Article
Biochemistry & Molecular Biology
Lucisabel Medina-Chavez, Christian Camacho, Jorge Arturo Martinez-Rodriguez, Blanca Estela Barrera-Figueroa, Dawn H. Nagel, Piyada Juntawong, Julian Mario Pena-Castro
Summary: Plant genes that oscillate in networks coordinate internal processes with external cues, contributing to increased fitness. This study investigated the dynamic changes in response to submergence stress during different times of the day in a model monocotyledonous plant. Transcriptome analysis revealed rhythmic processes and changes in clock genes, photosynthesis-related genes, growth suppressors, hormone-related genes, and signaling genes involved in mitochondria and carbohydrate metabolism. Additionally, the study demonstrated the alteration of clock genes in response to submergence stress in Arabidopsis thaliana. These findings provide insights into the chronocultural strategies and diurnal-associated tolerance mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Joachim De Jonghe, Tomasz S. Kaminski, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte E. Handford, Gregory M. Findlay, Magdalena Zernicka-Goetz, Sarah A. Teichmann, Florian Hollfelder
Summary: The authors developed spinDrop, a technique that increases gene detection and reduces noise in droplet microfluidics, to generate a high-quality molecular atlas of mouse brain development.
NATURE COMMUNICATIONS
(2023)
Review
Plant Sciences
Diana Lucia Zuluaga, Emanuela Blanco, Giacomo Mangini, Gabriella Sonnante, Pasquale Luca Curci
Summary: This review summarizes the progress made in transcriptomic resources related to durum wheat in the field of plant omics. It focuses on the mechanisms of the crop's response to abiotic and biotic stresses and the research methods used in relevant studies. The results show that mining and analyzing transcriptomic databases can help accelerate durum wheat breeding.
Article
Plant Sciences
Jie Yang, Zhixuan Tang, Wuyue Yang, Qianhui Huang, Yuqing Wang, Mengfan Huang, Hui Wei, Guoyuan Liu, Bolin Lian, Yanhong Chen, Jian Zhang
Summary: In this study, the Trihelix gene family was analyzed in Salix matsudana, an ornamental forest tree. A total of 78 Trihelix transcription factors were identified and classified into four subfamilies. The expression pattern analysis revealed that these genes play different roles in response to flooding stress, with SmTTF30 showing enhanced tolerance to flooding stress when overexpressed in Arabidopsis thaliana.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Alessia Buratin, Stefania Bortoluzzi, Enrico Gaffo
Summary: Circular RNAs (circRNAs) are closed transcripts involved in regulatory pathways and disease mechanisms. Standard differential expression assessment methods may not perform well on circRNA expression data. We compared different pipelines and found that Limma-Voom had the most consistent performance, while some single-cell RNA-seq (scRNA-seq) methods also performed well. Increasing the number of replicates improved the performance of all methods. Careful design and choice of differential expression analysis methods are important for circRNA expression studies.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Sini Junttila, Johannes Smolander, Laura L. Elo
Summary: This study compared 18 methods for identifying differential states (DS) changes between conditions in multisubject scRNA-seq data, and found that pseudobulk methods and mixed models performed best, showing superior statistical performance compared to naive single-cell methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Horticulture
Si Long, Qian Liu, Huan Guo, Xuan Li, Xiangkai You, Bowen Liu, Shuanghong Gao, Suyun Wen, Tie -Yuan Liu, Yuefei Xu
Summary: This study investigated the physiological and transcriptional changes of two tall fescue cultivars under lowlight stress. The results showed that Arid 3 exhibited better growth characteristics and photosynthetic gas exchange compared to Airlie. Gene expression analysis revealed that differentially expressed genes were mainly involved in 'cell part' and 'glutathione metabolism'. Transcription factors and genes related to chlorophyll metabolism and photosynthesis also showed different expression levels between the two cultivars. This study provides insights into the different photosynthetic responses of tall fescue cultivars to lowlight stress.
