Developmental Expression Profiles Research Articles

EB-SUN, a new microtubule plus-end tracking protein in Drosophila.

Microtubule (MT) regulation is essential for oocyte development. In Drosophila, MT stability, polarity, abundance, and orientation undergo dynamic changes across developmental stages. In our effort to identify novel microtubule-associated proteins that regulate MTs in the Drosophila ovary, we identified a previously uncharacterized gene, CG18190, whichencodes a novel MT end-binding (EB) protein, which we propose to name EB-SUN. We show that EB-SUN colocalizes with EB1 at growing MT plus-ends in Drosophila S2 cells. Tissue-specific and developmental expression profiles from Paralog Explorer reveal that EB-SUN is predominantly expressed in the ovary and early embryos, while EB1 is ubiquitously expressed. Furthermore, as early as oocyte determination, EB-SUN comets are highly concentrated in oocytes during oogenesis. EB-SUN knockout (KO) results in decreased MT density at the onset of mid-oogenesis (stage 7) and delays oocyte growth during late mid-oogenesis (stage 9). Combining EB-SUN KO with EB1 knockdown (KD) in germ cells significantly further reduces MT density at stage 7. Hatching assays of single protein depletion reveal distinct roles for EB-SUN and EB1 in early embryogenesis, likely due to differences in theirexpression and binding partners. Notably, all eggs from EB-SUN KO/EB1 KD females fail to hatch, suggesting partial redundancy between these proteins.

RNAi targeting Nav and CPR via leaf delivery reduces adult emergence and increases the susceptibility to λ-cyholthin in Tuta absoluta (Meyrick)

The tomato leafminer, Tuta absoluta (Meyrick), one of the most economically destructive pests of tomato, causes severe yields losses of tomato production globally. Rapid evolution of insecticide resistance requires the development of alternative control strategy for this pest. RNA interference (RNAi) represents a promising, innovative control strategy against key agricultural insect pests, which has recently been licensed for Colorado Potato Beetle control. Here two essential genes, voltage-gated sodium channel (Nav) and NADPH-cytochrome P450 reductase (CPR) were evaluated as targets for RNAi using an ex vivo tomato leaf delivery system. Developmental stage-dependent expression profiles showed TaNav was most abundant in adult stages, whereas TaCPR was highly expressed in larval and adult stages. T. absoluta larvae feeding on tomato leaflets treated with dsRNA targeting TaNav and TaCPR showed significant knockdown of gene expression, leading to reduction in adult emergence. Additionally, tomato leaves treated with dsRNA targeting these two genes were significantly less damaged by larval feeding and mining. Furthermore, bioassay with LC30 doses of λ-cyholthin showed that silencing TaNav and TaCPR increased T. absoluta mortality about 32.2 and 17.4%, respectively, thus indicating that RNAi targeting TaNav and TaCPR could increase the susceptibility to λ-cyholthin in T. absoluta. This study demonstrates the potential of using RNAi targeting key genes, like TaNav and TaCPR, as an alternative technology for the control of this most destructive tomato pests in the future.

Odorant binding protein 18 increases the pathogen resistance of the imported willow leaf beetle, Plagiodera versicolora.

Insect odorant-binding proteins (OBPs) are a class of small molecular weight soluble proteins. In the past few years, OBPs had been found to work as carriers of ligands and play a crucial role in olfaction and various other physiological processes, like immunity. A subset of insect OBPs had been found to be expressed differently and play a function in immunity of fungal infection. However, there are few studies on the role of OBPs in immunity of bacterial infection. To identify the immune-related OBPs of Plagiodera versicolora after infected by Pseudomonas aeruginosa, we determined the mortality of P. versicolora to P. aeruginosa and selected the time point of 50% mortality of larvae to collect samples for RNA-seq. RNAi technology was used to investigate the function of immune-related OBPs after P. aeruginosa infection. RNA-seq data shows that PverOBP18 gene significantly up-regulated by 1.8-fold and further RT-qPCR affirmed its expression. Developmental expression profile showed that the expression of PverOBP18 was highest in the pupae, followed by the female adults, and lower in the 1st-3rd larvae and male adults with lowest in eggs. Tissue expression profiling showed that PverOBP18 was dominantly expressed in the epidermis. RNAi knockdown of PverOBP18 significantly reduced the expression of bacterial recognition receptor gene PGRP and antibacterial peptide gene Attacin and reduced the resistance of P. versicolora to P. aeruginosa infection. Our results indicated that PverOBP18 gene increased the pathogen resistance of P. versicolora by cooperating with the immune genes and provided valuable insights into using OBPs as targets to design novel strategies for management of P. versicolora.

