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Identification,Phylogeny and Expressional Profiles of Peptidoglycan Recognition Protein(PGRP)gene family in Sinonovacula constricta

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Journal of Ocean University of China 2022年第4期21卷 1051-1060页

作者： MENG Yiping LÜLiyuan DAI Wenfang ZHANG Weiwei LIN Zhihua DONG Yinghui School of Marine Sciences Ningbo UniversityNingbo 315010China Zhejiang Key Laboratory of Aquatic Germplasm Resource College of Biological&Environmental SciencesZhejiangWanli UniversityNingbo 315100China Ninghai Institute of Mariculture Breeding and Seed Industry Zhejiang Wanli UniversityNinghai 315604China

Peptidoglycan recognition protein(PGRP)plays a vital role in invertebrate innate immunity system as a specific pattern recognition receptor for peptidoglycan.Bivalves possess various PGRP systems for self-defense;however,it has not been characterized in razor clam Sinonovacula constricta.In this study,eight PGRP coding sequences were identified and analyzed from S.constricta genome,which are designated as ScPGRP-S1,ScPGRP-S2,ScPGRP-S3,ScPGRP-S4,ScPGRP-S5,ScPGRP-S6,ScPGRP-S7,ScPGRP-S8.The results of molecular evolutionary analyses showed that all eight ScPGRP genes were highly conserved and exhi-bited a typical PGRP/amidase_2 domain as PGRP genes in other mollusks.Moreover,the presence of signal peptides was predicted in ScPGRP-S2,ScPGRP-S3 and ScPRP-S6,while a transmembrane structure only existed in ScPGRP-S6.Notably,a tertiary struc-ture analysis indicated that no disulfide bond was observed in ScPGRP-S5 and ScPGRP-S7.The mRNA transcripts analysis of ScPGRPs revealed that the high expression patterns of ScPGRP-S1 and ScPGRP-S4 were found in mantle,adductor muscle and foot,while those of ScPGRP-S2,ScPGRP-S3 and ScPGRP-S6 were observed in hepatopancreas.Furthermore,the temporal expression profiles of ScPGRPs in the hepatopancreas were analyzed by qPCRafter Gram-negative Vibrio parahaemolyticus and Gram-positive Staphylococcus aureus challenges.The mRNA expressions of ScPGRP-S2,ScPGRP-S3 and ScPGRP-S6 could be induced by V.pa-rahaemolyticus and S.aureus.Overall,our findings indicated that ScPGRPs were involved in the immune defense against invaders,which constituted a comprehensive understanding of the potential role of PGRP genes in S.constricta.

关键词： Sinonovacula constricta peptidoglycan recognition protein gene family gene expression

Genome-wide identification and characterization of the abiotic-stress-responsive lipoxygenase gene family in diploid woodland strawberry(Fragaria vesca)

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Journal of Integrative Agriculture 2022年第7期21卷 1982-1996页

作者： LI Zhi-qi XIE Qian YAN Jia-hui CHEN Jian-qing CHEN Qing-xi College of Horticulture Fujian Agriculture and Forestry UniversityFuzhou 350002P.R.China Horticultural Plant Biology and Metabolomics Center of Haixia Institute of Science and Technology Fujian Agriculture and Forestry UniversityFuzhou 350002P.R.China

Lipoxygenase(LOXs)is a kind of dioxygenase without heme and iron,which plays an important role in the development and adaptation of many plants to the environment.However,the study of strawberry LOX gene family has not been reported.In this study,14 LOX genes were identified from the diploid woodland strawberry genome.The phylogenetic tree divides the FvLOX gene into two subfamilies:9-LOX and 13-LOX.gene duplication event analysis showed that whole-genome duplication(WGD)/segmental duplication and dispersed duplication effectively promoted the expansion of strawberry LOX family.QRT-PCR analysis showed that FvLOX genes were expressed in different tissues.Expression profile analysis showed that FvLOX1 and FvLOX8 were up-regulated under low temperature stress,FvLOX3 and FvLOX7 were up-regulated under drought stress,FvLOX6 and FvLOX9 were up-regulated under salt stress,FvLOX2,FvLOX3 and FvLOX6 were up-regulated under salicylic acid(SA)treatment,FvLOX3,FvLOX11 and FvLOX14 were up-regulated under methyl jasmonate(MeJA)treatment,FvLOX4 and FvLOX14 were up-regulated under abscisic acid(ABA)treatment.Promoter analysis showed that FvLOX genes were involved in plant growth and development and stress response.We analyzed and identified the whole genome of strawberry FvLOX family and characterized a variety of FvLOX candidate genes involved in abiotic stress response.This study laid a theoretical and empirical foundation for the response mechanism of strawberry to abiotic stress.

