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Journal of Environmental Sciences 2023年第3期125卷 480-491页

作者： Biran Zhu Ziniu Wang Lei Lei Yongyong Guo Jian Han Bingsheng Zhou State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China School of Basic Medical Sciences Hubei University of Chinese MedicineWuhan 430065China State Key Laboratory of Environmental Chemistry and Ecotoxicology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China

Cadmium (Cd),a ubiquitous environmental hazardous heavy metal,poses a significant threat to the health of aquatic organisms,including *** the toxic profile of Cd is well recognized,little is known regarding the overall view of toxic responses to varying aquatic environmental parameters (e.g.,water hardness) at an individual ***,differences in water hardness were partially mimicked by adjusting Ca^(2+)levels in E3 *** an in vivo model,zebrafish embryos were exposed to variable Ca^(2+)levels (NV,normal Ca^(2+);LV,low Ca^(2+);HV,high Ca^(2+)) alone or combined with 30.7μg/L Cd^(2+)(NC,LC,and HC,respectively) until 144 hr *** genome-wide transcriptome revealed differentially expressed genes between *** enrichment analysis found that biological processes related to metabolism,particularly lipid metabolism,were significantly disrupted in NC and LC treatments,while a remission was observed in the HC *** assays confirmed that the decrease in Ca^(2+)enhanced synthesis,inhibited mobilization and increased the storage of lipids in Cd^(2+)*** study suggests that the toxic effect of Cd on biological pathways will be influenced by Ca^(2+),which will improve the toxicological understanding and facilitate accurate assessment of Cd.

关键词： Cadmium Calcium Zebrafish larvae transcriptome Metabolism disorder

transcriptome Analysis of Crassostrea sikamea (♀) × Crassostrea gigas (♂) Hybrids Under and After Thermal Stress

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Journal of Ocean University of China 2022年第1期21卷 213-224页

作者： ZHANG Xuekai FAN Chao ZHANG Xingzhi LI Qiongzhen LI Yangchun MA Peizhen YUE Shaobo HUO Zhongming WANG Zhaoping Fisheries College Ocean University of ChinaQingdao 266003China Guangxi Academy of Fisheries Sciences Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy AquacultureNanning 530021China

Crossbreeding is an effective approach to manage the genetic decline in ***-way hybrids of Crassostrea sikamea(♀)and Crassostrea gigas(♂)have advantages in growth traits and adaptation to high ***,we used high-throughput sequencing to analyze the molecular processes in the hybrids under and after thermal *** hybrids were cultured in the seawater with an increasing temperature from 25℃to 40℃during 10 hours,which is regarded as the thermal stress *** the temperature decreased from 40℃to 25℃within 2 h,which is regarded as the recovery *** this study,1293 significant diffe-rentially expressed genes(DEGs)were obtained under thermal stress,of which 576 were upregulated and 717 were downregulated,and 740 significant differentially expressed genes(DEGs)were obtained in the recovery stage,of which the number of upregulated and downregulated genes was 409 and 331,*** antigen processing and presentation,NOD-like,and NF-kappa B path-ways were significantly enriched during the thermal stress *** MAPK and PPAR signaling pathways were significantly enrich-ed during the recovery *** HSP70,HSP90,and CANX genes were strongly and rapidly upregulated in the control/thermal stress groups but were slightly less upregulated in the thermal stress/recovery *** results indicate that the innate immune system or nonspecific immunity was deployed to protect interior tissues from thermal *** addition,85%of the mutual DEGs were involved in bidirectional regulation(up/down or down/up)when the oysters were removed from the thermal stress to *** study provides preliminary insight into the molecular response of ***(♀)and ***(♂)hybrids to thermal stress and provides a basis for future studies on temperature-adaptation and the possible expansion of hybrid breeding.

