Article
Biochemical Research Methods
Bin Li, Wen Zhang, Chuang Guo, Hao Xu, Longfei Li, Minghao Fang, Yinlei Hu, Xinye Zhang, Xinfeng Yao, Meifang Tang, Ke Liu, Xuetong Zhao, Jun Lin, Linzhao Cheng, Falai Chen, Tian Xue, Kun Qu
Summary: This study compares 16 integration methods using 45 paired datasets and 32 simulated datasets, finding that Tangram, gimVI, and SpaGE perform best in predicting RNA transcript distribution, while Cell2location, SpatialDWLS, and RCTD are top-performing methods for cell type deconvolution. The benchmark pipeline provided in the study helps researchers in selecting optimal integration methods for their datasets. The comprehensive benchmarking analysis presented in this work evaluates computational methods integrating spatial and single-cell transcriptomics data for transcript distribution prediction and cell type deconvolution.
Article
Biochemistry & Molecular Biology
Ming Chen, Lin Guo, Muthusamy Ramakrishnan, Zhangjun Fei, Kunnummal K. Vinod, Yulong Ding, Chen Jiao, Zhipeng Gao, Ruofei Zha, Chunyue Wang, Zhimin Gao, Fen Yu, Guodong Ren, Qiang Wei
Summary: The rapid growth of Moso bamboo is associated with cell division and elongation, gibberellin, cytokinin, auxin, abscisic acid, and mechanical pressure. This study provides insight into the mechanisms underlying the rapid growth of Moso bamboo.
Article
Plant Sciences
Yangang Lan, Lin Wu, Min Wu, Huanlong Liu, Yameng Gao, Kaimei Zhang, Yan Xiang
Summary: In this study, a transcriptome analysis of moso bamboo shoots during early elongation stages revealed key candidate genes regulating plant hormone signal transduction, sugar and starch metabolism, and energy metabolism pathways. The cytokinin-signaling pathway was continuously active in the three successive elongation stages, indicating its importance in moso bamboo growth. Additionally, key genes involved in sugar, starch metabolism, and energy conversion were found to play essential roles in energy production and substrate synthesis during shoot growth.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Plant Sciences
Tao Li, Huihui Wang, Yaxin Zhang, Huiyuan Wang, Zeyu Zhang, Xuqing Liu, Zekun Zhang, Kai Liu, Deming Yang, Hangxiao Zhang, Lianfeng Gu
Summary: This study examines the cellular processes and epigenetic mechanisms underlying the fast growth of Moso bamboo shoots. The results show that internode cells elongate and lignin biosynthesis and GT43 gene expression are upregulated with shoot height. Additionally, differences in N-6-methyladenine (m(6)A) modification rate, DNA methylation levels, and poly(A) tail lengths are observed between shoots of different heights. The findings provide valuable insights into the post-transcriptional regulations responsible for the fast growth of Moso bamboo shoots.
Article
Agricultural Engineering
Yangang Lan, Feng Pan, Kaimei Zhang, Linna Wang, Honxia Liu, Chengzhi Jiang, Feng Chen, Min Wu, Yan Xiang
Summary: This study analyzed the expression patterns of 154 bZIP genes in response to drought using transcriptome data from public databases, and identified a key candidate gene, PhebZIP47, which exhibited strong induction under drought and ABA conditions. Transgenic Arabidopsis and rice overexpressing PhebZIP47 showed enhanced resistance to drought, supporting the role of PhebZIP47 in drought tolerance. Transcriptome analysis revealed that PhebZIP47 regulated a large number of differentially expressed genes (DEGs) involved in drought tolerance and ABA signaling pathways. Moreover, the transgenic plants displayed reduced sensitivity to exogenous ABA treatment.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Forestry
Haiyue Wang, Lin Guo, Ruofei Zha, Zhipeng Gao, Fen Yu, Qiang Wei
Summary: The Moso bamboo leaf has evolved special histological structures, metabolic pathways and a cold stress-tolerant transcriptome to adapt to the cold weather. These adaptations include more trichomes, fewer fusiform cells, lower stomata density and higher levels of stress-resistant metabolites. The cold stress response network involves trehalose, glutathione, flavonoid metabolism, DNA repair, reactive oxygen species degradation, stress-associated genes and abiotic stress-related plant hormones.
