Expression Patterns In Different Tissues Research Articles

Genome-wide investigation of WRKY transcription factors in sweet osmanthus and their potential regulation of aroma synthesis.

WRKY transcription factors, one of the largest transcription factor families, play important roles in regulating the synthesis of secondary metabolites. In sweet osmanthus (Osmanthus fragrans), the monoterpenes have been demonstrated as the most important volatile compounds, and the W-box, which is the cognate binding site of WRKY transcription factors, could be identified in most of the terpene-synthesis-related genes' promoters. However, the role of the WRKY family in terpene synthesis in sweet osmanthus has rarely been examined. In this study, 154 WRKY genes with conserved WRKY domain were identified and classified into three groups. The group II was further divided into five subgroups, and almost all members of IId contained a plant zinc cluster domain. Eight OfWRKYs (OfWRKY7/19/36/38/42/84/95/139) were screened from 20 OfWRKYs for their flower-specific expression patterns in different tissues. Simultaneously, the expression patterns of OfWRKYs and emission patterns of volatile compounds during the flowering process were determined and gas chromatography-mass spectrometry results showed that monoterpenes, such as linalool and ocimene, accounted for the highest proportion, contributing to the floral scent of sweet osmanthus in two cultivars. In addition, correlation analysis revealed the expression patterns of OfWRKYs (OfWRKY7/19/36/139) were each correlated with distinct monoterpenes (linalool, linalool derivatives, ocimene and ocimene derivatives). Subcellular localization analysis showed that p35S::GFP-OfWRKY7/38/95/139 were localized in the nucleus and OfWRKY139 had very strong transactivation activity. Collectively, the results indicated potential roles of OfWRKY139 and OfWRKYs with plant zinc cluster domain in regulating synthesis of aromatic compounds in sweet osmanthus, laying the foundation for use of OfWRKYs to improve the aroma of ornamental plants.

Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues

BackgroundDendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysaccharide at the transcription level, we performed de novo transcriptome sequencing for the first time to produce a comprehensive transcriptome of D. moniliforme.ResultsIn our study, a database of 562,580 unigenes (average length = 1115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, we identified 1204 carbohydrate-active related unigenes against CAZy database, including 417 glycosyltransferase genes (GTs), 780 glycoside hydrolases (GHs), 19 carbohydrate esterases (CEs), 75 carbohydrate-binding modules (CBMs), and 44 polysaccharide lyases (PLs). In the cellulose synthase family, 21 differential expression genes (DEGs) related to polysaccharide were identified. Subsequently, the tissue-specific expression patterns of the genes involved in polysaccharide pathway were investigated, which provide understanding of the biosynthesis and regulation of DMP at the molecular level. The two key enzyme genes (Susy and SPS) involved in the polysaccharide pathway were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR.ConclusionsWe determined the content of polysaccharides from Dendrobium moniliforme under different tissues, and we obtained a large number of differential genes by transcriptome sequencing. This database provides a pool of candidate genes involved in biosynthesis of polysaccharides in D. moniliforme. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb.

Functional analysis of two MyoDs revealed their role in the activation of myomixer expression in yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782)

Myoblast determination protein (MyoD), a muscle-specific basic helix-loop-helix (bHLH) transcription factor, plays a pivotal role in regulating skeletal muscle growth and development. However, the regulation mechanism of MyoD has not been determined in marine fishes. In the present study, we isolated the MyoD1 (AlMyoD1) and MyoD2 (AlMyoD2) genomic sequences and analyzed the expression patterns in different tissues of yellowfin seabream (Acanthopagrus latus). The open reading frame (ORF) sequences of AlMyoD1 and AlMyoD2 encoded 297 and 271 amino acids possessing three common characteristic domains, respectively, containing a myogenic basic domain, a bHLH domain, and a ser-rich region (helix III). Phylogenetic and genome structure analyses exhibited classic phylogeny and highly conserved exon/intron architecture. Furthermore, the AlMyoD1 and AlMyoD2 transcription levels were higher in white muscle than in the other tissues. In order to further study AlMyoD function in muscle, promoter sequence analysis found that several E-box binding sites were present. Additionally, binding sites of Almyomixer involved in mammal myoblast fusion, which expression was also the highest in white muscle, were found in the promoter of AlMyoD. Pomoter activity assays further confirmed that both AlMyoD1 and AlMyoD2 can dramatically activate Almyomixer expression, and the AlMyoD1 M2 and AlMyoD2 M5 E-box binding sites were functionally important for Almyomixer transcription based on mutation analysis and electrophoretic mobile shift assays (EMSA). In summary, two MyoDs play a core role in Almyomixer regulation and may promote myofibre formation during muscle development and growth by regulating Almyomixer expression.