关键词： lipoxygenase gene family strawberry abiotic stress expression pattern cis-acting element

Molecular characterization of the SAUR gene family in sweet cherry and functional analysis of PavSAUR55 in the process of abscission

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Journal of Integrative Agriculture 2023年第6期22卷 1720-1739页

作者： HOU Qian-dong HONG Yi WEN Zhuang SHANG Chun-qiong LI Zheng-chun CAI Xiao-wei QIAO Guang WEN Xiao-peng Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Life Sciences/Institute of Agro-bioengineeringGuizhou UniversityGuiyang 550025P.R.China College of Forestry/Institute for Forest Resources&Environment of Guizhou Guizhou UniversityGuiyang 550025P.R.China

Small auxin up RNA(SAUR) is a large gene family that is widely distributed among land plants. In this study, a comprehensive analysis of the SAUR family was performed in sweet cherry, and the potential biological functions of PavSAUR55 were identified using the method of genetic transformation. The sweet cherry genome encodes 86 SAUR members, the majority of which are intron-less. These genes appear to be divided into seven subfamilies through evolution. gene duplication events indicate that fragment duplication and tandem duplication events occurred in the sweet cherry. Most of the members mainly underwent purification selection pressure during evolution. During fruit development, the expression levels of Pav SAUR16/45/56/63 were up-regulated, and conversely, those of Pav SAUR12/61were down-regulated. Due to the significantly differential expressions of PavSAUR13/16/55/61 during the fruitlet abscission process, they might be the candidate genes involved in the regulation of physiological fruit abscission in sweet cherry. Overexpression of PavSAUR55 in Arabidopsis produced earlier reproductive growth, root elongation, and delayed petal abscission. In addition, this gene did not cause any change in the germination time of seeds and was able to increase the number of lateral roots under abscisic acid(ABA) treatment. The identified SAURs of sweet cherry play a crucial role in fruitlet abscission and will facilitate future insights into the mechanism underlying the heavy fruitlet abscission that can occur in this fruit crop.

关键词： sweet cherry small auxin up RNA gene family expression profile fruitlet abscission

Protein Disulfide Isomerase and Its Potential Function on Endoplasmic Reticulum Quality Control in Diatom Phaeodactylum tricornutum

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Phyton-International Journal of Experimental Botany 2024年第1期93卷 137-150页

作者： Yanhuan Lin Hua Du Zhitao Ye Shuqi Wang Zhen Wang Xiaojuan Liu Zhangzhou Institute of Technology ZhangzhouChina Guangdong Provincial Key Laboratory of Marine Biotechnology Guangdong Provincial Key Laboratory of Marine Disaster Prediction and PreventionCollege of SciencesShantou UniversityShantouChina

PDI is a molecular chaperone and plays an important role in Endoplasmic Reticulum quality control (ERQC).PDI participates in the refolding of the misfolded/unfolded proteins to maintain cellular homeostasis under differentstresses. However, bioinformatic characteristics and potential functions of PDIs in diatom Phaeodactylumtricornutum (Pt) are still unknown so far. Hence, the genome-wide characteristics of PtPDI proteins in P. tricornutumwere first studied via bioinformatic and transcriptomic methods. 42 PtPDI genes were identified from thegenome of P. tricornutum. The motif, protein structure, classification, number of introns, phylogenetic relationship,and the expression level of 42 PtPDI genes under the tunicamycin stress were analyzed. A pair of tandemduplicated genes (PtPDI15 and PtPDI18) was observed in P. tricornutum. The 42 PtPDIs with different genecharacteristics were divided into three independent clades, indicating different evolutional relationships and functionsof these PtPDIs. The 14 up-regulated PtPDI genes under the tunicamycin treatment might have a positiveeffect on the ER quality control of the unfolded/misfolded proteins, while the 7 down-regulated PtPDIs mightnegatively affect the ERQC. The characteristics of all 42 PtPDIs and their proposed working model here providea comprehensive understanding of the PtPDIs gene family. The differential expression of 21 PtPDIs will be usefulfor further functional study in the ERQC.

