Similar Motifs Research Articles

Identification of GA2ox Family Genes and Expression Analysis under Gibberellin Treatment in Pineapple (Ananas comosus (L.) Merr.).

Gibberellin (GAs) plays an important regulatory role in the development and growth of pineapple (Ananas comosus (L.) Merr.). Bioinformatics was used to confirm the differential expression of GA2 gibberellin oxidase gene AcGA2oxs in the pineapple genome, which laid the foundation for exploring its role in pineapple. In this study, 42 GA2ox genes (AcGA2oxs) were identified in the pineapple genome, named from AcGA2ox1 to AcGA2ox42, and divided into four groups according to phylogenetic analysis. We also analyzed the gene structure, conserved motifs and chromosome localization of AcGA2oxs. AcGA2oxs within the same group had similar gene structure and motifs composition. Collinear analysis and cis-element analysis provided the basis for understanding the evolution and function of GA2ox genes in pineapple. In addition, we selected different tissue parts to analyze the expression profile of AcGA2oxs, and the results show that 41 genes were expressed, except for AcGA2ox18. AcGA2ox18 may not be expressed in these sites or may be pseudogenes. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the GA2ox gene family under different concentrations of GA3 treatment, and it was found that AcGA2ox gene expression was upregulated in different degrees under GA3 treatment. These results provide useful information for further study on the evolution and function of the GA2ox family in pineapple.

RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.

The 3D structures of RNA play a critical role in understanding their functionalities. There exist several computational methods to study RNA 3D structures by identifying structural motifs and categorizing them into several motif families based on their structures. Although the number of such motif families is not limited, a few of them are well-studied. Out of these structural motif families, there exist several families that are visually similar or very close in structure, even with different base interactions. Alternatively, some motif families share a set of base interactions but maintain variation in their 3D formations. These similarities among different motif families, if known, can provide a better insight into the RNA 3D structural motifs as well as their characteristic functions in cell biology. In this work, we proposed a method, RNAMotifComp, that analyzes the instances of well-known structural motif families and establishes a relational graph among them. We also have designed a method to visualize the relational graph where the families are shown as nodes and their similarity information is represented as edges. We validated our discovered correlations of the motif families using RNAMotifContrast. Additionally, we used a basic Naïve Bayes classifier to show the importance of RNAMotifComp. The relational analysis explains the functional analogies of divergent motif families and illustrates the situations where the motifs of disparate families are predicted to be of the same family. Source code publicly available at https://github.com/ucfcbb/RNAMotifFamilySimilarity.

Genome-Wide Identification, Evolution and Expression Profile Analysis of NAC Transcription Factor in Simmondsia chinensis.

NAC transcription factors (TFs) are one of the largest plant-specific gene families and play important roles in plant growth, development, and the biotic and abiotic stress response. Although the sequencing of Jojoba (Simmondsia chinensis) has been completed, the genome-wide identification and analysis of its NAC TFs has not been reported. In this study, a total of 57 genes were identified in Jojoba, which were divided into eight groups based on phylogenetic analysis. The genes clustered in the same groups have a similar gene structure and motif distribution. Based on the analysis of cis-elements in NAC TFs, nine cis-acting elements were identified in the promoter region that involved in light response, hormonal response, and stress response. Synteny analysis showed a greater collinearity between Jojoba and V. vinifera than Arabidopsis thaliana. The 24 genes in the Jojoba NAC TFs are derived from fragment replication, which may be the main source of NAC amplification. Gene expression analysis identified seven genes that were highly expressed in seeds. The differential expression analysis of NAC TFs in cotyledon and embryonic axis tissues showed that the expression of 10 genes was up-regulated and 1 gene was down-regulated. This study provides more information on the classification, gene structure, conserved motif, and evolution of NAC TFs in Jojoba, facilitating further exploration of their specific functional analysis in Jojoba seed development.