Genome-wide identification, phylogenetic and expression analysis of SBP-box gene family in barley (Hordeum vulgare L.)

The SQUAMOSA PROMOTER BINDING PROTEIN box (SBP-box) gene family is a unique family of transcription factors in plants, which is found widely in green plants. This family functions involve many aspects of crop genetic improvement, such as yield, floral period, and stress resistances; therefore, it has an important practical application value. In this study, 14 non-redundant SBP-box genes were identified and isolated in barley (Hordeum vulgare L.) using Hordeum vulgare.IBSC_v2 in combination with bioinformatics analysis. The results revealed that 13 of these genes were unevenly distributed on five chromosomes, and another gene has not been anchored yet. Sequence alignments demonstrated that each SBP protein has highly conserved functional elements (zinc finger structure and nuclear localization signal sequence). Gene structure analysis indicated their diversified exon-introns structure. Phylogenetic analysis was used to classify the barley SBP-box genes into five subfamilies (D–H). Each subfamily was found to contain similar protein motifs and gene structures. Expression profiles based on the barley RNA-seq database found that the barley SBP-box gene family expresses the highest amount in the inflorescence and showed different expression patterns in different tissues and different stages. Overall, the results indicated that the barley SBP-box gene family is relatively conserved in evolution and function, and plays a crucial role in many stages of barley plant growth development. Our results provide a theoretical reference for subsequent studies of molecular regulation and genetic breeding of SBP-box family genes in barley growth and development.

Tissue-specific transcriptome for Dendrobium officinale reveals genes involved in flavonoid biosynthesis

Dendrobium officinale is a kind of crop and precious herbal that is widely distributed in China. We applied transcriptomics to investigate the flavonoids and their biosynthesis-related genes from different tissues. Total flavonoid was determined in three different tissues. In this study, nine cDNA libraries were generated from Dendrobium officinale. A total of 530 million (70.73%) of the high-quality reads were successfully mapped to the reference genome of Dendrobium officinale and nine libraries were combined and assembled into 24,927 non-redundant genes. We mapped all of these genes to reference pathways in the KEGG database to identify polysaccharide and secondary metabolites pathways in which the genes may be involved. We outlined the biosynthetic pathway of flavonoids and identified putative genes, which provide understanding of the biosynthesis and regulation of Dendrobium officinale flavonoids at the molecular level. We identified five CHS genes from Dendrobium officinale and characterized the CHS gene family. The flavonoid-related key enzyme genes were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. These data on flavonoid genes obtained in this work will be useful in understanding the molecular mechanisms of different tissues in Dendrobium officinale.

Four Decades After the Discovery of Regenerating Islet-Derived (Reg) Proteins: Current Understanding and Challenges.

Regenerating islet-derived (Reg) proteins have emerged as multifunctional agents with pro-proliferative, anti-apoptotic, differentiation-inducing and bactericidal properties. Over the last 40 years since first discovered, Reg proteins have been implicated in a gamut of maladies including diabetes, various types of cancer of the digestive tract, and Alzheimer disease. Surprisingly though, a consensus is still absent on the regulation of their expression, and molecular underpinning of their function. Here, we provide a critical appraisal of recent findings in the field of Reg protein biology. Specifically, the structural characteristics are reviewed particularly in connection with established or purported functions of different members of the Reg family. Moreover, Reg expression patterns in different tissues both under normal and pathophysiological conditions are summarized. Putative receptors and cascades reported to relay Reg signaling inciting cellular responses are presented aiming at a better appreciation of the biological activities of the distinct Reg moieties. Challenges are also discussed that have hampered thus far the rapid progress in this field such as the use of non-standard nomenclature for Reg molecules among various research groups, the existence of multiple Reg members with significant degree of homology and possibly compensatory modes of action, and the need for common assays with robust readouts of Reg activity. Coordinated research is warranted going forward, given that several research groups have independently linked Reg proteins to diseased states and raised the possibility that these biomolecules can serve as therapeutic targets and biomarkers.