关键词： oyster hybrids gill thermal stress recovery transcriptome

transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

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Science China(Life Sciences) 2016年第2期59卷 164-171页

作者： Changsong Zou Qiaolian Wang Cairui Lu Wencui Yang Youping Zhang Hailiang Cheng Xiaoxu Feng Mtawa Andrew Prosper Guoli Song State Key Laboratory of Cotton Biology Institute of Cotton Research Chinese Academy of Agricultural Sciences

Long noncoding RNAs （lncRNAs） play important roles in various biological regulatory processes in yeast, mammals, and plants. However, no systematic identification of lncRNAs has been reported in Gossypium arboreum. In this study, the strand-specific RNA sequencing （ssRNA-seq） of samples from cotton fibers and leaves was performed, and lncRNAs involved in fiber initiation and elongation processes were systematically identified and analyzed. We identified 5,996 lncRNAs, of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs （lincRNAs） and natural antisense transcripts （IncNAT）, respectively. LincRNAs and lncNATs are similar in many aspects, but have some differences in exon number, exon length, and transcript length. Expression analysis revealed that 51.9% of lincRNAs and 54.5% of lncNATs transcripts were preferentially expressed at one stage of fiber development, and were significantly highly expressed than protein-coding tran- scripts （21.7%）. During the fiber and rapid elongation stages, rapid and dynamic changes in lncRNAs may contribute to fiber development in cotton. This work describes a set of lncRNAs that are involved in fiber development. The characterization and expression analysis of lncRNAs will facilitate future studies on their roles in fiber development in cotton.

关键词： long noncoding RNAs strand specific RNA sequencing fiber transcriptome expression

transcriptome exploration to provide a resource for the study of Auricularia heimuer

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Journal of Forestry Research 2020年第5期31卷 1881-1887页

作者： Jian Zhang Tingting Sun Shixin Wang Li Zou College of Forestry Northeast Forestry UniversityHarbin 150040People’s Republic of China Department of Food Engineering Harbin UniversityHarbin 150086People’s Republic of China

Auricularia heimuer,an edible jelly fungus,is in considerable demand in Asia due to its high nutritive,economic and medicinal ***-Seq was used to investigate and analyze the mycelium transcriptome of *** for gene discovery.A total of 26,857 unigenes with an N50 length of 1333 bp were assembled by de novo *** addition,unigenes were annotated by publicly available databases,including gene descriptions,gene ontology(GO),clusters of orthologous group(COG),Kyoto Encyclopedia of Genes and Genomes(KEGG)metabolic pathways,and protein family(Pfam)*** was also studied for its wood degradation ***-eight putative FOLymes(fungal oxidative lignin enzymes)and 251 CAZymes(carbohydrate-active enzymes)were located from *** *** study provides a comprehensive sequence resource for *** at the transcriptional level,which will lay a strong foundation for functional genomics studies and gene discovery of this promising fungus.

关键词： Auricularia heimuer transcriptome Carbohydrate active enzymes Lignin degradation Nextgeneration sequencing

transcriptome analysis reveals the effects of alkali stress on root system architecture and endogenous hormones in apple rootstocks

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Journal of Integrative Agriculture 2019年第10期18卷 2264-2271页

作者： LIU Xuan LIANG Wei LI Yu-xing LI Ming-jun MA Bai-quan LIU Chang-hai MA Feng-wang LI Cui-ying State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple College of Horticulture Northwest A&F University

Soil alkalinity is a major factor that restricts the growth of apple *** analyze the response of apple roots to alkali stress, the root structure and endogenous hormones of two apple rootstocks, Malus prunifolia (alkali-tolerant) and Malus hupehensis (alkali-sensitive), were compared. To understand alkali tolerance of M. prunifolia at the molecular level, transcriptome analysis was performed. When plants were cultured in alkaline conditions for 15 d, the root growth of M. hupehensis with weak alkali tolerance decreased significantly. Analysis of endogenous hormone levels showed that the concentrations of indole-3-acetic acid (IAA) and zeatin riboside (ZR) in M. hupehensis under alkali stress were lower than those in the control. However, the trend for IAA and ZR in M. prunifolia was the opposite. The concentration of abscisic acid (ABA) in the roots of the two apple rootstocks under alkali stress increased, but the concentration of ABA in the roots of M. prunifolia was higher than that in M. hupehensis. The expression of IAA-related genes ARF5, GH3.6, SAUR36, and SAUR32 and the Cytokinin (CTK)-related gene IPT5 in M. prunifolia was higher than those in the control, but the expression of these genes in M. hupehensis was lower than those in the control. The expression of ABA-related genes CIPK1 and AHK1 increased in the two apple rootstocks under alkali stress, but the expression of CIPK1 and AHK1 in M. prunifolia was higher than in M. hupehensis. These results demonstrated that under alkali stress, the increase of IAA, ZR, and ABA in roots and the increase of the expression of related genes promoted the growth of roots and improved the alkali tolerance of apple rootstocks.