Cross-reactivity trends when selecting scFv antibodies against snake toxins using a phage display-based cross-panning strategy

Antibodies with cross-reactive binding and broad toxin-neutralizing capabilities are advantageous for treating indications such as infectious diseases and animal envenomings. Such antibodies have been successfully selected against closely related antigens using phage display technology. However, the mechanisms driving antibody cross-reactivity typically remain to be elucidated. Therefore, we sought to explore how a previously reported phage display-based cross-panning strategy drives the selection of cross-reactive antibodies using seven different snake toxins belonging to three protein (sub-)families: phospholipases A2, long-chain α-neurotoxins, and short-chain α-neurotoxins. We showcase how cross-panning can increase the chances of discovering cross-reactive single-chain variable fragments (scFvs) from phage display campaigns. Further, we find that the feasibility of discovering cross-reactive antibodies using cross-panning cannot easily be predicted by analyzing the sequence, structural, or surface similarity of the antigens alone. However, when antigens share the (exact) same functions, this seems to increase the chances of selecting cross-reactive antibodies, which may possibly be due to the existence of structurally similar motifs on the antigens.

Temperature -and pressure-dependent branching ratios for 2,6-dimethylheptyl radicals (C9H19) + O2 reaction: An ab initio and RRKM/ME approach on a key component of bisabolane biofuel

Chemical kinetics mechanisms contain elementary reactions and associated Arrhenius rate parameters are necessary to understand the modeling of hydrocarbon autoignition chemistry. The complexity of such mechanisms is increased due to interest in operating next-generation combustion strategies in the low-temperature region (≤1000 K), which is governed by O2-addition to alkyl radicals (R), subsequent radical isomerization and decomposition steps thereafter. In this work, we report theoretically the reaction of molecular oxygen to the four isomers of 2,6-dimethylheptyl radicals (C9H19). The stationary points on potential energy surfaces (PES), rate constants, and branching ratios from C9H19 isomers initiated by O2 has been investigated by a combination of ab initio/density functional theory (CBS-QB3) and advanced statistical rate theory i.e., microcanonical variational transition state theory (μCVTST) and Rice-Ramsperger-Kassel-Marcus (RRKM)/master equation (ME) simulations. The temperature- and pressure-dependent rate constants and branching ratios over temperature range 400 K–1000 K (with an interval of 50 K) and with different pressures 0.001, 0.01, 0.1, 1, 10 and 100 bar were computed. The RRKM/ME calculations reveal for addition of O2 to the primary radical, 2,6-dimethylhept-1-yl + O2 reaction, the formation of 2-iso-butyl-4-methyl-tetrahydrofuran (a five membered cyclic ether) + OH via concerted C–C and O–O bond scission of primary-secondary QOOH and formation of ROO-1 is the kinetically favorable pathway below 600 K. For 2,6-dimethylhept-2-yl + O2, three competitive favorable channels lead to the formation of 5-iso-propyl-2,2-dimethyl-tetrahydrofuran + OH, a five membered cyclic ether formed coincident with OH in a chain-propagating step from decomposition of tertiary-secondary hydroperoxyalkyl (QOOH), formation of a six membered cyclic ether i.e., 2,2,6,6-tetramethylpyran and ROO-2, however at higher temperature (>900 K) and 2–6-dimethyl-2-heptene is contributed equally over other products. For 2,6-dimethylhept-3-yl + O2 reaction, leading to 5-iso-propyl-2,2-dimethyltetrahydrofuran + OH (same products as in ROO-2) from decomposition of secondary–tertiary hydroperoxyalkyl (QOOH). For 2,6-dimethylhept-4-yl + O2 reaction, it reveals the formation of chain-propagation channels leading to iso-butene + methyl-isobutanal + OH. The results of this study reveals the importance of temperature- and pressure-dependent branching ratios, which is necessary to understand the low temperature internal combustion mechanism. The unimolecular rate constants were also compared with the previously reported values for 2,6-dimethylheptyl radical + O2 and similar reaction system i.e., 2,5-dimethylhexyl radical + O2. The updated rate constants and branching ratios may also serve as general prototypes for low-temperature oxidation of branched alkanes of next-generation biofuels with similar structural motifs, such as bisabolane and farnesane.

