Genome- Wide Analysis and Characterization of the TRX Gene Family in Upland Cotton

Thioredoxins (TRX) are small molecules of proteins that are present in all organisms. TRXs play an important role in diverse functions of plant growth and development. In this study, we performed genome-wide, characterization and expression levels of TRX gene family in cotton. A total of 150 GhTRX proteins were identified in upland cotton and classified into five subfamilies based on their domain compositions. Phylogenetic tree analysis divided TRX genes into seven subgroups. GhTRX genes covered all upland cotton chromosomes, with duplicated gene events. Ka/Ks ratio of three gene pairs was less than 1, suggesting purifying selection. The functions of GhTRX genes were studied using gene ontology, protein localization, and promoter analysis. Furthermore, six GhTRX genes were randomly selected to examine their expression level in cotton development and under various exogenous treatments. The genes showed high expressions in various tissues and at different stages of leaf senescence, also showed high expression under abscisic acid, ethylene, drought, and salinity. This study reveals the first report of TRX family genes in upland cotton. However further studies are needed to elucidate their specific functions in cotton plant.     

Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development

Phospholipase D is one of the crucial enzymes involved in lipid mediated signaling, triggered during various developmental and physiological processes. Different members of PLD gene family have been known to be induced under different abiotic stresses and during developmental processes in various plant species. In this report, we are presenting a detailed microarray based expression analysis and expression profiles of entire set of PLD genes in rice genome, under three abiotic stresses (salt, cold and drought) and different developmental stages (3-vegetative stages and 11-reproductive stages). Seven and nine PLD genes were identified, which were expressed differentially under abiotic stresses and during reproductive developmental stages, respectively. PLD genes, which were expressed significantly under abiotic stresses exhibited an overlapping expression pattern and were also differentially expressed during developmental stages. Moreover, expression pattern for a set of stress induced genes was validated by real time PCR and it supported the microarray expression data. These findings emphasize the role of PLDs in abiotic stress signaling and development in rice. In addition, expression profiling for duplicated PLD genes revealed a functional divergence between the duplicated genes and signify the role of gene duplication in the evolution of this gene family in rice. This expressional study will provide an important platform in future for the functional characterization of PLDs in crop plants.     

Genome-wide identification and characterisation of F-box family in maize

F-box-containing proteins, as the key components of the protein degradation machinery, are widely distributed in higher plants and are considered as one of the largest known families of regulatory proteins. The F-box protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, systematic analysis of the F-box family in maize (Zea mays) has not been reported yet. In this paper, we identified and characterised the maize F-box genes in a genome-wide scale, including phylogenetic analysis, chromosome distribution, gene structure, promoter analysis and gene expression profiles. A total of 359 F-box genes were identified and divided into 15 subgroups by phylogenetic analysis. The F-box domain was relatively conserved, whereas additional motifs outside the F-box domain may indicate the functional diversification of maize F-box genes. These genes were unevenly distributed in ten maize chromosomes, suggesting that they expanded in the maize genome because of tandem and segmental duplication events. The expression profiles suggested that the maize F-box genes had temporal and spatial expression patterns. Putative cis-acting regulatory DNA elements involved in abiotic stresses were observed in maize F-box gene promoters. The gene expression profiles under abiotic stresses also suggested that some genes participated in stress responsive pathways. Furthermore, ten genes were chosen for quantitative real-time PCR analysis under drought stress and the results were consistent with the microarray data. This study has produced a comparative genomics analysis of the maize ZmFBX gene family that can be used in further studies to uncover their roles in maize growth and development.     

The phytocyanin gene family in rice (Oryza sativa L.): genome-wide identification, classification and transcriptional analysis

Background

Phytocyanins (PCs) are plant-specific blue copper proteins involved in electron transport, and a large number of known PCs are considered to be chimeric arabinogalactan proteins (AGPs). To date there has not been a genome-wide overview of the OsPC gene family. Therefore, as the first step and a useful strategy to elucidate the functions of OsPCs, there is an urgent need for a thorough genome-wide analysis of this gene family.

