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Evolutionary Transients in the Rice Transcriptome

Jun Wang, Jianguo Zhang, Ruiqiang Li, Hongkun Zheng, Jun Li, Yong Zhang, Heng Li, Peixiang Ni, Songgang Li, Shengting Li, Jingqiang Wang, Dongyuan Liu (+7 others)
2010 Genomics, Proteomics & Bioinformatics  
Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may-in principle-be attributable  ...  to what we will refer to as "evolutionary transients", referring here to both the process and the genes that have gone or are undergoing this process.  ...  Transients in Rice Transcriptome  ... 
doi:10.1016/s1672-0229(10)60023-x pmid:21382590 pmcid:PMC5054128 fatcat:gg3x4taq3nf4rarigdsll7davq

BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development

Ming-Che Shih, Ming-Lun Chou, Jin-Jun Yue, Cheng-Tran Hsu, Wan-Jung Chang, Swee-Suak Ko, De-Chih Liao, Yao-Ting Huang, Jeremy JW Chen, Jin-Ling Yuan, Xiao-Ping Gu, Choun-Sea Lin
2014 BMC Plant Biology  
The expression patterns of these genes were most similar to the rice homologs, except BeMADS18 and BeMADS34, and were highly similar to the floral development ABCDE model in rice.  ...  Combination of the two datasets resulted in high transcriptome quality and increased length of the sequence reads.  ...  Acknowledgements We thank Shu-Chen Shen from the Confocal Microscopic Core Facility at Academia Sinica for assistance in confocal microscopy images.  ... 
doi:10.1186/1471-2229-14-179 pmid:24989161 pmcid:PMC4087239 fatcat:q5ae6cyj2vf2fotwihql26gmci

Identification and Characterization of the Basic Helix-Loop-Helix Transcription Factor Family in Pinus massoniana

Yu Chen, Peihuang Zhu, Fan Wu, Xiaofeng Wang, Jinfeng Zhang, Kongshu Ji
2020 Forests  
In this study, we identified 88 bHLH genes from four transcriptomes of Masson pine and performed bioinformatics analysis. These genes were divided into 10 groups in total.  ...  Research on the bHLH family in animals is more extensive than that in plants, and members of the family in plants are classified according to the classification criteria for those in animals.  ...  Acknowledgments: Thanks to Ziyuan Hao for his support and help in data analysis. Conflicts of Interest: The authors declare no conflict of interest. Forests 2020, 11, 1292  ... 
doi:10.3390/f11121292 fatcat:hngvetirqvhwticwzuff7igszi

Conserved Transcriptional Regulatory Programs Underlying Rice and Barley Germination

Li Lin, Shulan Tian, Shawn Kaeppler, Zongrang Liu, Yong-Qiang (Charles) An, Norman Johnson
2014 PLoS ONE  
and contribute to the ancient characteristics of germination preserved in barley and rice.  ...  To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination  ...  Disclaimer Note Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval  ... 
doi:10.1371/journal.pone.0087261 pmid:24558366 pmcid:PMC3928125 fatcat:qqpthp5325e3firso7jawvp4mu

TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

Kangming Jin, Yujun Wang, Renying Zhuo, Jing Xu, Zhuchou Lu, Huijin Fan, Biyun Huang, Guirong Qiao
2022 Frontiers in Plant Science  
This study provides useful insights into the evolutionary patterns and molecular functions of the TCP transcription factors in Ma bamboo and provides a valuable reference for further research on the regulatory  ...  Additionally, the transcriptome analysis of the bamboo shoot buds at different developmental stages helped to clarify the underlying functions of the TCP members during the growth of bamboo shoots.  ...  resist several biotic and abiotic stresses in the long-term evolutionary process.  ... 
doi:10.3389/fpls.2022.884443 fatcat:x6jbezql3vbdvf6uopy7sxcsza

Genome-Wide Characterization and Expression of Two-Component System Genes in Cytokinin-Regulated Gall Formation in Zizania latifolia

Lili He, Feng Zhang, Xiaozhen Wu, Yanmei Hu, LiLi Dong, Walter Dewitte, Bo Wen
2020 Plants  
These TCS genes have a close phylogenetic relationship with their rice counterparts.  ...  The swollen and juicy shoots are a popular vegetable in Asia. A key role for cytokinin action in this process was postulated. Here, trans-zeatin stimulated swelling in fungi-infected Z. latifolia.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/plants9111409 pmid:33105697 pmcid:PMC7690396 fatcat:gerwzemz2vb6lpzzko6dqdyoli

Auxin signalling: Ancestral pathways

Guillaume Tena
2015 Nature Plants  
Using transient expression in tobacco leaves the researchers validated the function of RhNUDX1 in the biosynthesis of geraniol, a monoterpene alcohol, in planta.  ...  However, 7-17% of the greenhouse gas methane in the atmosphere derives from rice farming.  ...  As a descendant of the earliest terrestrial plants, Marchantia is an interesting model for evolutionary studies of signalling pathways, and their importance in land colonization.  ... 
doi:10.1038/nplants.2015.122 pmid:27250553 fatcat:pv5flreanbaaxd4djntgnxg25y

Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton

Heng Sun, Meiling Hu, Jianying Li, Lin Chen, Meng Li, Shuqin Zhang, Xianlong Zhang, Xiyan Yang
2018 BMC Plant Biology  
NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of GhNAC genes.  ...  Transcriptome analysis and co-expression network indicated roles for GhNAC genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes.  ...  The transcriptome data sets of TM-1 in  ... 
doi:10.1186/s12870-018-1367-5 pmid:30041622 pmcid:PMC6057059 fatcat:c34g6epmkra6xhmdq7zdqvc5p4

From Bench to Barn: Plant Model Research and its Applications in Agriculture

Andrea Pitzschke
2013 Advancements in Genetic Engineering  
Acknowledgement I gratefully acknowledge the Austrian Science Foundation (FWF) for funding (Elise-Richter-Project V167-B09).  ...  The evolutionary much younger legume root nodule symbiosis has likely evolved from the ancient AM symbiosis.  ...  However, for various questions in molecular biology, transient expression systems are the method of choice.  ... 
doi:10.4172/2169-0111.1000110 fatcat:jokcndq7lnci3aq5646ay7goci

Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid

Hai Wang, Shengyan Li, Shouzhen Teng, Haisheng Liang, Hongjia Xin, Hongjiang Gao, Dafang Huang, Zhihong Lang, Ricardo Aroca
2017 PLoS ONE  
A transient expression assay using transfected maize protoplastswas established to examine the potential roles of DETFs in maize defense response and JA signaling, and this was used to show that ZmNAC60  ...  In this study, the genome-wide early responses in maize seedlings to Asian corn borer (ACB, Ostrinia furnacalis) and also to jasmonic acid(JA), the pivotal phytohormone controlling plant defense response  ...  David Jackson at Cold Spring Harbor Laboratory for kindly providing a comprehensive collection of PWMs of cis-elements in plants.  ... 
doi:10.1371/journal.pone.0177739 pmid:28520800 pmcid:PMC5433750 fatcat:k5audxlnovcmdjkrcuetuv4coe

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

Ming Luo, Jennifer M. Taylor, Andrew Spriggs, Hongyu Zhang, Xianjun Wu, Scott Russell, Mohan Singh, Anna Koltunow, Tetsuji Kakutani
2011 PLoS Genetics  
In plants, most imprinted genes have been identified in Arabidopsis endosperm, a transient structure consumed by the embryo during seed formation.  ...  Fifty-six of the 67 loci investigated were confirmed to be imprinted in the seed. Imprinted loci are not clustered in the rice genome as found in mammals.  ...  We thank Soussanith Nokham for processing of images; Narayana Upadhyaya for providing rice lines; and Jean Finnegan, Matt Tucker, Steve Swain, Tony Ashton, and Ben Trevaskis for critical reading of the  ... 
doi:10.1371/journal.pgen.1002125 pmid:21731498 pmcid:PMC3121744 fatcat:ocosvkbhajedjdz6r24hfzawlm

Ribogenomics: the Science and Knowledge of RNA

Jiayan Wu, Jingfa Xiao, Zhang Zhang, Xumin Wang, Songnian Hu, Jun Yu
2014 Genomics, Proteomics & Bioinformatics  
An all-out effort exceeding the magnitude of the Human Genome Project is of essence to construct just mammalian transcriptomes in multiple contexts including embryonic development, circadian and seasonal  ...  On the operational track, there are several diverse types of RNAs - their length distribution is perhaps the most simplistic stratification - involving in major cellular activities, such as chromosomal  ...  Acknowledgements This work was supported by the National Basic Research Program of China (Grant Nos. 2011CB944100 and  ... 
doi:10.1016/j.gpb.2014.04.002 pmid:24769101 pmcid:PMC4411354 fatcat:mudkhn4pizdydnpli55cwy44fq

CMYB1Encoding a MYB Transcriptional Activator Is Involved in Abiotic Stress and Circadian Rhythm in Rice

Min Duan, Peng Huang, Xi Yuan, Hui Chen, Ji Huang, Hongsheng Zhang
2014 The Scientific World Journal  
Moreover,CMYB1exhibited the transcriptional activation activity when transiently expressed in rice protoplast cells.  ...  Subcellular localization assay suggested thatCMYB1-GFP (green fluorescent protein) fusion protein was localized in the nuclei.  ...  In the present study, a novel MYB transcription factor gene CMYB1 was identified through transcriptome analysis in rice under cold stress.  ... 
doi:10.1155/2014/178038 pmid:24977183 pmcid:PMC3995101 fatcat:qixilsfz5bcntmg6hgsfcwdbfm

Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa)

Ming Wen, Munan Xie, Lian He, Yushuai Wang, Suhua Shi, Tian Tang
2016 Genome Biology and Evolution  
Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies.  ...  Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression  ...  .), the Science Foundation for Outstanding Young Teachers in Higher Education of Guangdong (Yq2013005) and the Fundamental Research Funds for the Central Universities (16lgjc75) to T.T., and the General  ... 
doi:10.1093/gbe/evw252 pmid:27797952 pmcid:PMC5203789 fatcat:6kq4lq77mve6ben2iib2jqb72u

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

Rupesh K. Deshmukh, Humira Sonah, Richard R. Bélanger
2016 Frontiers in Plant Science  
From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data.  ...  In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply  ...  Mosses, being primitive plants, are valuable for evolutionary studies, and the features observed in mosses are likely to be present in higher plants.  ... 
doi:10.3389/fpls.2016.01896 pmid:28066459 pmcid:PMC5167727 fatcat:5xi2utulpjgfrhdm74jzybk63e
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