Genome-Wide Analysis of ZAT Gene Family in Osmanthus fragrans and the Function Exploration of OfZAT35 in Cold Stress.

Osmanthus fragrans is a popular ornamental and odorant plant with high commercial value, but its cultivation and exploitation are limited by low temperature. The ZAT (zinc finger of Arabidopsis thaliana) genes as a subclass of the C2H2-type zinc finger proteins (C2H2-ZFP) family play essential roles in various abiotic stresses. However, their roles in cold stress response in O. fragrans remain unclear. This study identified 38 OfZATs, which could be divided into 5 subgroups based on the phylogenetic tree, with OfZATs in the same subgroup harboring similar gene structures and motif patterns. In addition, 49 segmental and 5 tandem duplication events were detected among OfZAT genes, while some OfZAT genes exhibited specific expression patterns in different tissues. Furthermore, two OfZATs were induced in salt stress and eight OfZATs responded to cold stress. Interestingly, OfZAT35 showed a continuously increasing expression trend under cold stress, while its protein showed nucleus localization with no transcriptional activation activity. Transiently transformed tobacco overexpressing OfZAT35 exhibited a significantly higher relative electrolyte leakage (REL) level and increased activities of superoxide dismutase (SOD), peroxidase (POD), and Ascorbate peroxidase (APX), while there was significantly decreased activity of catalase (CAT). Moreover, CAT, DREB3, and LEA5, which are associated with cold stress, were dramatically decreased after cold treatment in transiently transformed tobacco, suggesting that overexpression of OfZAT35 negatively regulated cold stress. This study provides a basis for exploring the roles of ZAT genes and contributes to uncovering the mechanism of ZAT-mediated cold stress response in O. fragrans.

Genome-Wide Analysis of Strictosidine Synthase-like Gene Family Revealed Their Response to Biotic/Abiotic Stress in Poplar.

The strictosidine synthase-like (SSL) gene family is a small plant immune-regulated gene family that plays a critical role in plant resistance to biotic/abiotic stresses. To date, very little has been reported on the SSL gene in plants. In this study, a total of thirteen SSLs genes were identified from poplar, and these were classified into four subgroups based on multiple sequence alignment and phylogenetic tree analysis, and members of the same subgroup were found to have similar gene structures and motifs. The results of the collinearity analysis showed that poplar SSLs had more collinear genes in the woody plants Salix purpurea and Eucalyptus grandis. The promoter analysis revealed that the promoter region of PtrSSLs contains a large number of biotic/abiotic stress response elements. Subsequently, we examined the expression patterns of PtrSSLs following drought, salt, and leaf blight stress, using RT-qPCR to validate the response of PtrSSLs to biotic/abiotic stresses. In addition, the prediction of transcription factor (TF) regulatory networks identified several TFs, such as ATMYB46, ATMYB15, AGL20, STOP1, ATWRKY65, and so on, that may be induced in the expression of PtrSSLs in response to adversity stress. In conclusion, this study provides a solid basis for a functional analysis of the SSL gene family in response to biotic/abiotic stresses in poplar.

Black box vs gray box: Comparing GAP and GPrep-DFTB for ruthenium and ruthenium oxide.

The increasing popularity of machine learning (ML) approaches in computational modeling, most prominently ML interatomic potentials, opened possibilities that were unthinkable only a few years ago-structure and dynamics for systems up to many thousands of atoms at an abinitio level of accuracy. Strictly referring to ML interatomic potentials, however, a number of modeling applications are out of reach, specifically those that require explicit electronic structure. Hybrid ("gray box") models based on, e.g., approximate, semi-empirical abinitio electronic structure with the aid of some ML components offer a convenient synthesis that allows us to treat all aspects of a certain physical system on the same footing without targeting a separate ML model for each property. Here, we compare one of these [Density Functional Tight Binding with a Gaussian Process Regression repulsive potential (GPrep-DFTB)] with its fully "black box" counterpart, the Gaussian approximation potential, by evaluating performance in terms of accuracy, extrapolation power, and data efficiency for the metallic Ru and oxide RuO2 systems, given exactly the same training set. The accuracy with respect to the training set or similar chemical motifs turns out to be comparable. GPrep-DFTB is, however, slightly more data efficient. The robustness of GPRep-DFTB in terms of extrapolation power is much less clear-cut for the binary system than for the pristine system, most likely due to imperfections in the electronic parametrization.