Article
Plant Sciences
Yandong Song, Chunju Peng, Qinjiao Wu, Shijie Tao, Tingting Mei, Zhihong Sun, Zhaojiang Zuo, Chunyu Pan, Yufeng Zhou, Guomo Zhou
Summary: This study investigated the photosynthetic and isoprene emission characteristics of Moso bamboo at different culm ages. The results showed that the effect of culm age on isoprene emission was different from that on photosynthesis, indicating that the isoprene emission rate was higher in old bamboo compared to mature bamboo. Therefore, considering culm age is important when establishing an isoprene emission model of Moso bamboo, and attention should be paid to the management of bamboo age structure and timely felling of aged bamboo to reduce environmental risk.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Chongyu Ye, Qiangfa Zeng, Keda Hu, Dongming Fang, Dirk Hoelscher, Huaqiang Du, Yongjun Shi, Yufeng Zhou, Frank Berninger, Tingting Mei, Guomo Zhou
Summary: Stem respiration is an important process in ecosystem carbon cycling. However, the measured efflux on the stem surface may not represent the actual respiration. This study proposes stem photosynthesis as an additional pathway and conducts experiments on newly sprouted bamboo to explore the partitioning of stem respiration.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Ruifang Ma, Jialu Chen, Bin Huang, Zhinuo Huang, Zhijun Zhang
Summary: In this study, 27 BBX genes were identified in the Moso bamboo genome, sharing highly similar structures and classified into three clusters. The PeBBX genes may be involved in the growth and development of bamboo shoots, with downstream target genes encoding enzymes related to plant photosynthesis and carbohydrate metabolism. The analysis provides valuable information for the functional validation and further studies of the BBX family.
Article
Multidisciplinary Sciences
Noor Pratap Singh, Michael I. Love, Rob Patro
Summary: Transcript abundance estimates always come with a certain level of uncertainty, which could pose challenges for downstream analyses like differential testing. TreeTerminus is a data-driven approach that groups transcripts into a tree structure, where leaves represent individual transcripts and internal nodes represent an aggregation of transcript sets. By constructing trees that reduce inferential uncertainty as we move up the topology, TreeTerminus enables flexible data analysis at different levels of resolution within the tree. Evaluations on simulated and experimental datasets show improved performance compared to transcripts (leaves) and other methods across multiple metrics.
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
Miaomiao Cai, Wenlong Cheng, Yucong Bai, Changhong Mu, Huifang Zheng, Zhanchao Cheng, Jian Gao
Summary: This study analyzed the characteristics of the general regulatory factors (GRFs) gene family in moso bamboo, and revealed their involvement in hormone response during bamboo shoot development.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biochemical Research Methods
Thomas Gatter, Peter F. Stadler
Summary: Research shows that multi-sample RNA-Seq experiments exhibit better stability and accuracy in RNA-seq assembly. The extended version of Ryuto can generate consensus transcriptomes and provide a better sensitivity-precision trade-off. Utilizing a (incomplete) reference for multi-sample assembly is an effective way to improve precision.
Article
Biotechnology & Applied Microbiology
Zhang Zhijun, Yu Peiyao, Huang Bing, Ma Ruifang, Kunnummal Kurungara Vinod, Muthusamy Ramakrishnan
Summary: This study provides a comprehensive analysis of the DoG gene family in moso bamboo, revealing their roles in various activities such as growth and development, stress response, and transcription regulation.
Article
Biology
Richard J. White, Eirinn Mackay, Stephen W. Wilson, Elisabeth M. Busch-Nentwich
Summary: In zebrafish, differentially expressed genes are often over-represented on the same chromosome as the mutation, due to different levels of expression of alleles from different genetic backgrounds. This has implications for interpreting the results and pathways in RNA-seq experiments.