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Preliminary analysis of two NAC transcription factor expression patterns in Larix olgensis

Journal of Forestry Research 2022年第2期33卷 601-609页

作者： Qing Cao Peiqi An Sufang Zhang Junhui Wang Hanguo Zhang Lei Zhang State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040People’s Republic of China Chinese Academy of Forestry Beijing 100000People’s Republic of China

The NAC transcription factor family is plant-specific with various biological functions.However,there are few studies on the NAC gene involving coniferous species.Bioinformatics research and expression analysis of NAC genes in Larix olgensis can be used to analyse the function of the NAC gene in the future.Screening of excellent genetic materials and molecular breeding have been utilized to cultivate high-quality,stress-resistant larches.According to the transcriptome data for L.olgensis,the genes Uni-gene81490 and Unigene70699 with complete ORFs(open reading frames)were obtained by conserved domain analy-sis and named LoNAC1 and LoNAC2,respectively.The cDNAs of LoNAC1 and LoNAC2 were 1971 bp and 1095 bp in length,encoding 656 and 364 amino acids,respectively.The molecular weights of the proteins encoded by the two genes were predicted to be 72.61 kDa and 41.13 kDa,and subcellular localization analysis indicated that the proteins were concentrated in the nucleus.The results of real-time quantitative PCR analysis showed that at different growth stages and in different tissues of L.olgensis,the relative expression levels of the two NAC genes were highest in the stem,and the expression differences were more obvious in non-lignified tissues.After drought,salt and alkali stress and hormone treatment,expression was induced to different degrees.The expression levels of LoNAC1 and LoNAC2 in semi-lignified L.olgensis were higher than in the other two periods(non-lignified and lignified),and expression levels significantly increased under drought and salt stress.Relative expression levels changed under hormone treatment.It is speculated that these two genes may not only be related to drought and salt stress and secondary growth but may also be induced by hormones such as abscisic acid.Overall,LoNAC1 and LoNAC2 are genetic materials that can be used for molecular breeding of larch.

关键词： Larix olgensis NAC transcription factor Bioinformatics analysis expression patterns

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Assignment and expression patterns of porcine muscle-specific isoform of phosphoglycerate mutase gene

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Journal of Genetics and Genomics 2008年第5期35卷 257-260页

作者： Haifang Qiu Shuhong Zhao Xuewen Xu Martine Yerle Bang Liu Lab of Molecular Biology and Animal Breeding Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education Huazhong Agricultural University Wuhan 430070 China INRA Laboratoire de Génétique Cellulaire Castanet-Toloson 31326 France

It has been reported that the muscle-specific isoform （type M, PGAM2） of phosphoglycerate mutase （PGAM） is a housekeeping enzyme; it catalyzes the conversion of 3-phosphoglycerate into 2-phosphoglycerate in the glycolysis process to release energy. It is encoded by the Pgam2 gene. In this study, the cDNA of the porcine Pgam2 was cloned. This gene contains an open reading frame of 765 bp encoding a protein of 253 residues, and the predicted protein sequences share high similarity with other mammalians, 96% identity with humans, and 94% identity with mouse and rats. Pgam2 was mapped to SSC18q13-q21 by the RH panel. In this region, there are several QTLs, such as fat ratio, lean percentage, and diameter of muslce fiber, which affect meat production and quality. The reverse transcriptase-polymerase chain reaction revealed that the porcine Pgam2 gene was mainly expressed in the muscle tissue （skeletal muscle and cardiac muscle）, and was expressed highly at skeletal muscle development stages （embryonic periods： 33, 65, and 90 days post-conception （dpo）; postnatal pigs： 4 days and adult）. This indicates that the Pgam2 gene plays an important role in muscle growth and development. In addition, it was demonstrated that PGAM2 locates both in cytoplasm and nuclei, and takes part in the glycometabolism process of cytoplasm and nuclei.

关键词： assignment expression patterns subcellular localization porcine pgma2

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Analyses of the NAC Transcription Factor Gene Family in Gossypium raimondii Ulbr.:Chromosomal Location,Structure,Phylogeny,and expression patterns

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Journal of Integrative Plant Biology 2013年第7期55卷 663-676页

作者： Haihong Shang Wei Li Changsong Zou Youlu Yuan State Key Laboratory of Cotton Biology Institute of Cotton Researchthe Chinese Academy of Agricultural Sciences

NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor （NAC-TF） genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 （55%） were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on tran- scriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii.