Plato’s Phaedrus and Symposium in the Pseudo-Clementine Homilies

Abstract The presence of Plato and Platonic philosophy in the late antique Christian novel, the Pseudo-Clementine Homilies, has been underexamined. The present article takes a twofold approach: first, it discusses Platonic references and allusions in the disputes between Appion the grammarian and Clement, a follower of the apostle Peter (Homiliae Clementinae 4–6), and links them to the rest of the Homilistic narrative. Plato’s dialogues of the Symposium and, in particular, the Phaedrus turn out to be insightful philosophical and literary frameworks by means of which the Homilist reflects on the value of eros, paideia, rhetoric and philosophy, the value of written discourse, and truth. Secondly, this article also compares the Pseudo-Clementine Homilies with (other) novels and narratives from the Second Sophistic that intertextually engage with similar Platonic motifs and passages. My analysis reveals how the Homilist, as a Christian novelist with strong philosophical (and one might say Sophistic) interests, is a remarkable member of the late antique, cultural dialogue, in which the reception of Plato’s dialogues took place.

The Influence of Giovanni Piranesi’s Etchings on the Works of Mstislav Dobuzhinsky

The relevance of the article’s topic is determined by the fact that the etchings of Giovanni Battista Piranesi, one of Mstislav Valerianovich Dobuzhinsky’s favorite artists, have never been specifically examined as artistic sources of his work.The scientific novelty of this article lies in the fact that it is the first attempt to analyze the influence of G.B. Piranesi’s etchings on the works of M.V. Dobuzhinsky. The author uses a complex method that combined the source analysis of the artist’s memoirs and letters, the traditional formal analysis of his works in comparison with Piranesi’s etchings and architectural monuments of Ancient Rome. The article also examines the industrial city motifs in Charles Dickens’ novels “The Old Curiosity Shop” and “Little Dorrit”. This made it possible to significantly expand and deepen the existing understanding of the historical, artistic and literary sources of architectural motifs and architectural fantasies in M.V. Dobuzhinsky’s works.The article reveals that G.B. Piranesi’s etchings from the series “Carceri” and “Vedute di Roma” influenced Dobuzhinsky’s fantasy drawings “Everyday life”, “Holiday” and the landscape “London. On the Bridge”. Piranesi’s etchings from these series also influenced Dobuzhinsky’s fantasy drawings of 1909—1921 on the theme of the city. In the early 1920s, some of the drawings were combined into the series “City Dreams”. The author also reveals the participation of industrial city images from Russian symbolist poetry, especially Valery Bryusov, in the formation of similar motifs in Dobuzhinsky’s works.

Molecular Characterization and Expression of CmobHLH Genes in Pumpkin

The transcription factor bHLH gene family plays fundamental roles in plant development and mitigating diverse biotic and abiotic stresses. However, the information of bHLH genes in pumpkin (Cucurbita moschata) is still unknown. In this current study, 222 CmobHLH genes were identified and mapped onto different chromosomes through bioinformatics analysis in pumpkin. CmobHLH and AtbHLH proteins could be classified into 19 subfamilies according to the phylogenetic tree. CmobHLH proteins within the same subfamily had similar motif composition and gene structures. Gene ontology (GO), cis-regulatory elements (CREs) and protein–protein interaction analyses suggested the potential regulatory roles of CmobHLH genes during the plant development process and abiotic stresses response in pumpkin. Tissue expression patterns based on transcriptome data demonstrated that CmobHLH genes were involved in pumpkin development process, and they had unique functions in different tissues. The expression patterns of five selected CmobHLH genes after exposure to abiotic stresses showed that the CmobHLH genes played varied roles in the stress responses of pumpkin to NaCl, waterlogging, cold, ABA and drought. In brief, these findings offer important information for further functional research of CmobHLH genes and resistance breeding in pumpkin.

