Article
Biotechnology & Applied Microbiology
Chenna Swetha, Anushree Narjala, Awadhesh Pandit, Varsha Tirumalai, P. Shivaprasad
Summary: This study improved a tool for validating sRNA targets with better accuracy and efficiency. Analysis of degradome data from wild and cultivated rice revealed multiple targeting differences under miRNA mediation and different mRNA targets of secondary sRNAs.
Article
Plant Sciences
Byron R. R. Manzanero, Krishnanand P. P. Kulkarni, Nicholi Vorsa, Umesh K. K. Reddy, Purushothaman Natarajan, Sathya Elavarthi, Massimo Iorizzo, Kalpalatha Melmaiee
Summary: This study investigated the genetic structure and relationships of 195 blueberry accessions using SNP markers generated from GBS data. The results revealed three major clusters of blueberry accessions, with V. boreale and V. darrowii, as well as V. myrsinites and V. tenellum, showing close genetic relationships. In addition, migration events and genetic divergence among blueberry species were identified through gene flow and admixture analysis.
Article
Plant Sciences
Salma Rouichi, Omar Idrissi, Quahir Sohail, Helene Marrou, Thomas R. Sinclair, Kamal Hejjaoui, Moez Amri, Michel Edmond Ghanem
Summary: Many wild lentil accessions have a lower breakpoint in transpiration rate response to increasing vapor pressure deficit (VPD) compared to cultivated lentil, suggesting that the limited-transpiration trait could be beneficial for water conservation and yield improvement in drought-prone areas. The transpiration rate response to high VPD varies greatly among wild lentil accessions, with 43 accessions exhibiting a breakpoint in their response. Field experiments also demonstrate that the breakpoint level positively affects yield and yield-related parameters. Selecting genotypes with a lower breakpoint could enhance lentil productivity in drought-prone areas.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Peiting Li, Pingping Lin, Zhenli Zhao, Zihong Li, Yanming Liu, Chaohua Huang, Guoqiang Huang, Liangnian Xu, Zuhu Deng, Yu Zhang, Xinwang Zhao
Summary: This study compared highly drought-resistant and weakly drought-resistant sugarcane genotypes to understand the molecular mechanisms of drought stress. The results showed physiological and transcriptomic differences between the two genotypes under drought stress. Signaling pathway activation, water deprivation response, and photosynthesis-related processes play important roles in drought tolerance in sugarcane.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Mu-Fan Geng, Xiu-Hua Wang, Mei-Xia Wang, Zhe Cai, Qing-Lin Meng, Xin Wang, Lian Zhou, Jing-Dan Han, Ji-Long Li, Fu-Min Zhang, Ya-Long Guo, Song Ge
Summary: Through whole transcriptomic sequencing, differences in susceptibility to drought stress among different samples were revealed, as well as identified specific transcription factors and genes critical in rice adaptation to drought. Additionally, unique drought-responsive genes or pathways in wild rice underscore the importance of wild resources in developing elite cultivars. The enrichment of drought-responsive genes in clusters or hotspots in the genome suggests a complex genetic architecture underlying drought tolerance traits.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Biochemical Research Methods
Sara Jalili, Kazem Arzani, Angela S. Prudencio, Juan A. Salazar, Pedro J. Martinez-Garcia, Naser Bouzari, Pedro Martinez-Gomez
Summary: Knowledge of the genetic potential of wild Prunus species is crucial for germplasm conservation and breeding strategies. This study analyzed cultivated sweet cherry and wild Cereus subgenus genotypes to understand their response to drought stress. Integrated morphological, physiological, genomic, and transcriptomic analyses were conducted, revealing differences in leaf morphology, gas exchange, and gene expression among the genotypes. The results contribute to understanding the molecular and physiological mechanisms of drought tolerance in cherries and emphasize the potential of wild cherries for drought resistance breeding programs.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Review
Plant Sciences
Paulina Koscielniak, Paulina Glazinska, Jacek Kesy, Marcin Zadworny
Summary: Despite being long-lived, trees are exposed to external stimuli and adverse environmental conditions, with certain trees like oaks evolving taproots to increase water acquisition. Little is known about the regulation of taproot growth through internal factors, such as genes and phytohormones, or the impact of external factors like drought. Further research is needed to understand the complex signaling pathways involved in taproot growth regulation.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Ranjita Thapa, Matthew Edwards, Matthew W. Blair
Summary: This study evaluated the genetic diversity in a collection of cultivated and wild species of Amaranthus using SNP markers, revealing high variability with an average polymorphism information content of 0.365. Population structure analysis identified two sub populations, and phylogeny demonstrated the relationships among the different species.