Comprehensive analysis of multiprotein bridging factor 1 family genes and SlMBF1c negatively regulate the resistance to Botrytis cinerea in tomato

BackgroundMultiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lycopersicum MBF1 (SlMBF1) gene family.ResultsIn total, five SlMBF1 genes were identified based on the tomato reference genome, and these genes were mapped to five chromosomes. All of the SlMBF1 proteins were highly conserved, with a typical MBF1 domain and helix-turn-helix_3 domain. In addition, the promoter regions of the SlMBF1 genes have various stress and hormone responsive cis-regulatory elements. Encouragingly, the SlMBF1 genes were expressed with different expression profiles in different tissues and responded to various stress and hormone treatments. The biological function of SlMBF1c was further identified through its overexpression in tomato, and the transgenic tomato lines showed increased susceptibility to Botrytis cinerea (B. cinerea). Additionally, the expression patterns of salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)- mediated defense related genes were altered in the transgenic plants.ConclusionsOur comprehensive analysis provides valuable information for clarifying the evolutionary relationship of the SlMBF1 members and their expression patterns in different tissues and under different stresses. The overexpression of SlMBF1c decreased the resistance of tomato to B. cinerea through enhancing the gene expression of the SA-mediated signaling pathway and depressing JA/ET-mediated signaling pathways. These results will facilitate future functional studies of the transcriptional co-activator family.

Cloning and expression analysis of metallothionein family genes in response to heavy metal stress in sugarcane (<italic>Saccharum officinarum</italic> L.)

Metallothioneins (MTs) are cysteine-rich, low-molecular-weight proteins. Plant MTs play important roles in detoxification and cellular redox regulation. In this study, hydroponic experiments of sugarcane ( Saccharum officinarum L. cv. Badila) were carried out to study the effects of CdCl2, ZnSO4, and CuCl2 treatments on plantlet growth. And then three kinds of heavy metal content in both shoots and roots of sugarcane were detected, showing an enrichment and tolerance ability to Cd2+, Zn2+, and Cu2+ in Badila seedlings. Three metallothionein genes, termed as ScMT 1 (accession number: KJ504373), ScMT 2-1-5 (accession number: MH191346), and ScMT 3 (accession number: KJ5043704), were isolated from Badila. ScMT 1 contained an open reading frame (ORF) of 228 bp encoding 75 amino acids residues. The first (52 bp) and second (176 bp) extrons of ScMT 1 were separated by an intron (283 bp). ScMT 2-1-5 contained an ORF of 246 bp encoding 81 amino acids residues. The first (64 bp), second (87 bp), and third (101 bp) extrons of ScMT2-1-5 were separated by two introns (483 bp and 853 bp). ScMT 3 contained an ORF of 198 bp encoding 65 amino acids residues. The first (50 bp) and second (148 bp) extrons of ScMT 3 were separated by an intron (259 bp). The deduce protein ScMT1, ScMT2-1-5, and ScMT3 were categorized into the subfamily of plant type1, type2, and type3 MTs, respectively. The expression profiles of the three genes under different heavy-metal stresses were investigated by real-time quantitative PCR (qRT-PCR) analysis. When treated with Cd2+, the expression of ScMT 2-1-5 was continuously and significantly up-regulated in both shoots and roots, while that of ScMT 1 showed a delayed up-regulation pattern. The expression of ScMT 3 showed a delayed up-regulation pattern in shoots and a trend of first raising and then suppressing in roots. The results suggested that ScMT 2-1-5 might play a more active role in response to Cd2+ in sugarcane while ScMT 3 might not, and ScMT 1 is involved in the molecular responses of Cd2+ stress at the later stage. When treated with Cu2+, the expression of ScMT 1 was continuously and significantly up-regulated, and that of ScMT 2-1-5 and ScMT 3 general up-regulated in shoots. As in the roots, the expression of both ScMT 1 and ScMT 2-1-5 showed a delayed up-regulation pattern which was significantly up-regulated at the later stage, while that of ScMT 3 significantly up-regulated at the early stage. It revealed that ScMT 1 cooperated with ScMT 2-1-5 and ScMT 3 is involved in the positive response to Cu2+ stress in roots, and might play a more positive role than ScMT 2-1-5 and ScMT 3, and the three genes are successively involved in the molecular responses of Cu2+ stress in roots. When treated with Zn2+, the expression of ScMT 1 and ScMT 3 increased only in shoots and roots, respectively. The expression of ScMT 2-1-5 was up-regulated at the early stage and then suppressed in both shoots and roots. It suggests that ScMT 1 and ScMT 3 mainly function in shoots and roots, respectively, when exposed to Zn2+ stress. ScMT 2-1-5 was involved in the molecular responses of Cd2+ stress at the early stage. ScMT 1, ScMT 2-1-5, and ScMT 3 showed similar or complementary expression patterns in different tissues of sugarcane when exposed to heavy metals, which revealed the functional diversity of sugarcane MTs in detoxification and cellular redox regulation, and their spatiotemporal coordination in mitigating or even preventing tissue injury caused by excessive heavy metals. The results provide a basic information for further research on mechanisms in the synergistic enhancement of tolerance to heavy metals for MTs family genes in the highly polyploid sugarcane.