Genome-Wide Identification of NAC Gene Family and Expression Analysis under Abiotic Stresses in Avena sativa.

In this study, a total of 177 NAC members were identified in Avena sativa, located on 21 chromosomes. Phylogenetic analysis showed that AsNAC proteins could be divided into seven subfamilies (I-VII), and that proteins in the same subfamily have similar protein motifs. Gene structure analysis found that NAC introns ranged from 1 to 17. Cis-element analysis of the promoter indicated that the gene family may have stress-related elements and growth regulation elements. Through qRT-PCR experiments, we speculated that AsNACs genes can respond to abiotic stresses such as cold, freezing, salt, and saline alkali. This study provides a theoretical basis for further exploring the function of the NAC gene family in A. sativa.

Genome-Wide Identification and Characterization of WRKY Transcription Factors and Their Expression Profile in Loropetalum chinense var. rubrum.

The WRKY gene family plays important roles in plant growth and development, as well as in the responses to biotic and abiotic stresses. Loropetalum chinense var. rubrum has high ornamental and medicinal value. However, few WRKY genes have been reported in this plant, and their functions remain unknown. To explore the roles that the WRKY genes play in L. chinense var. rubrum, we identified and characterized 79 LcWRKYs through BLAST homology analysis and renamed them (as LcWRKY1-79) based on their distribution on the chromosomes of L. chinense var. rubrum. In this way, according to their structural characteristics and phylogenetic analysis, they were divided into three groups containing 16 (Group I), 52 (Group II), and 11 (Group III) WRKYs, respectively. LcWRKYs in the same group have similar motifs and gene structures; for instance, Motifs 1, 2, 3, 4, and 10 constitute the WRKY domain and zinc-finger structure. The LcWRKY promoter region contains light response elements (ACE, G-box), stress response elements (TC-rich repeats), hormone response elements (TATC-box, TCA-element), and MYB binding sites (MBS, MBSI). Synteny analysis of LcWRKYs allowed us to establish orthologous relationships among the WRKY gene families of Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum L., Vitis vinifera L., Oryza sativa L., and Zea mays L.; furthermore, analysis of the transcriptomes of mature leaves and flowers from different cultivars demonstrated the cultivar-specific LcWRKY gene expression. The expression levels of certain LcWRKY genes also presented responsive changes from young to mature leaves, based on an analysis of the transcriptome in leaves at different developmental stages. White light treatment led to a significant decrease in the expression of LcWRKY6, 18, 24, 34, 36, 44, 48, 61, 62, and 77 and a significant increase in the expression of LcWRKY41, blue light treatment led to a significant decrease in the expression of LcWRKY18, 34, 50, and 77 and a significant increase in the expression of LcWRKY36 and 48. These results enable a better understanding of LcWRKYs, facilitating the further exploration of their genetic functions and the molecular breeding of L. chinense var. rubrum.

Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin.

The ERM (ezrin, radixin, and moesin) family of proteins and the related protein merlin participate in scaffolding and signaling events at the cell cortex. The proteins share an N-terminal FERM [band four-point-one (4.1) ERM] domain composed of three subdomains (F1, F2, and F3) with binding sites for short linear peptide motifs. By screening the FERM domains of the ERMs and merlin against a phage library that displays peptides representing the intrinsically disordered regions of the human proteome, we identified a large number of novel ligands. We determined the affinities for the ERM and merlin FERM domains interacting with 18 peptides and validated interactions with full-length proteins through pull-down experiments. The majority of the peptides contained an apparent Yx[FILV] motif; others show alternative motifs. We defined distinct binding sites for two types of similar but distinct binding motifs (YxV and FYDF) using a combination of Rosetta FlexPepDock computational peptide docking protocols and mutational analysis. We provide a detailed molecular understanding of how the two types of peptides with distinct motifs bind to different sites on the moesin FERM phosphotyrosine binding-like subdomain and uncover interdependencies between the different types of ligands. The study expands the motif-based interactomes of the ERMs and merlin and suggests that the FERM domain acts as a switchable interaction hub.

