玉米Dof转录因子家族基因的全基因组分析

Dof转录因子家族在植物生长发育和基因表达调控过程中具有重要的作用,本文利用公布的玉米基因组草图数据,利用生物信息学方法对玉米全基因组Dof基因的结构、系统进化关系和保守motif进行了分析。结果表明:玉米中共有18个Dof类型基因,命名为ZmDof1-ZmDof18,其蛋白质长度在211aa至618aa之间,通过系统进化树分析后,18个Dof基因可以明显的分为三类,此外玉米Dof基因的数目远远小于水稻和拟南芥,基因复制现象较少是玉米Dof基因数量较少的原因之一,MEME分析证实了Dof基因含有三个保守的motif。对玉米Dof类型基因的系统分析,将有助于玉米Dof类型基因的克隆和功能的进一步研究。     

Genome-wide identification and characterization of HSP70 gene family in four species of cotton

Heat shock proteins (HSPs) are important elements of the cellular group of molecular chaperones. Specifically, HSP70 proteins protect cells from being damaged when plants are exposed to environmental stresses. These proteins are catalysts that manage the correct folding of other proteins, and they play a key role in the development of tolerance against biotic and abiotic stresses. In the present study, 113 HSP70 genes were retrieved from the available genome assemblies of four cotton species, including Gossypium hirsutum, G. barbadense, G. arboreum, and G. raimondii. The HSP70 genes were clustered into 11 subfamilies based on phylogeny. One hundred and nine (109) gene duplications were found across these four species. Localization of genes revealed that several HSP70 genes reside in the cytoplasm. Synonymous and non-synonymous substitution rates revealed that functional segregation of HSP70 genes in cotton is due to purifying selection. Furthermore, HSP70 genes in cotton are expressed constitutively during developmental stages. These findings are valuable to understand the complex mechanism of HSP70 gene regulation that occurs in signaling pathways in response to plant stress.     

Genome-wide bioinformatics analysis of Dof transcription factor gene family of chickpea and its comparative phylogenetic assessment with Arabidopsis and rice

The genome mining of chickpea (Cicer arietinum L.) revealed a total of 37 putative Dof genes using NCBI BLAST search against the genome with a highly conserved Dof domain. The translated Dof proteins possessed 150–493 amino acid residues with molecular weight ranging from 16.9 to 54.4 kD and pI varied from 4.98 to 9.64 as revealed by ExPASy server ProtParam. The exon–intron organization showed predominance of intronless Dof genes in chickpea. The predicted Dof genes were distributed among the eight chromosomes with a maximum of 9 Dof genes present on chromosome 7 and a single Dof gene was found on chromosome 8.The predominance of segmental gene duplication as compared to tandem duplication was observed which might be the prime cause of Dof gene family expansion in chickpea. The cis-regulatory element analysis revealed the presence of light-responsive, hormone-responsive, endosperm-specific, meristem-specific and stress-responsive elements. Comprehensive phylogenetic analyses of Dof genes of chickpea with Arabidopsis, rice, soybean and pigeonpea revealed several orthologs and paralogs assisting in understanding the putative functions of CaDof genes. The functional divergence and site-specific selective pressures of chickpea Dof genes have been investigated. The bioinformatics-based genome-wide assessment of Dof gene family of chickpea attempted in the present study could be a significant step for deciphering novel Dof genes based on genome-wide expression profiling.     

Genome-wide identification,characterization and expression analysis of the LIM transcription factor family in quinoa

Lim family members play an important role in the regulation of plant cell development and stress response. However, there are few studies on LIM family in quinoa. In this study, we identified nine LIMS (named cqlim01-cqlim09) from quinoa, which were divided into three subfamilies (α Lim1, γ lim2 and δ lim2) according to phylogeny. The differences in gene structure and motif composition among different subfamilies have been observed. In addition, we studied the repetitive events of the members of the family. The Ka/Ks (non synchronous substitution rate / synchronous substitution rate) ratio analysis showed that the repetitive CqLIMs probably experienced purifying selection pressure. Promoter analysis showed that the family genes contained a variety of hormones, stress and tissue-specific expression elements, and protein interactions showed that these genes had actin stabilizing effect. In addition, QRT PCR results showed that all CqLIM genes were positively regulated under three stresses (low temperature, salt and ABA). These results provide a theoretical basis of further study of LIM gene in quinoa. Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-00988-2.     

花生MYB转录因子的鉴定与生物信息学分析

MYB转录因子是植物中重要的基因家族之一,参与多种生物学功能的调控.目前对花生(Arachis hypogaea)MYB转录因子家族的功能仍知之甚少,对花生中MYB转录因子的鉴定及生物信息学分析具有重要的意义.本研究在栽培花生中共鉴定出MYB转录因子443个,包括219个1R-MYB、209个2R-MYB、12个3R-...     