关键词： alkali stress apple rootstock endogenous hormone root architecture transcriptome analysis

transcriptome profiling using RNA-seq to provide insights into foxtail millet seedling tolerance to short-term water deficit stress induced by PEG-6000

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Journal of Integrative Agriculture 2019年第11期18卷 2457-2471页

作者： XU Bing-qin GAO Xiao-li GAO Jin-feng LI Jing YANG Pu FENG Bai-li College of Agronomy Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas Ministry of Science and Technology

Foxtail millet(Setaria italica L.)with high drought resistance,is grown widely in arid and semi-arid regions of the world,and it is a new model plant for genetic and molecular *** uncover the molecular mechanisms of stress-tolerance in different genotypes of foxtail millet,physiological analyses combined with transcriptional profiling were conducted using a time-course analysis on two foxtail millet genotypes Damaomao(DM)and Hongnian(HN).The genotype DM performed better than HN under water deficiency,with more moderate relative water content(RWC)and chlorophyll *** physiological and RNA-seq investigations revealed that the two genotypes possessed high conservatism in some vital biological pathways which respond to drought stress,involving hormone synthesis,proline,and soluble sugar synthesis,and reactive oxygen species(ROS)***,some genes related to these pathways showed different expression ***,the lower malondialdehyde(MDA)content in HN than DM may be explained by the observation that HN contained more activated genes in the ascorbate-glutathione cycle using KEGG pathway ***,abscisic acid(ABA)response genes,ROS scavengers which were probably involved in signaling responses,a set of enzymes involved in proline and soluble sugar synthesis,channel protein genes,and transcription factors,encompassed the early strategy of foxtail millet response to *** findings provide a comprehensive molecular view of how different foxtail millet genotypes respond to short-term osmotic stress.

关键词： transcriptome foxtail millet osmotic stress RNA-seq gene expression

transcriptome Analysis of Schwann Cells at Various Stages of Myelination Implicates Chromatin Regulator Sin3A in Control of Myelination Identity

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Neuroscience Bulletin 2022年第7期38卷 720-740页

作者： Bin Zhang Wenfeng Su Junxia Hu Jinghui Xu Parizat Askar Shuangxi Bao Songlin Zhou Gang Chen Yun Gu Jiangsu Key Laboratory of Neuroregeneration Co-innovation Center of NeuroregenerationJiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury RepairNMPAKey Laboratory for ResearchEvaluation of Tissue Engineering Technology ProductsNantong UniversityNantong 226001China

Enhancing remyelination after injury is of utmost importance for optimizing the recovery of nerve *** the formation of myelin by Schwann cells(SCs)is critical for the function of the peripheral nervous system,the temporal dynamics and regulatory mechanisms that control the progress of the s lineage through myelination require further ***,using in vitro co-culture models,gene expression profiling of laser capture-microdissected SCs at various stages of myelination,and multilevel bioinformatic analysis,we demonstrated that SCs exhibit three distinct transcriptional characteristics duringmyelination:the immature,promyelinating,and myelinating *** showed that suppressor interacting 3a(Sin3A)and 16 other transcription factors and chromatin regulators play important roles in the progress of ***3A knockdown in the sciatic nerve or specifically in SCs reduced or delayed the myelination of regenerating axons in a rat crushed sciatic nerve model,while overexpression of Sin3A greatly promoted the remyelination of ***,in vitro experiments revealed that Sin3A silencing inhibited SC migration and differentiation at the promyelination stage and promoted SC proliferation at the immature *** addition,SC differentiation and maturation may be regulated by the Sin3A/histone deacetylase2(HDAC2)complex functionally cooperating with Sox10,as demonstrated by rescue ***,these results complement the recent genome and proteome analyses of SCs during peripheral nerve myelin *** results also reveal a key role of Sin3A-dependent chromatin organization in promoting myelinogenic programs and SC differentiation to control peripheral myelination and *** findings may inform new treatments for enhancing remyelination and nerveregeneration.