Genome-wide identification and functional characterization of pectin methylesterase inhibitors associated with male sterility in wheat

Pectin methylesterase inhibitors (PMEIs) can specifically bind to pectin methylesterases (PMEs) and regulate their enzymatic activities to control the status of pectin methyl esterification, which plays crucial roles in stabilizing the cell wall properties during plant growth and development. Although the evolution and biological functions of the PMEI gene family in various plants have been well characterized, the role of PMEI genes in wheat was poorly understood. In this study, a total of 237 PMEI genes (TaPMEIs) were identified in wheat (Triticum aestivum L.), which were dispersed irregularly over 22 chromosomes and tissue-specific in their expression. They were divided into nine groups based on similar motif number and composition. Using quantitative real-time PCR analysis, we discovered that TaPMEI23 as the most abundant-expressed PMEI in anther and significantly upregulated expression in fertile anthers. Moreover, subcellular localization analysis indicated that TaPMEI23 was localized on the plasma membrane or cell wall. Effective silencing of the TaPMEI23 significantly influences the anther dehiscence, pollen activity, seed setting rate, and male fertility, suggesting that PMEIs are necessary for pollen development and male sterility. Our work provides novel insights into the functions of PMEIs in wheat.

Interaction of nucleoporins with nuclear transport receptors: a structural perspective.

Soluble nuclear transport receptors and stationary nucleoporins are at the heart of the nucleocytoplasmic transport machinery. A subset of nucleoporins contains characteristic and repetitive FG (phenylalanine-glycine) motifs, which are the basis for the permeability barrier of the nuclear pore complex (NPC) that controls transport of macromolecules between the nucleus and the cytoplasm. FG-motifs can interact with each other and/or with transport receptors, mediating their translocation across the NPC. The molecular details of homotypic and heterotypic FG-interactions have been analyzed at the structural level. In this review, we focus on the interactions of nucleoporins with nuclear transport receptors. Besides the conventional FG-motifs as interaction spots, a thorough structural analysis led us to identify additional similar motifs at the binding interface between nucleoporins andtransport receptors. A detailed analysis of all known human nucleoporins revealed a large number of such phenylalanine-containing motifs that are not buried in the predicted 3D-structure of the respective protein but constitute part of the solvent-accessible surface area. Only nucleoporins that are rich in conventional FG-repeats are also enriched for these motifs. This additional layer of potential low-affinity binding sites on nucleoporins for transport receptors may have a strong impact on the interaction of transport complexes with the nuclear pore and, thus, the efficiency of nucleocytoplasmic transport.

Functional identification of OsMADS6 and OsMADS17 in floral organ development in rice

AbstractRice floral organs are closely related to rice yield and quality, and MADS family genes play an important role in rice floral organ development. In this study, we identified functions of two MADS genes in floral organ development by bioinformatics analysis and CRISPR/Cas9 technology. Our results showed that MADS6 and MADS17 were a pair of highly homologous genes, which had highly similar sequences, motifs and expression profiles. The floral organs of mads6 and mads6/17 mutants were abnormal, whereas mads17 mutants showed no difference with wild type. Collectively, these results reveal that there are functional differentiations between conserved gene MADS6 and MADS17. Our findings provide a theoretical basis for further analysing the function of MADS family homologous genes and unravelling their molecular mechanism and regulatory network.