毛竹GRF转录因子家族的全基因组鉴定与分析

利用生物信息学方法,于毛竹(Phyllostachys edulis (Carr.) Lehaie)全基因组中鉴定获得18个GRF转录因子,并对其理化特性、保守结构域、系统发育关系、mi R396靶位点以及基因表达模式进行了分析。结果表明,18个Pe GRF蛋白长度为170～551 aa,分子量为18.5～58.8 k D;这些Pe GRF蛋白均具有QLQ和WRC结构域,部分Pe GRF含有FFD和TQL保守结构域。对毛竹、拟南芥(Arabidopsis thaliana (L.) Heynh)和水稻(Oryza sativa L.)的系统进化分析结果显示,毛竹18个GRF可分为3个亚类,且单子叶植物毛竹和水稻的GRF转录因子亲缘关系更近。mi R396靶位点预测分析结果发现,在13个Pe GRF基因序列的编码区存在毛竹mi R396结合位点; Pe GRF基因表达模式分析结果显示,Pe GRF主要在毛竹的竹笋中表达。     

Genome-wide identification of laccase gene family in three Phytophthora species

Phytophthora spp. is a primary pathogen in oomycete, causing economically and environmentally devastating epidemics of plants. Laccases have been found in all domains of life but have not been reported in oomycte. In this paper, laccase genes of Phytophthora spp. were identified in three genomes (Phytophthora capsici, Phytophthora sojae and Phytophthora ramorum). 18 laccase genes were identified in total, including four in P. capsici genome, six in P. sojae genome and eight in P. ramorum genome. Most of the predicted gene models shared typical fungal laccase character, possessing three conserved positions with one cysteine and ten histidine residues at these positions. Phylogenetic analysis illustrated that laccases from Phytophthora clustered into four clades, while fungal laccases clustered together. The results provided the theoretical ground for new hypotheses about the roles laccases in oomycetes and may guide the future research of these enzymes.     

重寄生枝孢菌SYC63中MYB转录因子鉴定及分析

【背景】V-myb禽成髓细胞瘤病毒癌基因同源物(v-myb avian myeloblastosis viral oncogene homolog, MYB)转录因子广泛存在于真菌中,在真菌的胁迫响应与致病性中发挥重要功能。枝孢菌(Cladosporium sp.)作为一类对锈菌有重寄生作用的真菌,具有极高的生防潜力,然而有关其MYB转录因子尚未见报道,对其MYB家族转录因子进行鉴定和表达分析,有助于理解枝孢菌在重寄生过程中发挥的作用。【目的】了解重寄生枝孢菌(Cladosporium cladosporioides) SYC63菌株中MYB转录因子家族种类数目及在重寄生过程中发挥的作用。【方法】利用生物信息学方法对其基本特性进行预测,并结合锈孢子诱导下的表达情况进行分析。【结果】枝孢菌SYC63中包含22个MYB转录因子家族基因,所有MYB转录因子均含有SANT结构域,分子量为28.26-239.05 kDa,等电点(isoelectric point, pI)为4.57-10.15,均为亲水蛋白;大多定位在细胞核,共有1R-MYB和2R-MYB两类,均含有响应病原菌的启动子结合位点...     

水稻Trihelix转录因子家族全基因组分析及功能预测

Trihelix转录因子家族在植物生长发育以及响应逆境胁迫等方面发挥着重要作用,但目前基于水稻全基因组水平鉴定和分析该基因家族的研究尚未见相关报道。本文利用生物信息学方法在水稻基因组数据库中鉴定到Trihelix家族成员31个,序列聚类和功能结构域分析发现该家族均含有高度保守的、特征性的Trihelix结构域;根据亲缘关系远近和结构域特点,将其分为5个亚家族(Ⅰ~Ⅴ)。通过与拟南芥、二穗短炳草和高粱中Trihelix家族的聚类分析发现,这4个物种中Trihelix家族的分类相一致,但每个物种均含有不同亚家族的成员,表明该基因家族的分化早于物种的分化。基于MEME程序分析水稻Trihelix转录因子家族的保守基序与聚类分析结果具有较高的一致性。染色体区段复制分析表明,部分Trihelix家族成员在水稻以及水稻与其他物种之间存在种内和种间的染色体区段复制;生物芯片数据分析发现,Trihelix基因家族在水稻不同组织中、以及对6种不同植物激素的响应呈现多样化的表达谱。采用RiceFREND在线数据库分析发现,水稻Trihelix转录因子家族的20个成员与其他蛋白存在互作关系。本研究结果初步明确了水稻Trihelix转录因子家族的进化特点、染色体分布、染色体区段复制关系、组织表达、激素应答,以及该家族蛋白与其他蛋白质的互作情况,为进一步揭示Trihelix转录因子家族的分子进化规律和生物学功能奠定了基础。