Characterization, Expression, and Interaction Analyses of OsMORF Gene Family in Rice.

The multiple organellar RNA editing factors (MORF) gene family plays a key role in organelle RNA editing in flowering plants. MORF genes expressions are also affected by abiotic stress. Although seven OsMORF genes have been identified in rice, few reports have been published on their expression patterns in different tissues and under abiotic stress, and OsMORF–OsMORF interactions. In this study, we analyzed the gene structure of OsMORF family genes. The MORF family members were divided into six subgroups in different plants based on phylogenetic analysis. Seven OsMORF genes were highly expressed in leaves. Six and seven OsMORF genes expressions were affected by cold and salt stresses, respectively. OsMORF–OsMORF interaction analysis indicated that OsMORF1, OsMORF8a, and OsMORF8b could each interact with themselves to form homomers. Moreover, five OsMORF proteins were shown to be able to interact with each other, such as OsMORF8a and OsMORF8b interacting with OsMORF1 and OsMORF2b, respectively, to form heteromers. These results provide information for further study of OsMORF gene function.

Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

Auxin regulates diverse aspects of growth and development. Furthermore, polar auxin transport, which is mediated by the PIN-FORMED (PIN) and AUXIN1/LIKE-AUX (AUX/LAX) proteins, plays a crucial role in auxin distribution. In this study, six PIN and four AUX/LAX genes were identified in ramie (Boehmeria nivea L.). We used qRT-PCR to characterize and analyze the two gene families, including phylogenetic relationships, intron/exon structures, cis-elements, subcellular localization, and the expression patterns in different tissues. The expression of these genes in response to indole-3-acetic acid (IAA) treatment and drought stress was also assessed; the results indicate that most of the BnAUX/LAX and BnPIN genes were regulated as a result of IAA treatment and drought stress. Our study provides insights into ramie auxin transporters and lays the foundation for further analysis of their biological functions in ramie fiber development and adaptation to environmental stresses.

Expression characterization and transcription regulation analysis of porcine Yip1 domain family member 3 gene.