Article
Horticulture
Johan Rodriguez Melo, Maria Laura Tonelli, Maria Carolina Barbosa, Federico Ariel, Zifan Zhao, Jianping Wang, Adriana Fabra, Fernando Ibanez
Summary: In this study, members of the LysM-RLK family in the peanut genome were identified and the evolutionary history of the family was reconstructed. These proteins are involved in symbiosis development and defense responses, and may play a role in the receptor network mediating the perception of Nod factors and chitosan.
Article
Plant Sciences
Hongyong Qiao, Danlei Gao, Tao Yuan
Summary: This study found that both wild and cultivated P. ludlowii species were able to flower and fruit normally, but wild species had a higher number of flowers and fruits, as well as higher soil available phosphorus and available potassium contents than cultivated species. The community assembly mechanisms of rhizosphere soil fungi in both wild and cultivated species were primarily stochasticity, with no significant differences between them. Cultivated species had a higher proportion of fungi that can easily cause diseases, and the network connections among fungi were weaker in cultivated species, which increased their susceptibility to external environmental interferences.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Ning Li, Qiang He, Juan Wang, Baike Wang, Jiantao Zhao, Shaoyong Huang, Tao Yang, Yaping Tang, Shengbao Yang, Patiguli Aisimutuola, Ruiqiang Xu, Jiahui Hu, Chunping Jia, Kai Ma, Zhiqiang Li, Fangling Jiang, Jie Gao, Haiyan Lan, Yongfeng Zhou, Xinyan Zhang, Sanwen Huang, Zhangjun Fei, Huan Wang, Hongbo Li, Qinghui Yu
Summary: Researchers constructed a tomato super-pangenome using chromosome-scale genomes of nine wild species and two cultivated accessions, revealing the genomic diversity and structural variation across wild and cultivated tomatoes.
Article
Plant Sciences
Arun Kumar C. Huded, Pavankumar Jingade, Manoj Kumar Mishra, Sezai Ercisli, Gulce Ilhan, Romina Alina Marc, Dan Vodnar
Summary: In this study, a NAC25-like transcription factor was isolated and characterized from different coffee species. The gene structure, variation, and expression of the NAC25 gene were analyzed. The study demonstrated differential expression of NAC25 in different tissues and revealed the independent evolution of NAC25 in coffee.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Shafaque Sehar, Muhammad Faheem Adil, Muhammad Zeeshan, Paul Holford, Fangbin Cao, Feibo Wu, Yizhou Wang
Summary: This study examined the genotypic responses to drought stress and potassium nutrition in Tibetan barley genotypes, finding that the wild barley genotype XZ5 exhibited the highest tolerance to drought stress due to its ability to retain potassium, higher ATPase activity, increased K+ and Ca2+ content, and enhanced antioxidative performance. These findings suggest that Tibetan wild barley genotypes could serve as a valuable genetic resource for improving potassium metabolism and combating drought stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Radka Vrancheva, Ivan Ivanov, Ivayla Dincheva, Ilian Badjakov, Atanas Pavlov
Summary: The study identified and quantified triterpenoids and other non-polar compounds in blueberry leaves using GC-MS and HPLC-DAD. Results showed significant differences in metabolite profiles among different Vaccinium species and populations, likely influenced by climatic and geographical conditions.
