATE35 and CcLTCS-CcCS jointly regulate the efflux and synthesis of citrate to enhance the resistance of pigeon pea under aluminum stress.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Review
Biotechnology & Applied Microbiology
Tien V. Vu, Ngan Thi Nguyen, Jihae Kim, Jong Chan Hong, Jae-Yean Kim
Summary: Prime editing technology uses an extended guide RNA to direct a fusion peptide to a specific location in the genome, enabling precise gene editing. This groundbreaking tool has potential in improving crop varieties, but efficiency limitations exist in certain plants.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Yan Xu, Jinyi Tan, Junxing Lu, Yuelin Zhang, Xin Li
Summary: Sclerotinia sclerotiorum causes white mold in economically important plants, and the discovery of SsGAP1 and SsRAS1/SsRAS2 genes as essential regulators of fungal development and virulence provides potential targets for controlling the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Xiaoyang Chen, Chen Liu, Hailin Wang, Qi Liu, Yaping Yue, Yuhang Duan, Zhaoyun Wang, Lu Zheng, Xiaolin Chen, Yaohui Wang, Junbin Huang, Qiutao Xu, Yuemin Pan
Summary: This study identified a secreted protein, Uv1809, as a key virulence factor in Ustilaginoidea virens-rice interactions. Uv1809 inhibits rice immunity and promotes infection by targeting and enhancing rice histone deacetylase OsSRT2-mediated histone deacetylation. CRISPR-Cas9 edited ossrt2 mutants showed broad-spectrum resistance to rice pathogens, indicating its potential as a genetic resource for breeding disease resistance.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Weishuai Bi, Jing Liu, Yuanyuan Li, Ziwei He, Yongming Chen, Tingting Zhao, Xiangxiu Liang, Xiaodan Wang, Xiangzong Meng, Daolong Dou, Guangyuan Xu
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Shengjie You, Yu Wu, Wen Li, Xiaofeng Liu, Qinlan Tang, Fengkun Huang, Yan Li, Hsihua Wang, Mingchun Liu, Yang Zhang
Summary: In this study, a transcription factor called SlERF.G3-Like in tomato was found to play a role in regulating ethylene synthesis, cell wall degradation, and the flavonoid pathway. The researchers also discovered the interaction between SlERF.G3-Like and the master ripening regulator SlRIN, and increased the production of resveratrol derivatives through genetic manipulation. These findings provide insights into the coordination of fruit maturation and metabolic changes in tomatoes, and have implications for metabolic engineering.
PLANT BIOTECHNOLOGY JOURNAL
(2024)
Article
Biotechnology & Applied Microbiology
Thomas R. Aalders, Mara de Sain, Fleur Gawehns, Nina Oudejans, Yoran D. Jak, Henk L. Dekker, Martijn Rep, Harrold A. van den Burg, Frank L. W. Takken
Summary: The TPL1 and TPL2 genes in tomato are closely associated with susceptibility to Fusarium wilt disease, and mutating these genes can enhance plant resistance to the disease.
PLANT BIOTECHNOLOGY JOURNAL
(2024)