Methodology/Principal Findings

In this study, a total of 62 OsPC genes were identified through a comprehensive bioinformatics analysis of the rice (Oryza sativa L.) genome. Based on phylogeny and motif constitution, the family of OsPCs was classified into three subclasses: uclacyanin-like proteins (OsUCLs), stellacyanin-like proteins (OsSCLs) and early nodulin-like proteins (OsENODLs). Structure and glycosylation prediction indicated that 46 OsPCs were glycosylphosphatigylinositol-anchored proteins and 38 OsPCs were chimeric AGPs. Gene duplication analysis revealed that chromosomal segment and tandem duplications contributed almost equally to the expansion of this gene family, and duplication events were mostly happened in the OsUCL subfamily. The expression profiles of OsPC genes were analyzed at different stages of vegetative and reproductive development and under abiotic stresses. It revealed that a large number of OsPC genes were abundantly expressed in the various stages of development. Moreover, 17 genes were regulated under the treatments of abiotic stresses.

Conclusions/Significance

The genome-wide identification and expression analysis of OsPC genes should facilitate research in this gene family and give new insights toward elucidating their functions in higher plants.     

Comparative expression profiles of maize genes from a water stress-specific cDNA macroarray in response to high-salinity, cold or abscisic acid

cDNA macroarray has become a useful tool to analyze expression profiles and compare the similarities and differences of various expression patterns. We have prepared a cDNA macroarray containing 190 maize expressed sequence tags (ESTs) specifically induced by water stress to analyze the expression profiles of maize seedlings under abscisic acid (ABA) treatment, high-salinity and cold stress conditions. The results indicated that 48 ESTs in leaves and 111 ESTs in roots were significantly up-regulated by ABA treatment, 36 ESTs in leaves and 41 ESTs in roots by high-salinity stress, 14 ESTs in leaves and 18 ESTs in roots by cold induction, whereas 22 ESTs were induced under all 3 stresses. Results from the hierarchical cluster analysis suggest that the leaves and roots of maize seedlings had different expression profiles after these stresses. The overlap analysis of different stress-induced ESTs indicated that there is more crosstalk between water stress and ABA and high-salinity stress than between water stress and cold stress. It will be helpful to study the precise function of the corresponding overlapping-induced genes for understanding the relationship and crosstalk between different stress signal pathways.     

The Glutaredoxin Family in Oxygenic Photosynthetic Organisms

Glutaredoxins (GRXs) are small redox proteins of the thioredoxin (TRX) superfamily. Compared to TRXs, much less information on the GRX family is available, especially in photosynthetic organisms since GRXs have been mainly studied in E. coli, yeast and mammal cells. The analysis of the TRX family in oxygenic photosynthetic organisms revealed an unsuspected multiplicity of TRXs but it is not known if the same situation holds for GRXs. Despite the availability of genome sequences from different oxygenic photosynthetic organisms, the number of GRXs and the different groups present in these organisms are still undescribed. This paper presents a comparative analysis of the GRX families present in Arabidopsis, Chlamydomonas and Synechocystis which were found to contain 30, 6 and 3 GRX genes, respectively. The putative subcellular localization of each GRX and its relative expression level, based on EST data, have been investigated. This analysis reveals the presence of three major classes of GRXs, the CPYC type, the CGFS type and a previously undescribed type, called the CC type that appears specific to higher plants. These data are discussed in view of recent results suggesting a complex cross-regulation between the TRX and GRX systems.     

Genome-wide exploration of the molecular evolution and regulatory network of mitogen-activated protein kinase cascades upon multiple stresses in Brachypodium distachyon

Background

Brachypodium distachyon is emerging as a widely recognized model plant that has very close relations with several economically important Poaceae species. MAPK cascade is known to be an evolutionarily conserved signaling module involved in multiple stresses. Although the gene sequences of MAPK and MAPKK family have been fully identified in B. distachyon, the information related to the upstream MAPKKK gene family especially the regulatory network among MAPKs, MAPKKs and MAPKKKs upon multiple stresses remains to be understood.