关键词： Cotton expression patterns NAC phylogeny structure,

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Detection of Cytokine expression patterns in the Peripheral Blood of Patients with Acute Leukemia by Antibody Microarray Analysis

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2014年第2期34卷 176-180页

作者：李青李梅吴耀辉朱晓健曾辰邹萍陈智超 Institute of Hematology Union Hospital Tongji Medical College Huazhong University of Science and Technology Department of Pediatric Hematology Union Hospital Fujian Medical University

The cytokines of acute leukemia （AL） patients have certain expression patterns, forming a complex network involved in diagnosis, progression, and prognosis. We collected the serum of different AL patients before and after complete remission （CR） for detection of cytokines by using an antibody chip. The expression patterns of cytokines were determined by using bioinformatics computational analysis. The results showed that there were significant differences in the cytokine expression patterns between AL patients and normal controls, as well as between acute myeloid leukemia （AML） and acute lymphoblastic leukemia （ALL）. In confirmatory test, ELISA revealed the expression of uPAR in AL. Moreover, the bioinformatic analysis showed that the differentially expressed cytokines among the AL groups were involved in different biological behaviors and were closely related with the development of the disease. It was concluded that the cytokine expression pattern of AL patients is significantly different from that of healthy volunteers. Also, differences of cytokine expression patterns exist between AML and ALL, and between before and after CR in the same subtype of AL, which holds important clinical significance for revealing disease progression.

关键词： cytokine microarray acute leukemia expression patterns bioinformatics

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Genome-wide expression patterns of calcium-dependent protein kinases in Toxoplasma gondii

Genome-wide expression patterns of calcium-dependent protein...

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中国畜牧兽医学会兽医寄生虫学分会第十三次学术研讨会

作者： Si-Yang Huang Jin-Lei Wang Nian-Zhang Zhang Jia Chen Xing-Quan Zhu State Key Laboratory of Veterinary Etiological Biology Lanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences

Background:Calcium-dependent protein kinases(CDPKs) were found in plants and some Apicomplexan parasites but not in animals or fungi.CDPKs have been shown to play important roles in various calcium-signaling pathways such as host cell invasion,egress and protein secretion in Toxoplasma gondii.The objectives of the present study were to examine the T.gondii CDPK genes expression patterns during different development stages and stress responses.Methods:We carried out a comprehensive expression analysis of CDPK genes based on previously published microarray datasets,and we also used real time quantitative RT-PCR to study ten T.gondii CDPK genes expression patterns under acid,alkali,high temperature and low temperature conditions.Results:Microarrays analysis indicated that some TgCDPK genes exhibited different expression levels in IFN-γstimuli conditions or at different developmental stages,suggesting that CDPK genes may play different roles in these processes.expression profiles under low temperature,high temperature,acid and alkaline indicated that most CDPK may be involved in regulating high temperature,acid and alkaline signaling pathways.Conclusions:We present a genome-wide expression analysis of CDPK genes in T.gondii for the first time,andthe mRNA levels change with abiotic and biotic stresses,suggesting functional roles in these processes.These results will provide a solid basis for future functional studies of the CDPK gene family in T.gondii.

关键词： Toxoplasma gondii Calcium-dependent protein kinases（CDPKs） expression patterns

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Comparative transcriptome profiling reveals different expression patterns in Xanthomonas oryzae pv.oryzae strains with putative virulence-relevant genes

Comparative transcriptome profiling reveals different expres...

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第十四届全国植物基因组学大会

作者： Fan Zhang Yongli Zhou Zhikang Li Institute of Crop Sciences National Key Facility for Crop Gene Resources and Genetic ImprovementChinese Academy of Agricultural Sciences

Xanthomonas oryzae pv.oryzae(Xoo) is the causal agent of rice bacterial blight, which is a major rice disease in tropical Asian countries.An attempt has been made to investigate gene expression patterns of three Xoo s... 详细信息

关键词： Xoo-rice interaction expression patterns virulence

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Cloning and Analysis expression patterns of Novel PPR Gene in Cotton

Cloning and Analysis Expression Patterns of Novel PPR Gene i...

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中国棉花学会2013年年会

作者： HE Peng LIU Xue-mei YU Jia-ning College of Life Sciences Shaanxi Normal University

PPR ( pentatricopeptide repeats protein ) gene family was widely found in terrestrial plants , and they were involved in plant development , organelle biogenesis , restoring of cytoplasmic male sterilities , post-translational processing and modification , cell signaling , and responses to environmental stresses.Currently , the PPR have been found in many eukaryotic genes , but little was researched in cotton.In this study , we cloned a novel PPRgene GhPPRH1in Gossypium hirsutum , which encoded 637amino acid residues.The tissue expression pattern of this gene indicated that GhPPRH1was high expression in roots , leaves and 15-day fibers , Cluster analysis showed that GhPPRH1shared closed relationship with a PPR in Prunus persica.

关键词： Gossypium hirsutum PPR protein expression patterns

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A major vernalization-independent QTL for tiller angle on chromosome arm 2BL in bread wheat

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The Crop Journal 2022年第1期10卷 185-193页

作者： Jiajun Liu Jieguang Zhou Huaping Tang Yang Tu Yang Mu Lulu Gou Qiantao Jiang Yaxi Liu Guoyue Chen Jirui Wang Pengfei Qi Wei Li Yunfeng Jiang Zehong Yan Houyang Kang Yuming Wei Xiujin Lan Youliang Zheng Jian Ma State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Triticeae Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina College of Agronomy Sichuan Agricultural UniversityChengdu 611130SichuanChina