Genome-wide analysis of the CDPK gene family and their important roles response to cold stress in white clover

ABSTRACT Calcium-dependent protein kinases (CDPKs) are an important class of calcium-sensitive response proteins that play an important regulatory role in response to abiotic stresses. To date, little is known about the CDPK genes in white clover. White clover is a high-quality forage grass with high protein content, but it is susceptible to cold stress. Therefore, we performed a genome-wide analysis of the CDPK gene family in white clover and identified 50 members of the CDPK genes. Phylogenetic analysis using CDPKs from the model plant Arabidopsis divided the TrCDPK genes into four groups based on their sequence similarities. Motif analysis showed that TrCDPKs within the same group had similar motif compositions. Gene duplication analysis revealed the evolution and expansion of TrCDPK genes in white clover. Meanwhile, a genetic regulatory network (GRN) containing TrCDPK genes was reconstructed, and gene ontology (GO) annotation analysis of these functional genes showed that they contribute to signal transduction, cellular response to stimuli, and biological regulation, all of which are important processes in response to abiotic stresses. To determine the function of TrCDPK genes, we analyzed the RNA-seq dataset and found that most TrCDPK genes were highly up-regulated under cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiments, implying that TrCDPK genes are involved in various gene regulatory pathways in response to cold stress. Our study may help to further investigate the function of TrCDPK genes and their role in response to cold stress, which is important for understanding the molecular mechanisms of cold tolerance in white clover and improving its cold tolerance.

Genome-Wide Identification of the Argonaute Protein Family and Its Expression Analysis under PEG6000, ABA and Heat Treatments in Populus alba × P. glandulosa

The argonaute (AGO) protein, as an important member of the small RNA (sRNA) regulatory pathway gene-silencing complex (RNA-induced silencing complex, RISC), is a key protein that mediates gene silencing and plays a key role in the recruitment of sRNAs. In this study, bioinformatics was used to identify the AGO gene family in poplar and study its expression in various tissues and in response to abiotic stress treatments. A total of 15 PtAGO genes were identified in poplar, which were unevenly distributed in 9 chromosomes. Most proteins were predicted to be located in the nucleus and chloroplast. The PtAGOs had similar motif structures and conserved motifs, except for PtAGO3. All the PtAGO genes could be clustered into 3 groups, and Group II, including PtAGO2/3/7, had the smallest number of exons, while the others had more than 20 exons. Cis-regulatory elements involved in light response, growth and development, abiotic stress and hormone-induced responses were found in the promoters of PtAGO members. Further expression analysis found that the PtAGO genes had tissue-specific expression patterns. For example, PtAGO7 and PtAGO10b were mainly expressed in the xylem and might be involved in secondary xylem development. Furthermore, abiotic stress tests, including heat, ABA and PEG treatments, showed that most PtAGO genes could respond quickly to ABA treatment, and multiple PtAGO genes were constantly regulated under heat-shock stress. These results provide a basis for the elucidation mechanism of PtAGO genes and further molecular breeding in poplar.

Genome-Wide Identification and Expression Analysis of the SWEET Gene Family in Annual Alfalfa (Medicago polymorpha).

SWEET (Sugars will eventually be exported transporter) proteins are a group of sugar transporters that are involved in sugar efflux, phloem loading, reproductive development, plant senescence, and stress responses. In this study, 23 SWEET transporter members were identified in the Medicago polymorpha genome, heterogeneously distributed on seven chromosomes. These MpSWEET genes were divided into four subfamilies, which showed similar gene structure and motif composition within the same subfamily. Seventeen MpSWEET genes encode seven transmembrane helices (TMHs), and all MpSWEET proteins possess conserved membrane domains and putative serine phosphorylation sites. Four and three pairs of MpSWEET genes were predicted to be segmentally and tandemly duplicated, respectively, which may have contributed to their evolution of M. polymorpha. The results of microarray and RNA-Seq data showed that some MpSWEET genes were specifically expressed in disparate developmental stages (including seedling stage, early flowering stage, and late flowering stage) or tissues such as flower and large pod. Based on protein network interaction and expression patterns of MpSWEET genes, six MpSWEET genes were selected for further quantitative real-time PCR validation in different stress treatments. qRT-PCR results showed that MpSWEET05, MpSWEET07, MpSWEET12, MpSWEET15, and MpSWEET21 were significantly upregulated for at least two of the three abiotic stress treatments. These findings provide new insights into the complex transcriptional regulation of MpSWEET genes, which facilitates future research to elucidate the function of MpSWEET genes in M. polymorpha and other legume crops.