Article
Biochemistry & Molecular Biology
Carlos Lopez-Ortiz, Yadira Pena-Garcia, Menuka Bhandari, Venkata Lakshmi Abburi, Purushothaman Natarajan, John Stommel, Padma Nimmakayala, Umesh K. Reddy
Summary: This study analyzed miRNA contents in cultivated and wild pepper species, revealing differentially expressed miRNAs across species and tissues. Key pathways regulated by miRNAs during pepper fruit ripening include amino acids, sugar and nucleotide metabolism, and starch and sucrose metabolism. Predicted miRNA-target gene interactions provide insights into the mechanisms regulating flowering time and fruit development in Capsicum species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Dahai Liu, Li Liu, Kui Duan, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou, Yun Zheng
Summary: The study found that the transcriptional activities of hundreds of TEs were dynamically regulated during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells. Furthermore, certain Long Terminal Repeats (LTRs) and integrase elements of MacERV3 were transiently activated during the early stages of conversion and potentially bound by critical transcription factors for reprogramming such as KLF4 and ETV5. These results suggest a conserved mechanism in primates for converting fibroblast cells to stem cells through the activation of certain ERVs.
Article
Biotechnology & Applied Microbiology
Yaping Yan, Shuchao Ren, Yanchao Duan, Chenyu Lu, Yuyu Niu, Zhengbo Wang, Briauna Inglis, Weizhi Ji, Yun Zheng, Wei Si
Summary: The study found that A53T transgenic monkeys with early Parkinson's symptoms exhibited higher diversity in gut microbiota and significantly elevated specific metabolites, with the altered metabolites mainly associated with mitochondrial dysfunction.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Biochemistry & Molecular Biology
Chandra Obul Reddy Puli, Yun Zheng, Yong-Fang Li, Guru Jagadeeswaran, Angbaji Suo, Bingbing Jiang, Pradeep Sharma, Robert Mann, Govindan Ganesan, Nirmali Gogoi, Asha Srinivasan, Aparna Kakani, Vijaya Gopal Kakani, Abdelali Barakat, Ramanjulu Sunkar
Summary: This study analyzed the miRNA profiles in leaves of sorghum exposed to individual drought, heat, or combined stresses, identifying differentially regulated miRNA families and confirming 48 target genes. The results showed stronger miRNA regulation under heat or combination of heat and drought compared to drought alone, providing insights into miRNA-guided gene regulations under combined stresses.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Shiyong Guo, Jun Yang, Bingbing Jiang, Nan Zhou, Hao Ding, Guangchen Zhou, Shuai Wu, Angbaji Suo, Xingwang Wu, Wenping Xie, Wanran Li, Yulong Liu, Wei Deng, Yun Zheng
Summary: This study identified miRNA editing sites and SNPs in the brains of Huntington's disease (HD) patients, and found significantly different editing levels in the prefrontal cortex. Furthermore, the edited hsa-mir-10b was shown to downregulate GTPBP10, which may contribute to the progression of HD.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Han Lin, Shiyong Guo, Song Li, Jihong Shen, Jianfeng He, Yun Zheng, Zhenhua Gao
Summary: This study identified differentially expressed mRNAs and miRNAs in acute urethral injuries, and found that they are involved in various biological processes and signaling pathways. These findings contribute to the understanding and treatment of urethral injuries.
