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Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms

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Journal of Integrative Plant Biology 2022年第11期64卷 2111-2125页

作者： Yuqi Nie Liangyu Guo Fuqiang Cui Yirong Shen Xiaoxue Ye Deyin Deng Shuo Wang Jianhua Zhu Wenwu Wu State Key Laboratory of Subtropical Silviculture School of Forestry and BiotechnologyZhejiang A&F UniversityHangzhou 311300China institute of Tropical biosciences and Biotechnology Chinese Academy of Tropical Agricultural SciencesHaikou 571101China School of Life Sciences Anhui Agricultural UniversityHefei 230036China Department of Plant Science and Landscape Architecture University of MarylandCollege ParkMaryland 20742USA

The C-repeat binding factors/dehydrationresponsive element binding protein 1 s(CBFs/DREB1 s)have been identified as major regulators of cold acclimation in many angiosperm ***,their origin and evolutionary process associated to cold responsiveness are still *** integrating multi-omics data of genomes,transcriptomes,and CBFs/DREB1 s genome-wide binding profiles,we unveil the origin and evolution of CBFs/DREB1 s and their regulatory *** collinearity and phylogeny analyses show that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREBⅢgene.A subsequent event of e-whole genome duplication led to two CBF/DREB1 archetypes(CladesⅠandⅡ)in ancient *** contrast to cold-insensitivity of Clade I and their parent DREBⅢgenes,CladeⅡevolved a further innovation in cold-sensitive response and was stepwise expanded in eudicots and monocots by independent *** geological time,the duplication events were mainly enriched around the Cretaceous-Paleogene(K-Pg)boundary and/or in the Late Cenozoic Ice Age,when the global average temperature significantly ***,the duplicated CBF/DREB1 genes contributed to the rewiring of CBFs/DREB1 s-regulatory network for cold ***,our results highlight an origin and convergent evolution of CBFs/DREB1 s and their regulatory network probably for angiosperms adaptation to global cooling.

关键词： CBF/DREB1 cold acclimation global cooling ice age K-Pg boundary paleotemperature tandem duplication(TD) whole genome duplication(WGD)

Analysis of the genotoxic potential of low concentrations of Malathion on the Allium cepa cells and rat hepatoma tissue culture

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Journal of Environmental Sciences 2015年第10期27卷 102-111页

作者： Jaqueline Bianchi Mario Sérgio Mantovani Maria Aparecida Marin-Morales Department of Biology Institute of BiosciencesSao Paulo State University(UNESP) Department of General Biology Biological Science CentreUniv Estadual de Londrina

Based on the concentration of Malathion used in the field, we evaluated the genotoxic potential of low concentrations of this insecticide on meristematic and F1 cells of Allium cepa and on rat hepatoma tissue culture（HTC cells）. In the A. cepa, chromosomal aberrations（CAs）, micronuclei（MN）, and mitotic index（MI） were evaluated by exposing the cells at 1.5,0.75, 0.37, and 0.18 mg/m L of Malathion for 24 and 48 hr of exposure and 48 hr of recovery time. The results showed that all concentrations were genotoxic to A. cepa cells. However,the analysis of the MI has showed non-relevant effects. Chromosomal bridges were the CA more frequently induced, indicating the clastogenic action of Malathion. After the recovery period, the higher concentrations continued to induce genotoxic effects, unlike the observed for the lowest concentrations tested. In HTC cells, the genotoxicity of Malathion was evaluated by the MN test and the comet assay by exposing the cells at 0.09, 0.009, and0.0009 mg/5 m L culture medium, for 24 hr of exposure. In the comet assay, all the concentrations induced genotoxicity in the HTC cells. In the MN test, no significant induction of MN was observed. The genotoxicity induced by the low concentrations of Malathion presented in this work highlights the importance of studying the effects of low concentrations of this pesticide and demonstrates the efficiency of these two test systems for the detection of genetic damage promoted by Malathion.

关键词： HTC Chromosomal aberration Micronuclei Comet assay Pesticide

Benzydamine hydrochloride ameliorates ethanol-induced inflammation in RAW 264.7 macrophages by stabilizing redox homeostasis

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Asian Pacific Journal of Tropical Biomedicine 2024年第2期14卷 73-81,I0006-I0009页

作者： Tiasha Dasgupta Venkatraman Manickam Department of Biomedical Sciences School of Biosciences and TechnologyVellore Institute of TechnologyVellore 632014Tamil NaduIndia

Objective:To evaluate the protective effect of benzydamine hydrochloride against ethanol-induced oxidative stress and inflammation in RAW 264.7 ***:RAW 264.7 macrophages were treated with ethanol(100 mM)and benzydamine hydrochloride(7.5μM).The imflammatory status was confirmed by measuring pro-(TNF-αand IL-6)and anti-inflammatory(IL-10)cytokines through ELISA and RT-PCR *** oxygen species generation and mitochondrial membrane potential were investigated to study the protective role of benzydamine hydrochloride against ethanol-induced oxidative *** detection was also investigated using flow cytometry and acridine orange/ethidium bromide ***:Benzydamine hydrochloride significantly decreased the secretion of TNF-αand IL-6,as well as the generation of reactive oxygen species inside the cells,thereby stabilizing the mitochondrial membrane potential and reducing DNA *** ethanol-induced cellular necrosis was also reversed by the administration of benzydamine ***:Benzydamine hydrochloride ameliorates ethanol-induced cell apoptosis and inflammation in RAW macrophages.

