Article
Biochemistry & Molecular Biology
Yongfeng Song, Zhichao Lv, Yue Wang, Chunxiang Li, Yue Jia, Yong Zhu, Mengna Cao, Yu Zhou, Xing Zeng, Zhenhua Wang, Lin Zhang, Hong Di
Summary: Seed storability is an important trait for grain quality and germplasm conservation. This study identified miRNAs and target genes involved in seed storability in maize by miRNA sequencing and analysis. Transcriptome sequencing and RT-PCR confirmed six pairs of differentially expressed miRNAs associated with seed storability, along with their negative target genes. The enrichment analysis suggested that the regulation of seed storability involves ethylene activation signaling pathway, hormone synthesis and signal transduction, and plant organ morphogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Yuhua Fu, Pengyu Fan, Lu Wang, Ziqiang Shu, Shilin Zhu, Siyuan Feng, Xinyun Li, Xiaotian Qiu, Shuhong Zhao, Xiaolei Liu
Summary: This study utilized massive public data to improve the annotation of known miRNAs, identify a large number of novel miRNAs, and predict target genes for all pig miRNAs. The correlation-based strategy provided a new perspective for predicting target genes of miRNAs, offering additional evidence of expression compared with traditional methods, and is applicable to other nonmodel organisms with incomplete annotation information.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Forestry
Zhiquan Wang, Fengjiao Zhang, Qin Shi, Rui Zhang, Yunlong Yin, Chaoguang Yu
Summary: This study aimed to discover the miRNAs responding to salt stress. Small RNA sequencing was performed in the salt-tolerant Taxodium hybrid 'Zhongshanshan 405' and 52 differentially expressed miRNAs were found. Enrichment analysis of target genes showed that miRNAs may play key roles in regulating the tolerance to salt stress in 'Zhongshanshan 405'. The study also identified two important genes regulated by miRNAs under salt treatment, which can be selected for future research.
Article
Plant Sciences
Claudia Gutierrez-Garcia, Shiek S. S. J. Ahmed, Sathishkumar Ramalingam, Dhivya Selvaraj, Aashish Srivastava, Sujay Paul, Ashutosh Sharma
Summary: This study utilized high-throughput sequencing technology to analyze the miRNA profile of Murraya koenigii and identified miRNAs associated with secondary metabolite biosynthesis. The results showed that these miRNAs targeted key enzymes in the terpenoid backbone and flavonoid biosynthesis pathways. The sequencing results were validated by qPCR. This is the first report of the miRNA profile of Murraya koenigii, providing valuable information for studying the involvement of miRNAs in secondary metabolism.
Article
Genetics & Heredity
Jiefei Nai, Tieming Ma, Yingjie Liu, Yunwei Zhou
Summary: In this study, high-throughput sequencing was used to identify known and new miRNAs in the Chrysanthemum variety Niu 9717. The miRNAs were found to form miRNA-target pairs with mRNAs in the root and leaf, and were involved in pathways related to hormone signaling during plant growth and development.
Article
Veterinary Sciences
Aiyou Wen, Wei Zhang, Jingen Xu, Kunping Wang, Hong Hu
Summary: The study found that eccDNAs and ecDNAs are present in both Wei pig (WP) and Large White pig (LP), and they both have sizes large enough to carry one or several partial or complete genes. These findings have expanded our understanding of circular DNA in pigs and will serve as a reference for using pigs as a medical model and discovering new genetic markers for selecting high-quality breeds.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Obstetrics & Gynecology
Yihong Luo, Long Cui, Lina Chen, Lele Wang, Kaiyuan Ji, Huishu Liu
Summary: This study identified differentially expressed lncRNAs in the human myometrium during labor and non-labor using RNA sequencing and bioinformatic analysis. The enriched analysis showed that these lncRNAs are associated with mRNA splicing, ferroptosis, FGFR, and NOTCH signaling pathways.
REPRODUCTIVE SCIENCES
(2022)
Article
Rheumatology
Rodrigo Coutinho de Almeida, Ahmed Mahfouz, Hailiang Mei, Evelyn Houtman, Wouter den Hollander, Jamie Soul, Eka Suchiman, Nico Lakenberg, Jennifer Meessen, Kasper Huetink, Rob G. H. H. Nelissen, Yolande F. M. Ramos, Marcel Reinders, Ingrid Meulenbelt
Summary: Through transcriptomic data, two distinct OA subtypes were identified in cartilage tissue, characterized by unique OA pathophysiological processes in cartilage as well as clinical features. Analysis of preserved cartilage samples revealed differences in gene expression related to chemokine pathways, and integration of clinical data showed differences in joint space narrowing and osteophyte scores between subtypes. Further research and data integration are needed for personalized care and improved treatment responses.
Review
Chemistry, Physical
Na Li, Qingqing Cai, Qing Miao, Zeshi Song, Yuan Fang, Bijie Hu
Summary: Sequencing technology is increasingly being used in clinical laboratories, with metagenomic next-generation sequencing (mNGS) emerging as an attractive method for comprehensive detection and classification of microorganisms. However, there are still several challenges to be overcome in clinical practice.