ObjectiveThe Yip1 domain family (YIPF) proteins were proposed to function in endoplasmic reticulum (ER) to Golgi transport and maintenance of the morphology of the Golgi, which were homologues of yeast Yip1p and Yif1p. YIPF3, the member 3 of YIPF family was a homolog of Yif1p. The aim of present study was to investigate the expression and regulation mechanism of porcine YIPF3.MethodsQuantitative realtime polymerase chain reaction (qPCR) was used to analyze porcine YIPF3 mRNA expression pattern in different tissues and pig kidney epithelial (PK15) cells stimulated by polyinosine-polycytidylic acid (poly [I:C]). Site-directed mutations combined with dual luciferase reporter assays and electrophoretic mobility shift assay (EMSA) were employed to reveal transcription regulation mechanism of porcine YIPF3.ResultsResults showed that the mRNA of porcine YIPF3 (pYIPF3) was widely expressed with the highest levels in lymph and lung followed by spleen and liver, while weak in heart and skeletal muscle. Subcellular localization results indicated that it expressed in Golgi apparatus and plasma membranes. Upon stimulation with poly (I:C), the level of this gene was dramatically up-regulated in a time- and concentration-dependent manner. pYIPF3 core promoter region harbored three cis-acting elements which were bound by ETS proto-oncogene 2 (ETS2), zinc finger and BTB domain containing 4 (ZBTB4), and zinc finger and BTB domain containing 14 (ZBTB14), respectively. In which, ETS2 and ZBTB4 both promoted pYIPF3 transcription activity while ZBTB14 inhibited it, and these three transcription factors all played important regulation roles in tumorigenesis and apoptosis.ConclusionThe pYIPF3 mRNA expression was regulated by ETS2, ZBTB4, and ZBTB14, and its higher expression in immune organs might contribute to enhancing ER to Golgi transport of proteins, thus adapting to the immune response.

Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium.

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

Osteoblast-specific expression of Panx3 is dispensable for postnatal bone remodeling.

Since cost-effective osteoanabolic treatment options remain to be established, it is relevant to identify specific molecules physiologically regulating osteoblast differentiation and/or activity that are principally accessible as drug targets. Specific or predominant gene expression in a given cell type often predicts a relevant function in the respective tissue. Thus, we aimed to identify genes encoding membrane-associated proteins with selective expression in differentiated osteoblasts. We therefore applied an unbiased approach, i.e. Affymetrix Gene Chip hybridization, to compare global gene expression in primary murine osteoblasts at two stages of differentiation. For the most strongly induced genes we analyzed their expression pattern in different tissues, which led us to identify known and unknown osteoblast differentiation markers with predominant expression in bone. One of these genes was Panx3, encoding a transmembrane hemichannel with ill-defined function in skeletal remodeling. To decipher the role of Panx3 in osteoblasts we first generated Panx3-fl/fl mice carrying a Runx2-Cre transgene. Using undecalcified histology followed by bone-specific histomorphometry we did not observe any significant difference between 24 weeks old Cre-negative and Cre-positive littermates. We additionally generated and analyzed mice with ubiquitous Panx3 deletion, where a delay of endochondral ossification did not translate into a detectable skeletal phenotype after weaning, possibly explained by compensatory induction of Panx1. Of note, newborn Panx3-deficient mice displayed significantly reduced serum glucose levels, which was not the case in older animals. Our findings demonstrate that Panx3 expression in osteoblasts is not required for postnatal bone remodeling, which essentially rules out its suitability as a target protein for osteoanabolic medication.

Multifaceted Mass Spectrometric Investigation of Neuropeptide Changes in Atlantic Blue Crab, Callinectes sapidus, in Response to Low pH Stress.

The decrease of pH level in the water affects animals living in aquatic habitat, such as crustaceans. The molecular mechanisms enabling these animals to survive this environmental stress remain unknown. To understand the modulatory function of neuropeptides in crustaceans when encountering drops in pH level, we developed and implemented a multifaceted mass spectrometric platform to investigate the global neuropeptide changes in response to water acidification in the Atlantic blue crab, Callinectes sapidus. Neural tissues were collected at different incubation periods to monitor dynamic changes of neuropeptides under different stress conditions occurring in the animal. Neuropeptide families were found to exhibit distinct expression patterns in different tissues and even each isoform had its specific response to the stress. Circulating fluid in the crabs (hemolymph) was also analyzed after 2-h exposure to acidification, and together with results from tissue analysis, enabled the discovery of neuropeptides participating in the stress accommodation process as putative hormones. Two novel peptide sequences were detected in the hemolymph that appeared to be involved in the stress-related regulation in the crabs.