关键词： Protein disulfide isomerase gene family Endoplasmic Reticulum quality control Phaeodactylum tricornutum

Genome-Wide Identification and Expression Analysis of the Phytocyanin gene family in Nicotiana tabacum

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Phyton-International Journal of Experimental Botany 2023年第5期92卷 1469-1492页

作者： Peiling Wang Xiaohong Xu Yong Li Hecui Zhang Xuejie Zhang Siru Zhou Yimei Liu Yunyan Feng Tonghong Zuo Liquan Zhu School of Agronomy and Biotechnology Engineering Research Center of South Upland AgricultureMinistry of EducationSouthwest UniversityChongqing400715China Tobacco Science Research Institute of Chongqing Tobacco Company Chongqing400715China Chongqing Qianjiang Tobacco Branch Company Chongqing Institute of Tobacco Science Chongqing400715China

Phytocyanin(PC)is a class of plant-specific blue copper proteins involved in electron transport,plant growth,development,and stress resistance.However,PC proteins have not been systematically evaluated in tobacco plants.We determined the whole-genome sequences of the PC family in the tobacco cultivar‘K326.’The transcriptome data were used to analyze the expression of the NtPC family at different development stages and tissue-specific genes.Real-time fluorescence quantitative analysis was used to analyze the expression of the NtPC gene family under low temperature and methyl jasmonate stress.The tobacco NtPC family contained 110 members and was divided into four subfamilies:early nodulin-like protein(NtENODL),uclacyanin-like protein,stellacyanin1-like protein,and plantacyanin-like protein.According to phylogenetic and structural analyses,the NtPC family could be divided into eight structural types.Fifty-three NtPCs were randomly distributed on 22 of 24 tobacco chromosomes.Collinearity analysis revealed 33 pairs of genes belonging to the NtPC family.gene ontology analysis showed that the PC genes are components of the plasma membrane and may participate in plasma membrane-related functions.The NtPC family contained numerous elements related to hormonal and abiotic stress responses and was specifically expressed in the tobacco prosperous,maturation,and budding periods.Tissue-specific expression analysis showed that some genes were tissue specific.The expression of NtENODL58 and other genes was significantly induced by low-temperature and methyl jasmonate stress.Thus,the NtPC gene family plays an important role in plant stress response.

关键词： Tobacco phytocyanin gene family bioinformatics gene expression

Genome-wide identification and expression profiling of the YUCCA gene family in Brassica napus

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Oil Crop Science 2022年第3期7卷 103-111页

作者： Ka Zhang Jinfang Zhang Cheng Cui Liang Chai Benchuan Zheng Jun Jiang Haojie Li Jinxing Tu Crop Research Institute Sichuan Academy of Agricultural SciencesChengdu610066China National Key Laboratory of Crop genetic Improvement National Sub-Center of Rapeseed Improvement in WuhanCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China

Auxin is essential for plant growth and development,also closely related to plant architecture.YUCCA(YUC)proteins catalyse the rate-limiting step for endogenous auxin biosynthesis.In this study,we identified 57 Bn YUC genes in Brassica napus(rapeseed)genome,located on 17 chromosomes.Among them,A09 chromosome contained the most Bn YUCs as 6.Phylogenetic tree showed that all Bn YUC members were divided into 2 evolutionary clusters,including 7 sub-groups.Among the sub-groups,Clade I-C consisted 20 members,evolved independently from Arabidopsis thaliana,and motif 10 was unique.Genomic collinearity analysis showed that YUC collinear gene pairs widely existed in Brassica species,indicating that this family has a high retention rate in the evolution.Expression profile suggested that the Bn YUC family genes tended to express in specific growth/development stages as well as suffering stress/hormone treatments.It suggested that dominant expression of specific members existed with each development stage or treatment,indicating that each Bn YUC might have a clear division of work,and play a given biological function.This work was expected to build a basis for further study of the involvement of Bn YUC in growth,development and stress response.