Article
Environmental Sciences
Man Ning, Huimin Li, Zheng Xu, Lei Chen, Yiliang He
Summary: This study developed a new methodology combining flow cytometric analysis and high-throughput sequencing for monitoring picophytoplankton in a clean reservoir, discovering more species of Pico-Cyanobacteria and Pico-Eukaryotes to improve monitoring accuracy.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biotechnology & Applied Microbiology
Marcelino Martinez Nunez, Magali Ruiz Rivas, Josefat Gregorio Jorge, Pedro Fernando Vera Hernandez, Silvia Luna Suarez, Stefan de Folter, Ricardo A. Chavez Montes, Flor de Fatima Rosas Cardenas
Summary: Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. In this study, small RNAs from seedlings of the Amaranthus hypocondriacus variety Gabriela under different stress conditions were sequenced, leading to the identification of 53 genuine miRNA clusters. Target gene analysis suggests that conserved amaranth miRNAs play roles in growth, development, and stress responses.
Article
Plant Sciences
Enfang Qi, Xiaoxia Jia, Wei Huang, Guohong Wen, Heping Lv, Jianwu Li, Zhang Li
Summary: By comparing four different color potato varieties, 12 transcriptomic libraries were constructed to identify miRNAs and target genes associated with anthocyanin formation. The study discovered 4199 new miRNAs and screened some important miRNAs and target genes. Functional annotation analysis also identified several key regulatory pathways. These findings provide a scientific basis for developing colorful or functional potatoes.
ACTA PHYSIOLOGIAE PLANTARUM
(2023)
Article
Agriculture, Dairy & Animal Science
Shi Yin, Jingwen Zhou, Liuqing Yang, Yujie Yuan, Xianrong Xiong, Daoliang Lan, Jian Li
Summary: This study investigates the transcriptome dynamics of microRNA (miRNA) in yak corpus luteum (CL) at different developmental stages. The findings reveal key miRNAs and target genes associated with the formation, function, and regression of the CL. The results provide valuable insights into the regulatory mechanisms and gene networks of miRNA in the estrous cycle of yaks.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Fereshteh Ahmadi-Teshniz, Behrouz Shiran, Sadegh Mousavi-Fard, Hossein Fallahi, Bojana Banovic Deri
Summary: This study identified 21 conserved miRNAs in Fritillaria imperialis using RNAseq and qRT-PCR, shedding light on their expression patterns and roles in different tissues and developmental stages. The findings could provide valuable insights for ensuring the survival, preservation, and utilization of crown imperial, with potential applications in other plant species.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Microbiology
Jianhui Zhao, Jingwei Shui, Lipei Luo, Cailing Ao, Hongqing Lin, Yuanhao Liang, Li Wang, Haiying Wang, Hongliang Chen, Shixing Tang
Summary: Precise genotyping is essential for understanding the epidemiology and clinical manifestations of Chlamydia trachomatis infection. This study used NGHTS to identify different genotypes and mixed-genotype infections of C. trachomatis, and found association between mixed-genotype infections and worse vaginal cleanliness and cervical SIL.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Wayne L. Morris, M. Carmen Alamar, Rosa M. Lopez-Cobollo, Javier Canete Castillo, Mark Bennett, Jeroen Van der Kaay, Jennifer Stevens, Sanjeev Kumar Sharma, Karen McLean, Andrew J. Thompson, Leon A. Terry, Colin G. N. Turnbull, Glenn J. Bryan, Mark A. Taylor
JOURNAL OF EXPERIMENTAL BOTANY
(2019)
Article
Biology
Pirita Paajanen, George Kettleborough, Elena Lopez-Girona, Michael Giolai, Darren Heavens, David Baker, Ashleigh Lister, Fiorella Cugliandolo, Gail Wilde, Ingo Hein, Iain Macaulay, Glenn J. Bryan, Matthew D. Clark
Article
Plant Sciences
Cristiane P. G. Calixto, Nikoleta A. Tzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. S. Brown
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Plant Sciences
Ying Wang, Muhammad Abdul Rehman Rashid, Xianping Li, Chunguang Yao, Lili Lu, Jianming Bai, Yanshan Li, Ningsheng Xu, Qiongfen Yang, Linhai Zhang, Glenn J. Bryan, Qijun Sui, Zhechao Pan
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Biochemistry & Molecular Biology
Guenter G. Lehretz, Sophia Sonnewald, Csaba Hornyik, Jose M. Corral, Uwe Sonnewald
Article
Agronomy
Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo M. Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, Alan Humphries, David Jordan, Zacharia Kehel, Shiv Kumar, Sandy Jan Labarosa, Loi Huu Nguyen, Emma Mace, Susan McCouch, Ken McNally, David F. Marshall, Erick Owuor Mikwa, Iain Milne, Damaris Achieng Odeny, Mariola Plazas, Jaime Prohens, Loren H. Rieseberg, Roland Schafleitner, Shivali Sharma, Gordon Stephen, Huynh Quang Tin, Abou Togola, Emily Warschefsky, Peter Werner, Paul D. Shaw
Summary: The management and distribution of experimental data from prebreeding projects is crucial for uptake of germplasm into breeding and research programs. The use of a common informatics platform across multiple species provides economies of scale and reduces barriers for researchers to access and share data. The updates to the Germinate platform highlight its value in distributing prebreeding data and demonstrate the benefits of a shared informatics platform for breeding and research communities.