关键词： Alcohol Benzydamine hydrochloride Inflammation Oxidative stress Apoptosis

Genome-wide association analysis for stripe rust resistance in spring wheat(Triticum aestivum L.) germplasm

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Journal of Integrative Agriculture 2020年第8期19卷 2035-2043页

作者： Sher MUHAMMAD Muhammad SAJJAD Sultan Habibullah KHAN Muhammad SHAHID Muhammad ZUBAIR Faisal Saeed AWAN Azeem iqbal KHAN Muhammad Salman MUBARAK Ayesha TAHIR Muhammad UMER Rumana KEYANI Muhammad InamAFZAL Irfan MANZOOR Javed Iqbal WATTOO Aziz-ur REHMAN Department of Bioinformatics and Biotechnology GC UniversityFaisalabad 38090Pakistan Department of biosciences COMSATS University Islamabad(CUI)Islamabad 45550Pakistan Centre of agricultural Biochemistry and Biotechnology(CABB) University of AgricultureFaisalabad 38000Pakistan Department of Plant Breeding and Genetics University of AgricultureFaisalabad 38000Pakistan Department of Biotechnology Faculty of Life SciencesUniversity of Central PunjabLahore 54000Pakistan Wheat Research institute Ayub Agricultural Research Institute(AARI)Faisalabad 38950Pakistan

Stripe rust is a continuous threat to wheat crop all over the *** causes considerable yield losses in wheat crop every *** deployment of adult plant resistance(APR)genes in newly developing wheat cultivars is the most judicious strategy to combat this ***,we dissected the genetics underpinning stripe rust resistance in Pakistani wheat *** association panel of 94 spring wheat genotypes was phenotyped for two years to score the infestation of stripe rust on each accession and was scanned with 203 polymorphic *** on D’measure,linkage disequilibrium(LD)exhibited between loci distant up to 45 c ***-trait associations(MTAs)were determined using mixed linear model(MLM).Total 31 quantitative trait loci(QTLs)were observed on all 21 wheat *** QTLs were newly discovered as well as 19 QTLs and 35 previously reported Yr genes were validated in Pakistani wheat *** major QTLs were ***.2 AL and ***.3 BS(PVE,11.9%).Dissection of genes from the newly observed QTLs can provide new APR genes to improve genetic resources for APR resistance in wheat crop.

关键词： wheat Puccinia striiformis LD GWAS MTA PCoA

Genome-wide analyses on transcription factors and their potential microRNA regulators involved in maize male fertility

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The Crop Journal 2021年第6期9卷 1248-1262页

作者： Ziwen Li Taotao Zhu Shuangshuang Liu Yilin Jiang Haoyun Liu Yuwen Zhang Ke Xie Jinping Li Xueli An Xiangyuan Wan Zhongzhi International institute of agricultural biosciences Biology and Agriculture Research CenterUniversity of Science and Technology BeijingBeijing 100024China Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding Beijing International Science and Technology Cooperation Base of Bio-Tech BreedingBeijing 100192China

Anther development is a programmed biological process crucial to plant male reproduction. Genomewide analyses on the functions of transcriptional factor(TF) genes and their microRNA(miRNA) regulators contributing to anther development have not been comprehensively performed in maize. Here, using published RNA-Seq and small RNA-Seq(sRNA-Seq) data from maize anthers at ten developmental stages in three genic male-sterility(GMS) mutants(ocl4, mac1, and ms23) and wild type W23, as well as newly sequenced maize anther transcriptomes of ms7-6007 and lob30 GMS mutants and their WT lines, we analyzed and found 1079 stage-differentially expressed(stage-DE) TF genes that can be grouped into six(premeiotic, meiotic, postmeiotic, premeiotic-meiotic, premeiotic-postmeiotic, and meiotic-postmeiotic clusters) expression clusters. Functional enrichment combined with cytological and physiological analyses revealed specific functions of genes in each expression cluster. In addition, 118 stage-DE miRNAs and99 miRNA-TF gene pairs were identified in maize anthers. Further analyses revealed the regulatory roles of zma-miR319 and zma-miR159 as well as ZmMs7 and ZmLOB30 on ZmGAMYB expression. Moreover,ZmGAMYB and its paralog ZmGAMYB-2 were demonstrated as novel maize GMS genes by CRISPR/Cas9 knockout analysis. These results extend our understanding on the functions of miRNA-TF gene regulatory pairs and GMS TF genes contributing to male fertility in plants.