关键词： Brassica napus YUCCA(YUC) Auxin biosynthesis gene family Plant architecture

Oxidative stress drives divergent evolution of the glutathione peroxidase(GPX)gene family in mammals

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Integrative Zoology 2021年第5期16卷 696-711页

作者： Ran TIAN Yuepan GENG Ying YANG Inge SEIM Guang YANG Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjingJiangsuChina Integrative Biology Laboratory College of Life SciencesNanjing Normal UniversityNanjingJiangsuChina School of Biology and Environmental Science Queensland University of TechnologyBrisbaneQueenslandAustralia

The molecular basis for adaptations to extreme environments can now be understood by interrogating the everincreasing number of sequenced genomes.Mammals such as cetaceans,bats,and highland species can protect themselves from oxidative stress,a disruption in the balance of reactive oxygen species,which results in oxidative injury and cell damage.Here,we consider the evolution of the glutathione peroxidase(GPX)family of antioxidant enzymes by interrogating publicly available genome data from 70 mammalian species from all major clades.We identified 8 GPX subclasses ubiquitous to all mammalian groups.Mammalian GPX gene families resolved into the GPX4/7/8 and GPX1/2/3/5/6 groups and are characterized by several instances of gene duplication and loss,indicating a dynamic process of gene birth and death in mammals.Seven of the eight GPX subfamilies(all but GPX7)were under positive selection,with the residues under selection located at or close to active sites or at the dimer interface.We also reveal evidence of a correlation between ecological niches(e.***.high oxidative stress)and the divergent selection and gene copy number of GPX subclasses.Notably,a convergent expansion of GPX1 was observed in several independent lineages of mammals under oxidative stress and may be important for avoiding oxidative damage.Collectively,this study suggests that the GPX gene family has shaped the adaption of mammals to stressful environments.

关键词： adaptive evolution gene family glutathione peroxidase mammals oxidative stress

In silico genome-wide identification,phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula

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Journal of Integrative Agriculture 2017年第7期16卷 1576-1591页

作者： ZHENG Xing-wei YI Deng-xia SHAO Lin-hui LI Cong Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijing 100193P.R.China

The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.

关键词： R2R3-MYB Medicago truncatula gene family stress response function prediction

Genome-wide analysis of the calcium-dependent protein kinase gene family in Gossypium raimondii

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Journal of Integrative Agriculture 2015年第1期14卷 29-41页

作者： LI Li-bei YU Ding-wei ZHAO Feng-li PANG Chao-you SONG Mei-zhen WEI Heng-ling FAN Shu-li YU Shu-xun State Key Laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural Sciences

Plant calcium-dependent protein kinases （CDPKs） play important roles in diverse physiological processes by regulating the downstream components of calcium signaling. To date, only a few species of the plant CDPK gene family have been functionally identified. In addition, there has been no systematic analysis of the CDPK family in cotton. Here, 41 putative cotton CDPK （GrCDPK） genes were identified via bioinformatics analysis of the entire genome of Gossypium raimondii and were classified into four groups based on evolutionary relatedness. gene structure analysis indicated that most of these GrCDPK genes share a similar intron-exon structure （7 or 8 exons）, strongly supporting their close evolutionary relationships. Chromosomal distributions and phylogenetics analysis showed that 13 pairs of GrCDPK genes arose via segmental duplication events. Furthermore, using microarray data of upland cotton （G. hirsutum L.）, comparative profiles analysis of these GhCDPKs indicated that some of the encoding genes might be involved in the responses to multiple abiotic stresses and play important regulatory roles during cotton fiber development. This study is the first genome-wide analysis of the CDPK family in cotton, and it will provide valuable information for the further functional characterization of cotton CDPK genes.

关键词： GrCDPK cotton stress gene family expression