Article
Microbiology
Sarah Harvey, Priyanka Kumari, Dmitry Lapin, Thomas Griebel, Richard Hickman, Wenbin Guo, Runxuan Zhang, Jane E. Parker, Jim Beynon, Katherine Denby, Jens Steinbrenner
Article
Multidisciplinary Sciences
Carolina Sansaloni, Jorge Franco, Bruno Santos, Lawrence Percival-Alwyn, Sukhwinder Singh, Cesar Petroli, Jaime Campos, Kate Dreher, Thomas Payne, David Marshall, Benjamin Kilian, Iain Milne, Sebastian Raubach, Paul Shaw, Gordon Stephen, Jason Carling, Carolina Saint Pierre, Juan Burgueno, Jose Crosa, HuiHui Li, Carlos Guzman, Zakaria Kehel, Ahmed Amri, Andrzej Kilian, Peter Wenzl, Cristobal Uauy, Marianne Banziger, Mario Caccamo, Kevin Pixley
NATURE COMMUNICATIONS
(2020)
Article
Plant Sciences
Ibtissam Jabre, Saurabh Chaudhary, Wenbin Guo, Maria Kalyna, Anireddy S. N. Reddy, Weizhong Chen, Runxuan Zhang, Cornelia Wilson, Naeem H. Syed
Summary: Research suggests that nucleosome positioning affects cold-induced alternative splicing in plants. In Arabidopsis thaliana, different types of alternative splicing events are closely linked to characteristic nucleosome occupancy levels. Internal regions of protein-coding exons, known as exitrons, exhibit distinct nucleosome positioning patterns compared to other alternatively spliced regions.
Article
Biochemistry & Molecular Biology
Wenbin Guo, Nikoleta A. Tzioutziou, Gordon Stephen, Iain Milne, Cristiane P. G. Calixto, Robbie Waugh, John W. S. Brown, Runxuan Zhang
Summary: 3D RNA-seq is a powerful tool for comprehensive analysis of RNA-seq data, with user-friendly features, rapid and accurate analysis of differential gene expression and alternative splicing.
Article
Ecology
Sanjeev Kumar Sharma, Karen McLean, Richard J. Colgan, Debbie Rees, Stephen Young, Mads Sonderkaer, Leon A. Terry, Colin Turnbull, Mark A. Taylor, Glenn J. Bryan
Summary: The study highlights the importance of long-term tuber storage in potato crops, while considering the needs of the seed potato industry for rapid emergence. Through genetic analysis and innovative methods, the research reveals a complex genetic architecture for tuber sprouting and sprout growth, with multiple consistent QTL identified across two growing seasons.
Article
Plant Sciences
Pingtao Ding, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, Chang Liu, Xiaoqi Feng, Runxuan Zhang, Klaas Vandepoele, Dan MacLean, Jonathan D. G. Jones
Summary: This study combines RNA-seq and ATAC-seq to investigate the effects of cell-surface and intracellular receptor-mediated immunity activation on gene expression and chromatin accessibility. The results reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Dominika Lewandowska, Jamie Orr, Miriam Schreiber, Isabelle Colas, Luke Ramsay, Runxuan Zhang, Robbie Waugh
Summary: This study used high-resolution mass spectrometry to analyze the development of barley anthers, identifying over 6100 non-redundant proteins including 82 known and putative meiotic proteins. Although protein abundance was relatively stable throughout prophase I, dynamic variations in 336 proteins were quantified. This research provides new insights into the development of the male reproductive organ in small grain cereals during meiotic prophase I.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biology
Wenbin Guo, Max Coulter, Robbie Waugh, Runxuan Zhang
Summary: Different genotypes within a species have variable numbers of specific genes and different structures of core genes. The use of a common reference genome can lead to the loss of genotype-specific information and generate erroneous or incomplete results in transcriptomics analysis. In this study, genotype-specific and common reference-based Reference Transcript Datasets (RTDs) were assembled using RNA-seq data from cultivated barley. The results showed that the genotype-specific RTD had a higher diversity of transcripts and alternative splicing events, while the common reference-based RTD missed a significant proportion of transcripts and had less accurate transcript assemblies.
LIFE SCIENCE ALLIANCE
(2022)
Article
Biotechnology & Applied Microbiology
Richard I. Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald, David W. Burt