SCIENTIA HORTICULTURAE
(2022)
Article
Biochemistry & Molecular Biology
Pedro L. Baldoni, Yunshun Chen, Soroor Hediyeh-zadeh, Yang Liao, Xueyi Dong, Matthew E. Ritchie, Wei Shi, Gordon K. Smyth
Summary: Differential expression analysis of RNA-seq is commonly used in bioinformatics. However, transcript-level quantifications are more uncertain due to the ambiguity of sequence reads. To address this issue, a new method is proposed to estimate the overdispersion caused by read-to-transcript ambiguity and generate scaled transcript counts, which improves the efficiency and accuracy of differential analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xingen Zhang, Jing Liu, Yuanxiang Huang, Hongying Wu, Xiaolin Hu, Beijiu Cheng, Qing Ma, Yang Zhao
Summary: In this study, physiological and comparative transcriptome analyses were conducted to investigate the response of maize seedlings to salt stress. The results revealed differences in salt tolerance between two maize inbred lines, cmh15 and CM37, at both physiological and transcriptomic levels. Gene ontology analysis showed that photosynthesis-related and oxidation-reduction processes played crucial roles in the response to salt stress. Furthermore, differences were observed in the hormone signaling pathway and regulation patterns of transcription factors between cmh15 and CM37 under salt stress. This study provides valuable insights into the molecular networks involved in salt stress tolerance of maize seedlings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Luis Abraham Chaparro-Encinas, Gustavo Santoyo, Juan Jose Pena-Cabriales, Luciano Castro-Espinoza, Fannie Isela Parra-Cota, Sergio de los Santos-Villalobos
Summary: Increasing temperature has a significant impact on durum wheat growth and gene expression, resulting in decreased traits and 283 differentially expressed genes. The enriched GO terms indicate involvement in photosynthetic acclimation, respiration, and lipid biosynthesis, among other physiological processes.
Article
Biotechnology & Applied Microbiology
Yu Hamaguchi, Chao Zeng, Michiaki Hamada
Summary: This study compared the mappability of three different human gene annotations (GENCODE, RefSeq, and NONCODE) to evaluate its impact on DE analysis. The results showed that increasing mappability improved the performance of DE analysis, particularly in the quantification step, suggesting that excluding unnecessary gene models from gene annotations could enhance DE analysis.
Article
Multidisciplinary Sciences
Zhanlin Chen, William C. King, Aheyon Hwang, Mark Gerstein, Jing Zhang
Summary: Recent advances in single-cell sequencing technologies have led to new opportunities for studying the gene expression profile and transcriptome dynamics of individual cells. In this study, the authors propose DeepVelo, a neural network-based method that models complex transcriptome dynamics by simulating continuous changes in gene expression over time within cells. DeepVelo was applied to analyze transcriptome dynamics at different time scales and identify developmental driver genes through perturbation analysis.
Article
Multidisciplinary Sciences
Lei Yu, Xinlei Wang, Quanhua Mu, Sindy Sing Ting Tam, Danson Shek Chun Loi, Aden K. Y. Chan, Wai Sang Poon, Ho-Keung Ng, Danny T. M. Chan, Jiguang Wang, Angela Ruohao Wu
Summary: Single-cell multi-omics provides a unique perspective on tumor cellular heterogeneity. We developed scONE-seq, a versatile method for single-cell whole-genome RNA sequencing that is compatible with frozen biobanked samples. By comparing with existing methods, we demonstrated the performance of scONE-seq in various aspects and identified a unique transcriptionally normal-like tumor clone in a frozen astrocytoma sample, suggesting the potential of scONE-seq in uncovering previously unidentified discoveries in tumor biology.
Review
Plant Sciences
Dilip Kumar, Pulugurtha Bharadwaja Kirti
Summary: Peanut is a segmental allotetraploid with high tolerance to biotic and abiotic stresses. Studying differential gene expression can help identify genes and regulatory pathways related to stress tolerance, providing a better understanding of resistance mechanisms and aiding in the development of stress-tolerant plants through genetic manipulation.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Nazanin Amirbakhtiar, Ahmad Ismaili, Mohammad-Reza Ghaffari, Raheleh Mirdar Mansuri, Sepideh Sanjari, Zahra-Sadat Shobbar
Summary: This study investigated the transcriptome of wheat leaves in a salt-tolerant cultivar to identify genes and mechanisms involved in response to salinity stress. The results indicated that genes associated with phenylpropanoid biosynthesis, transporters, transcription factors, and hormone signal transduction pathways might play roles in salt tolerance. Validation of gene expression patterns using real-time PCR showed consistency with RNA-sequencing results, suggesting potential applications in enhancing salt tolerance in wheat through genetic engineering or molecular breeding.