关键词： (Re)myelination Schwann cells Sin3A transcriptome Peripheral nerve injury

transcriptome Analysis During Tetrasporogenesis of Gracilariopsis lemaneiformis and Preliminary Study of the Expressions of Its Meiotic Genes

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Journal of Ocean University of China 2023年第2期22卷 541-554页

作者： ZHU Weifang YANG Ze XU Di YANG Jinxin ZHANG Yingyue PAN Xiaohui The Key Laboratory of Marine Genetics and Breeding Ministry of EducationCollege of Marine Life SciencesOcean University of ChinaQingdao 266003China

The transcriptomes of three different parts of the fertile tetrasporophyte of Gracilariopsis lemaneiformis,including tip(T),middle(M),and subjacent(S)parts,with a gradual tetrasporangium maturity were analyzed and compared to identify the genes involved in the process of *** number of differentially expressed genes(DEGs)for the Gple-S versus Gple-T comparison was 10296,and the numbers of DEGs for the Gple-S versus Gple-M and Gple-T versus Gple-M comparisons were 7435 and 1337,*** Ontology and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed,and the results showed the enrichment of 132 KEGG pathways(corrected Ptranscriptome comparison indicated that in the T part,the meiosis,ribosome,and RNA transport-related genes were mostly up-regulated compared with those in the other two *** the M part,the genes related to ribosomes and the endoplasmic reticulum were also up-regulated compared with those in the lower ***,in the S part,the genes associated with photosynthesis were mostly up-regulated,which might be helpful to the recovery from spore formation and release.

关键词： Gracilariopsis lemaneiformis transcriptome tetrasporogenesis meiosis related genes

transcriptome analysis of carotenoid biosynthesis in Dunaliella salina under red and blue light

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Journal of Oceanology and Limnology 2020年第1期38卷 177-185,I0016-I0018页

作者： LI Yuanxiang CAI Xuehua GU Wenhui WANG Guangce Key Laboratory of Experimental Marine Biology Institute of OceanologyCenter for Ocean Mega-ScienceChinese Academy of SciencesQingdao 266071China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266071China College of Earth Sciences University of Chinese Academy of SciencesBeijing 100049China

The quality of light is an important abiotic factor that affects the growth and development of photosynthetic *** this study,we exposed the unicellular green alga Dunaliella salina to red(660 nm)and blue(450 nm)light and analyzed the cell growth,total carotenoid content,and *** growth of *** was enhanced by illumination with red light,whereas blue light was not able to promote the algal *** contrast,the total carotenoid content increased under both red and blue *** RNA of *** was sequenced and the transcriptomic response of algal cells to red and blue light was *** transcripts encoding for the blue light receptor cryptochrome were identified,and transcripts involved in the carotenoid metabolism were up-regulated under both red and blue *** encoding for photoprotective enzymes related to the scavenging of reactive oxygen species were up-regulated under blue *** present transcriptomic study provides a more comprehensive understanding of carotenoid biosynthesis in *** under different wavelengths of light.

关键词： blue light carotenoid Dunaliella red light transcriptome

transcriptome analysis of sugar beet root maggot （Tetanops myopaeformis） genes modulated by the Beta vulgaris host

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Insect Science 2018年第2期25卷 222-234页

作者： Haiyan Li Ann C. Smigocki USDA-ARS Molecular Plant Pathology Laboratory Beltsville Maryland US

Sugar beet root maggot （SBRM, Tetanops myopaeformis von R6der） is a major but poorly understood insect pest of sugar beet （Beta vulgaris L.）. The molecular mecha- nisms underlying plant defense responses are well documented, however, little information is available about complementary mechanisms for insect adaptive responses to overcome host resistance. To date, no studies have been published on SBRM gene expression pro- filing. Suppressive subtractive hybridization （SSH） generated more than 300 SBRM ESTs differentially expressed in the interaction of the pest with a moderately resistant （F1016） and a susceptible （F1010） sugar beet line. Blast2GO v. 3.2 search indicated that over 40% of the differentially expressed genes had known functions, primarily driven by fruit fly D. melanogaster genes. Expression patterns of 18 selected EST clones were confirmed by RT-PCR analysis. Gene Ontology （GO） analysis predicted a dominance of metabolic and catalytic genes involved in the interaction of SBRM with its host. SBRM genes function- ing during development, regulation, cellular process, signaling and under stress conditions were annotated. SBRM genes that were common or unique in response to resistant or susceptible interactions with the host were identified and their possible roles in insect responses to the host are discussed.

关键词： Beta vulgaris resistant sugar beet root maggot suppressive subtractivehybridization susceptible transcriptome