Editorial Material
Biochemical Research Methods
Yun Zheng
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Junpeng Zhang, Yun Zheng, Juan Xu
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Neurosciences
Xingwang Wu, Huaide Yang, Han Lin, Angbaji Suo, Shuai Wu, Wenping Xie, Nan Zhou, Shiyong Guo, Hao Ding, Guangchen Zhou, Zhichao Qiu, Hong Shi, Jun Yang, Yun Zheng
Summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with unclear pathogenesis. Recent research has shown that miRNAs are edited in various ways, especially in the central nervous system. This study analyzed miRNA-seq samples from ASD patients and normal controls, and identified 70 significantly different editing sites in the superior frontal gyrus samples of ASD patients. Increased expression of ADAR1 was found to be consistent with the increased editing level of hsa-mir-376a-1_9_A_g in ASD-SFG samples. This study provides new insights into the mechanism of ASD.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Genetics & Heredity
Yikun Zhou, Jianmei Liu, Shuai Wu, Wanran Li, Yun Zheng
Summary: Weiss-Kruszka syndrome (WSKA) is a rare disease caused by mutations in the ZNF462 gene. A new mutation site is reported in this study, and further research is needed to understand the role of this gene in the development of WSKA.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Chenyu Lu, Shuchao Ren, Wenping Xie, Zhigang Zhao, Xingwang Wu, Shiyong Guo, Angbaji Suo, Nan Zhou, Jun Yang, Shuai Wu, Yun Zheng
Summary: By analyzing small RNA sequencing profiles of brain tissues of 43 PD patients and 88 normal controls, researchers found that there were significantly different editing levels of 362 miRNA editing sites in the prefrontal cortices of PD patients compared to normal controls. They also experimentally validated that the significantly increased expression of miR-497-5p directly represses OPA1 and VAPB, contributing to enhanced progressive neurodegeneration in PD patients. These findings provide new insights into the mechanistic understanding, novel diagnostics, and therapeutic clues of PD.
Article
Biochemistry & Molecular Biology
Wenping Xie, Jun Yang, Nan Zhou, Hao Ding, Guangchen Zhou, Shuai Wu, Shiyong Guo, Wanran Li, Lei Zhang, Huaide Yang, Chunyi Mao, Yun Zheng
Summary: This study explored the miRNA editing patterns in three subtypes of leukemia and identified hundreds of miRNA editing sites. Differential editing of miRNAs was observed in different subtypes of leukemia. The predicted targets of edited miRNAs were also investigated, providing insights into the functional relevance of miRNA editing in leukemia.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Editorial Material
Genetics & Heredity
Yun Zheng, Zexuan Zhu
FRONTIERS IN GENETICS
(2023)
Review
Cell Biology
Wanran Li, Yun Zheng
Summary: Alzheimer's disease (AD) is a neurodegenerative disease that affects memory, language, and thinking. Over 55 million people were diagnosed with AD or other forms of dementia worldwide in 2020. MicroRNAs (miRNAs) have been found to play important roles in AD development and have potential applications in diagnosis and treatment. Extracellular vesicles (EVs) containing miRNAs are present in body fluids and are involved in cell-to-cell communication. This study summarizes the dysregulated miRNAs in EVs derived from different body fluids and brain tissues of AD patients, and discusses their potential functions and applications in AD. Certain miRNAs, such as miR-125b-5p and miR-9-5p, show promise as diagnostic markers and potential therapeutic targets for AD.
Editorial Material
Biotechnology & Applied Microbiology
Esra Busra Isik, Michelle D. Brazas, Russell Schwartz, Bruno Gaeta, Patricia M. Palagi, Celia W. G. van Gelder, Prashanth Suravajhala, Harpreet Singh, Sarah L. Morgan, Hilyatuz Zahroh, Maurice Ling, Venkata P. Satagopam, Annette McGrath, Kenta Nakai, Tin Wee Tan, Ge Gao, Nicola Mulder, Christian Schonbach, Yun Zheng, Javier De Las Rivas, Asif M. Khan
Summary: Given the growing demand for bioinformatics expertise in the life sciences, a collective effort is required to proactively evaluate and address the challenges of educating and training life scientists with the requisite skills and competencies.
NATURE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Robert E. Paull, Najla Ksouri, Michael Kantar, Dessiree Zerpa-Catanho, Nancy Jung Chen, Gail Uruu, Jingjing Yue, Shiyong Guo, Yun Zheng, Ching Man Jennifer Wai, Ray Ming
Summary: Pineapple and ornamental bromeliads can be induced to flower by ethylene treatment, which activates ethylene response transcription factors and various genes involved in flower development. These candidate genes can be potential targets for genetic manipulation to understand their molecular roles in flower transition.