Relevance of Class I α-Mannosidases to Cassava Postharvest Physiological Deterioration.

Class I α-mannosidases (MNSs) play important roles in protein N-glycosylation. However, no data are currently available about MNSs in cassava (Manihot esculenta), of which the functions are therefore not known, particularly in relevance to postharvest physiological deterioration (PPD). A total of seven genes were identified from the cassava genome in the present study. Two (MeMNS2 and MeMNS6) of the seven genes may be pseudogenes, as indicated by sequence alignment and exon–intron organizations. Five MNSs could be classified into three subfamilies. Tissue-specific expression analysis revealed that MNS genes have distinct expression patterns in different tissues between sugar cassava and cultivated cassava varieties, indicating their functional diversity. A PPD response and defense model was proposed based on the transcription data of MNSs and genes involved in reactive oxygen species, signal transduction, and cell wall remodeling. The findings help in the understanding of PPD responses in cassava.

Genome-Wide Identification, Characterization and Expression Analysis of Xyloglucan Endotransglucosylase/Hydrolase Genes Family in Barley (Hordeum vulgare).

Xyloglucan endotransglucosylase/hydrolases (XTHs)—a family of xyloglucan modifying enzymes—play an essential role in the construction and restructuring of xyloglucan cross-links. However, no comprehensive study has been performed on this gene family in barley. A total of 24 HvXTH genes (named HvXTH1-24) and an EG16 member were identified using the recently completed genomic database of barley (Hordeum vulgare). Phylogenetic analysis showed that 24 HvXTH genes could be classified into three phylogenetic groups: (I/II, III-A and III-B) and HvXTH15 was in the ancestral group. All HvXTH protein members—except HvXTH15—had a conserved N-glycosylation site. The genomic location of HvXTHs on barley chromosomes showed that the 24 genes are unevenly distributed on the 7 chromosomes, with 10 of them specifically located on chromosome 7H. A structure-based sequence alignment demonstrates that each XTH possesses a highly conserved domain (ExDxE) responsible for catalytic activity. Expression profiles based on the barley genome database showed that HvXTH family members display different expression patterns in different tissues and at different stages. This study is the first systematic genomic analysis of the barley HvXTH gene family. Our results provide valuable information that will help to elucidate the roles of HvXTH genes in the growth and development of barley.

Genome-Wide Analysis and Hormone Regulation of Chitin Deacetylases in Silkworm.

Chitin deacetylases (CDAs) are a group of enzymes involved in chitin metabolism in insects; they play a critical role in molting, pupation, and the modification of chitin. In this study, we identified several CDAs in the silkworm, Bombyx mori (BmCDA), and investigated the effect of various hormones on their expression in B. mori larvae and embryo cell lines (BmE). Eight genes encoding BmCDAs were identified in the silkworm genome. They showed different expression patterns in different tissues, and were classified into three types based on where they were expressed: the exoskeleton, digestive organs, and genital organs. Moreover, we found that some BmCDAs showed upregulated expression during the molting period, especially during the fourth molting period in larvae. We also verified that the expression of BmCDA1–6 was upregulated by treatment with 20-hydroxyecdysone not only in larvae, but also in BmE cells. Interestingly, juvenile hormone analog treatment also upregulated the expression of some BmCDAs. The overexpression of several transcription factors revealed that the POU transcription factor POUM2 may play a major role in the regulation of BmCDA expression. Finally, the silencing of BmCDA1 and BmCDA2 did not lead to abnormal phenotypes or death, but may have led to delays in silkworm pupation. These results provide important information about lepidopteran insects in terms of chitin deacetylases and the regulation of their expression.

Genome-wide identification, characterization and in-silico profiling of genes encoding FAD (fatty acid desaturase) proteins in chickpea (Cicer arietinum L.)