Results

In this study, we have identified MAPKKKs which belong to the biggest gene family of MAPK cascade kinases. We have systematically investigated the evolution of whole MAPK cascade kinase gene family in terms of gene structures, protein structural organization, chromosomal localization, orthologs construction and gene duplication analysis. Our results showed that most BdMAPK cascade kinases were located at the low-CpG-density region, and the clustered members in each group shared similar structures of the genes and proteins. Synteny analysis showed that 62 or 21 pairs of duplicated orthologs were present between B. distachyon and Oryza sativa, or between B. distachyon and Arabidopsis thaliana respectively. Gene expression data revealed that BdMAPK cascade kinases were rapidly regulated by stresses and phytohormones. Importantly, we have constructed a regulation network based on co-expression patterns of the expression profiles upon multiple stresses performed in this study.

Conclusions

BdMAPK cascade kinases were involved in the signaling pathways of multiple stresses in B. distachyon. The network of co-expression regulation showed the most of duplicated BdMAPK cascade kinase gene orthologs demonstrated their convergent function, whereas few of them developed divergent function in the evolutionary process. The molecular evolution analysis of identified MAPK family genes and the constructed MAPK cascade regulation network under multiple stresses provide valuable information for further investigation of the functions of BdMAPK cascade kinase genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1452-1) contains supplementary material, which is available to authorized users.     

拟南芥AtWRKY25、AtWRKY26和AtWRKY33在非生物胁迫条件下的表达分析

WRKY 转录因子家族在调控植物逆境诱导反应、生长发育及其信号转导等方面起着重要的分子生物学功能。文章采用Northern 杂交的方法, 对拟南芥3个WRKY基因进行表达谱分析。结果表明: AtWRKY25、AtWRKY26和AtWRKY33受多种非生物逆境因子(温度因子、高盐、渗透胁迫和激素脱落酸)的影响, 其中低温和高盐对AtWRKY25、AtWRKY26和AtWRKY33的诱导尤为明显, 表明这3个AtWRKY基因可能在响应环境信号方面起着一定的作用。作为序列相似性较高的AtWRKY25、AtWRKY26和AtWRKY33对一些胁迫因子的表达模式呈现一定的相似性; 但AtWRKY33受高温的抑制和低温的快速诱导, 与另外两个基因的表达模式不同, 推测它们对温度胁迫因子的反应存在差异。此外, 对启动子序列的生物信息学分析发现, 3个基因的启动子包含多个与非生物逆境反应相关的顺式作用元件。     

Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum

Zinc finger genes comprise a large and diverse gene family. Based on their individual finger structures and spacing, zinc finger proteins are further divided into different families according to their specific molecular functions. Genes in the CCCH family encode zinc finger proteins containing a motif with three cysteines and one histidine. They play important roles in plant growth and development, and in response to biotic and abiotic stresses. However, the limited analysis of the genome sequence has meant that there is no detailed information concerning the CCCH zinc finger family in tomato (Solanum lycopersicum). Here, we identified 80 CCCH zinc finger protein genes in the tomato genome. A complete overview of this gene family in tomato was presented, including the chromosome locations, gene duplications, phylogeny, gene structures and protein motifs. Promoter sequences and expression profiles of putative stress-responsive members were also investigated. These results revealed that, with the exception of four genes, the 80 CCCH genes are distributed over all 12 chromosomes with different densities, and include six segmental duplication events. The CCCH family in tomato could be divided into 12 groups based on their different CCCH motifs and into eight subfamilies by phylogenetic analysis. Analysis showed that almost all CCCH genes contain putative stress-responsive cis-elements in their promoter regions. Nine CCCH genes chosen for further quantitative real-time PCR analysis showed differential expression patterns in three representative tomato tissues. In addition, their expression levels indicated that these genes are mostly involved in the response to mannitol, heat, salicylic acid, ethylene or methyl jasmonate treatments. To the best of our knowledge, this is the first report of a genome-wide analysis of the tomato CCCH zinc finger family. Our data provided valuable information on tomato CCCH proteins and form a foundation for future studies of these proteins, especially for those members that may play important roles in stress responses.