Tiller angle(TA)strongly influences plant architecture and grain yield in cereals.However,the genetic basis of TA in wheat is largely unknown.We identified three TA-related quantitative trait loci(QTL).One of them was QTa.sau-2 B-769,a major QTL localized on chromosome arm 2 BL.QTa.sau-2 B-769 was detected in seven environments,explaining 18.1%–51.1%of phenotypic variance.We developed a linked Kompetitive Allele-Specific Polymerase chain reaction(KASP)marker,KASP-AX-108792274,to further validate this locus in three additional populations in multiple environments.QTa.sau-2 B-769 increased TA by up to 24.9%in these populations.There were significant and positive correlations between TA and flag leaf angle(FLANG).However,TA was not correlated with plant height or anthesis date,suggesting that expression of QTa.sau-2 B-769 is independent of vernalization.Traes CS2 B01 G583800,a gene known to be involved in leaf angle regulation,was identified as the most likely candidate gene for QTa.sau-2 B-769.These results enrich our understanding of the mechanisms regulating wheat TA at maturity and may support precise mapping and cloning of gene(s)underlying QTa.sau-2 B-769.

关键词： Tiller angle QTL detection and validation Candidate genes expression patterns

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Genome-Wide Identification, Evolution and expression Analyses of GA2ox Gene Family in Brassica napus L.

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Phyton-International Journal of Experimental Botany 2023年第3期92卷 815-835页

作者： Yanhua Li Hualei Huang Youming Shi Shuqin Huang Tao Liu Changming Xiao Xiaoqing Tian Ping Zhao Xiaoyan Dai Taocui Huang Yan Zhou Chongqing Academy of Agricultural Sciences Chongqing401329China Chongqing Municipal Agricultural School Chongqing401329China Fengdu Agricultural Technology Service Center Chongqing408201China

Gibberellin 2-oxidases(GA2ox)are important enzymes that maintain the balance of bioactive GAs in plants.GA2ox genes have been identified and characterized in many plants,but these genes were not investigated in Brassica napus.Here,we identified 31 GA2ox genes in B.napus and 15 of these BnaGA2ox genes were distributed in the A and C subgenomes.Subcellular localization predictions suggested that all BnaGA2ox proteins were localized in the cytoplasm,and gene structure analysis showed that the BnaGA2ox genes contained 2–4 exons.Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups,including two C_(19)-GA2ox and two C_(20)-GA2ox clades.Group 4 is a C_(20)-GA2ox Class discovered recently.Most BnaGA2ox genes had a syntenic relationship with AtGA2ox genes.BnaGA2ox genes in the C subgenome had experienced stronger selection pressure than genes in the A subgenome.BnaGA2ox genes were highly expressed in specific tissues such as those involved in growth and development,and most of them were mainly involved in abiotic responses,regulation of phytohormones and growth and development.Our study provided a valuable evolutionary analysis of GA2ox genes in monocotyledons and dicotyledons,as well as an insight into the biological functions of GA2ox family genes in B.napus.

关键词： Brassica napus GA2ox gene family evolution expression patterns

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Genomic analysis of sugar transporter genes in peanut (Arachis hypogaea):Characteristic,evolution and expression profiles during development and stress

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Oil Crop Science 2022年第4期7卷 189-199页

作者： Zhijun Xu Lei Xu Xiaowen Hu Guangdong Engineering Technology Research Center for Dryland Water-saving Agriculture Zhanjiang Experiment StationChinese Academy of Tropical Agricultural SciencesZhanjiangGuangdongChina Zhanjiang Experimental and Observation Station for National Long-term Agricultural Green Development ZhanjiangGuangdongChina

Peanut(Arachis hypogaea L.) is an economically significant crop with aerial cleistogamous flowers and subterranean geocarpic fruit(pods).The formation of peanut pod requires movement of the embryo from air to ground and then development in the soil,which is a complex biological process involving transport and accumulation of sugars.Sugar transport proteins(STP) mediate the transport of monosaccharides in various physiological processes,including fertilization,ovary formation,and seed development.In this study,a total of 36 AhSTP genes(AhSTP1–36) containing the conserved sugar_tr motif were identified in the A.hypogaea genome.Phylogenetic analysis revealed that AhSTP genes were classified into four clades,and the arrangement of motifs in AhSTP proteins was similar within clades.Synteny analysis revealed that segmental duplication events have played an important role in the expansion of STP genes in peanut,and chromosome rearrangements might have facilitated the exchange of STP genes between the A and B sub-genomes.Transcriptome analyses revealed that the expression patterns of AhSTP genes varied among tissues.Hormone and abiotic stress treatments could upregulate or down-regulate the expression of AhSTP genes,and low temperature had a major effect on the expression of most AhSTP genes.Four AhSTP genes(AhSTP3,AhSTP9,AhSTP19,and AhSTP28) were specifically expressed in the pod,indicating that these genes might be involved in pod formation and development in peanut.The unique expression of these four genes during pod construction and development was confirmed in two different type cultivars using quantitative real-time PCR analysis.Our findings provide new insights into the STP gene family in peanut and will aid future functional studies of AhSTP genes.

关键词： Peanut STP gene Family Evolution expression patterns Pod development

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