Fatty acid desaturases (FADs) are involved in introducing double bonds into the hydrocarbon chains of fatty acids leading to the formation of unsaturated fatty acids. These unsaturated fatty acids are known to play important role in plant development and generating stress tolerance against various environmental stresses. In this study, 21 full-length FAD genes were identified in Desi chickpea (Cicer arietinum L.) and 18 FAD genes in Kabuli chickpea genome by a thorough annotation exercise. An extensive analysis was done to establish their chromosomal locations, construct a phylogeny, structure prediction, motif analysis, in-silico expression analysis and co-expression with other interconnected pathways. In desi chickpea, out of 21 FAD genes, 19 were located on seven chromosomes and two additional scaffolds whereas in Kabuli, out of 18 FAD genes, 17 were located on seven chromosomes and an additional scaffold. Identified soluble and membrane-bound CaFADs were phylogenetically clustered into four and eight subfamilies, respectively with their counterparts from other plants. It was observed that gene structures, motif composition and positions were highly conserved in each subfamily. Furthermore, in-silico gene expression analysis of CaFAD genes in various tissues as well as under abiotic stress conditions revealed differential expression patterns in different tissues and developmental stages. Nine FAD genes were down-regulated in all three abiotic stresses as compared to control. Whereas, five FAD genes were up-regulated in shoot tissue during drought, two FAD genes during salinity and three FAD genes were up-regulated during cold stress. In root tissue, 9 FAD genes were down-regulated and 3 FAD genes were up-regulated during all three abiotic stresses. In co-expression analysis, fatty acid synthesis, TAG synthesis genes and Jasmonic acid (JA) biosynthesis genes were expressed more during flower development and shoot apical meristem. JA signaling gene (CaJAR1) was also expressed more in bud, shoot apical meristem and seeds. No other relationship was observed with respect to modulation during abiotic stresses.

Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum)

BackgroundAP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis thaliana (A. thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of tartary buckwheat (Fagopyum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allowed us to study the tissue and expression profiles of AP2/ERF genes in tartary buckwheat on a genome-wide basis.ResultsIn this study, 134 AP2/ERF genes of tartary buckwheat (FtAP2/ERF) were identified and renamed according to the chromosomal distribution of the FtAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic tree analysis, namely, AP2 (15 members), ERF (116 members) and RAV (3 members). A total of 10 motifs were detected in tartary buckwheat AP2/ERF genes, and some of the unique motifs were found to be important for the function of AP2/ERF genes.ConclusionA comprehensive analysis of AP2/ERF gene expression patterns in different tissues and fruit development stages by quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of FtAP2/ERF genes and improvement of tartary buckwheat crops.

Genome-wide identification of Toll-like receptors in the Chinese soft-shelled turtle Pelodiscus sinensis and expression analysis responding to Aeromonas hydrophila infection

Toll-like receptors (TLRs) recognizing specific pathogen-associated molecular patterns play crucial roles in immune defence against pathogen invasion. Although recent advances in many species have reported the characterization and functional roles of TLRs in innate immunity, systematic knowledge of TLRs is still lacking in the Chinese soft-shelled turtle Pelodiscus sinensis. In this study, a genome-wide search was performed and identified 15 candidate PsTLR family genes in P. sinensis. Protein structure analysis revealed the conserved domain arrangements for these PsTLR proteins. Phylogenetic analysis indicated the evolutionary conservation of TLRs among various species. Additionally, a putative interaction network among PsTLR proteins was proposed and several functional partner proteins involved in TLR signalling pathway were predicted in P. sinensis. Expression profiling showed that these PsTLRs exhibited constitutive expression patterns in different tissues of P. sinensis. Moreover, several genes were highly expressed in the major immune organ spleen. Remarkably, the mRNA levels of PsTLR2-1, PsTLR4 and several TLR signalling molecules were significantly up-regulated in the spleen after Aeromonas hydrophila infection, indicating that PsTLRs and these genes responded to bacterial stress. These results provide rich information for the functional exploration of PsTLRs and will facilitate uncovering the molecular mechanisms underlying immune regulation in P. sinensis.