关键词： Transcription factor gene microRNA Anther development Male fertility Genic male sterility

ZmMS1/ZmLBD30-orchestrated transcriptional regulatory networks precisely control pollen exine development

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Molecular Plant 2023年第8期16卷 1321-1338页

作者： Quancan Hou Xueli An Biao Ma Suowei Wu Xun Wei Tingwei Yan Yan Zhou Taotao Zhu Ke Xie Danfeng Zhang Ziwen Li Lina Zhao Canfang Niu Yan Long Chang Liu WeiZhao FeiNi Jinping Li Daolin Fu Zhong-NanYang Xiangyuan Wan Research institute of Biology and Agriculture University of Science and Technology BeijingBeijing 100083China Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding Zhongzhi International Institute of Agricultural BiosciencesBeijing 100192China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTaianShandong 271018China Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China

Because of its significance for plant male fertility and,hence,direct impact on crop yield,pollen exine development has inspired decades of scientific ***,the molecularmechanismunderlying exine formation and thickness remains *** this study,we identified that a previously unrecognized repressor,ZmMS1/ZmLBD30,controls proper pollen exine development in *** an ms1 mutant with aberrantly thickened exine,we cloned a male-sterility gene,ZmMs1,which encodes a tapetum-specific lateral organ boundary domain transcription factor,*** thatZmMs1/ZmLBD30 is initially turned on by a transcriptional activation cascade of ZmbHLH51-ZmMYB84-ZmMS7,and then it serves as a repressor to shut down this cascade via feedback repression to ensure timely tapetal degeneration and proper level of *** activation-feedback repression loop regulating male fertility is conserved in maize and sorghum,and similar regulatory mechanism may also exist in other flowering plants such as rice and ***,these findings reveal a novel regulatory mechanism of pollen exine development by which a long-sought master repressor of upstream activators prevents excessive exine formation.

关键词： ZmMs1/ZmLBD30 LBD transcription factor feedback repression exine male sterility maize

Restauro-G:A Rapid Genome Re-Annotation System for Comparative Genomics

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Genomics, Proteomics & Bioinformatics 2007年第1期5卷 53-58页

作者： Satoshi Tamaki Kazuharu Arakawa Nobuaki Kono Masaru Tomita institute for Advanced biosciences Keio University Fujisawa 252-8520 Japan Department of Environ-mental Information Keio University Fujisawa 252-8520 Japan institute for Advanced biosciences Keio University Fujisawa 252-8520 Japan

of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLASTLike Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http：//***/ under the GNU General Public License.

关键词： bioinformatics software annotation G-language Genome Analysis Environment complete genomes

Foxtail millet:nutritional and eating quality,and prospects for genetic improvement

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Frontiers of agricultural Science and Engineering 2015年第2期2卷 124-133页

作者： Lu HE Bin ZHANG Xingchun WANG Hongying LI Yuanhuai HAN College of Agriculture Shanxi Agricultural UniversityTaigu 030801China institute of agricultural Bioengineering Shanxi Agricultural UniversityTaigu 030801China College of biosciences Shanxi Agricultural UniversityTaigu 030801China Key Laboratory of Loess Plateau Crop Gene Resources and Germplasm Ministry of AgricultureTaiyuan 030001China Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops Shanxi Agricultural UniversityTaigu 030801China

Foxtail millet is a minor yet important crop in some areas of the world,particularly northern *** has strong adaptability to abiotic stresses,especially drought,and poor *** also has high nutritional *** millet is rich in essential amino acids,fatty acids and minerals,and is considered to be one of the most digestible and non-allergenic grains available and has significant importance for human *** foxtail millet’s ability to adapt to abiotic stresses associated with climate change,it is more important than ever to develop breeding strategies that facilitate the increasing demand for high quality grain that better satisfies *** we review research on foxtail millet quality evaluation,appearance,cooking and eating quality at the phenotypic *** review analysis of the main nutrients in foxtail millet,their relationships and the biochemical and genetic factors affecting their *** addition,we review past progress in breeding this regionally important crop,outline current status of breeding of foxtail millet,and make suggestions to improve grain quality.

关键词： foxtail millet grain quality quality evaluation breeding for quality

Genomics approaches to unlock the high yield potential of cassava,a tropical model plant

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Frontiers of agricultural Science and Engineering 2014年第4期1卷 259-266页

作者： Shengkui ZHANG Ping’an MA Haiyan WANG Cheng LU Xin CHEN Zhiqiang XIA Meiling ZOU Xinchen ZHOU Wenquan WANG institute of Tropical biosciences&Biotechnology Chinese Academy of Tropical Agricultural SciencesHaikou 571101China Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture Haikou 571101China

Cassava,a tropical food,feed and biofuel crop,has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition,which makes it highly suitable as a model plant for tropical ***,the understanding of the metabolism and genomics of this important crop is *** recent breakthroughs in the genomics of cassava,including whole-genome sequencing and transcriptome analysis,as well as advances in the biology of photosynthesis,starch biosynthesis,adaptation to drought and high temperature,and resistance to virus and bacterial diseases,are reviewed *** of the new developments have come from comparative analyses between a wild ancestor and existing ***,the current challenges and future potential of cassava as a model plant are discussed.

关键词： cassava genomics yield potential adaptability tropical model