Molecular and functional characterization of heat-shock protein 70 in Aphis gossypii under thermal and xenobiotic stresses

Aphis gossypii, a globally distributed and economically significant pest of several crops, is known to infest a wide range of host plants. Heat shock proteins (Hsps), acting as molecular chaperones, are essential for the insect's environmental stress responses. The present study investigated the molecular characteristics and expression patterns of AgHsp70, a heat shock protein gene, in Aphis gossypii. Our phylogenetic analysis revealed that AgHsp70 shared high similarity with homologs from other insects, suggesting a conserved function across species. The developmental expression profiles of AgHsp70 in A. gossypii showed that the highest transcript levels were observed in the fourth instar nymphs, while the lowest levels were detected in the third instar nymphs. Heat stress and exposure to four different xenobiotics (2-tridecanone, tannic acid, gossypol, and flupyradifurone (4-[(2,2-difluoroethyl)amino]-2(5H)-furanone)) significantly up-regulated AgHsp70 expression. Knockdown of AgHsp70 using RNAi obviously increased the susceptibility of cotton aphids to 2-tridecanone, gossypol and flupyradifurone. Dual-luciferase reporter assays revealed that gossypol and flupyradifurone significantly enhanced the promoter activity of AgHsp70 at a concentration of 10 mg/L. Furthermore, we identified the transcription factor heat shock factor (HSF) as a regulator of AgHsp70, as silencing AgHSF reduced AgHsp70 expression. Our results shed light on the role of AgHsp70 in xenobiotic adaptation and thermo-tolerance.

Analysis of the differentially expressed genes in the combs and testes of Qingyuan partridge roosters at different developmental stages

BackgroundThe sexual maturity of chickens is an important economic trait, and the breeding of precocious and delayed puberty roosters is an important selection strategy for broilers. The comb serves as an important secondary sexual characteristic of roosters and determines their sexual precocity. Moreover, comb development is closely associated with gonad development in roosters. However, the underlying molecular mechanism regulating the sexual maturity of roosters has not yet been fully explored.ResultsIn order to identify the genes related to precocious puberty in Qingyuan partridge roosters, and based on the synchrony of testis and combs development, combined with histological observation and RNA-seq method, the developmental status and gene expression profile of combs and testis were obtained. The results showed that during the early growth and development period (77 days of age), the development of combs and testis was significant in the high comb (H) group versus the low comb (L) group (p < 0.05); however, the morphological characteristic of the comb and testicular tissues converged during the late growth and development period (112 days of age) in the H and L groups. Based on these results, RNA-sequencing analysis was performed on the comb and testis tissues of the 77 and 112 days old Qingyuan Partridge roosters with different comb height traits. GO and KEGG analysis enrichment analysis showed that the differentially expressed genes were primarily enriched in MAPK signaling, VEGF signaling, and retinol metabolism pathways. Moreover, weighted correlation network analysis and module co-expression network analysis identified WNT6, AMH, IHH, STT3A, PEX16, KPNA7, CATHL2, ROR2, PAMR1, WISP2, IL17REL, NDRG4, CYP26B1, and CRHBP as the key genes associated with the regulation of precocity and delayed puberty in Qingyuan Partridge roosters.ConclusionsIn summary, we identified the key regulatory genes of sexual precocity in roosters, which provide a theoretical basis for understanding the developmental differences between precocious and delayed puberty in roosters.

Astrocyte Involvement in Blood-Brain Barrier Function: A Critical Update Highlighting Novel, Complex, Neurovascular Interactions.

Neurological disorders have been linked to a defective blood-brain barrier (BBB), with dysfunctions triggered by stage-specific disease mechanisms, some of these being generated through interactions in the neurovascular unit (NVU). Advanced knowledge of molecular and signaling mechanisms in the NVU and the emergence of improved experimental models allow BBB permeability prediction and the development of new brain-targeted therapies. As NVU constituents, astrocytes are the most numerous glial cells, characterized by a heterogeneity that occurs as a result of developmental and context-based gene expression profiles and the differential expression of non-coding ribonucleic acids (RNAs). Due to their heterogeneity and dynamic responses to different signals, astrocytes may have a beneficial or detrimental role in the BBB's barrier function, with deep effects on the pathophysiology of (and on the progression of) central nervous system diseases. The implication of astrocytic-derived extracellular vesicles in pathological mechanisms, due to their ability to pass the BBB, must also be considered. The molecular mechanisms of astrocytes' interaction with endothelial cells at the BBB level are considered promising therapeutic targets in different neurological conditions. Nevertheless, a personalized and well-founded approach must be addressed, due to the temporal and spatial heterogeneity of reactive astrogliosis states during disease.

Identification and characterization of ecdysis-related neuropeptides in the lone star tick Amblyomma americanum.

The lone star tick, Amblyomma americanum, is an important ectoparasite known for transmitting diseases to humans and animals. Ecdysis-related neuropeptides (ERNs) control behaviors crucial for arthropods to shed exoskeletons. However, ERN identification and characterization in A. americanum remain incomplete. We investigated ERNs in A. americanum, assessing their evolutionary relationships, protein properties, and functions. Phylogeny, sequence alignment, and domain structures of ERNs were analyzed. ERN functionality was explored using enrichment analysis, and developmental and tissue-specific ERN expression profiles were examined using qPCR and RNAi experiments. The study shows that ERN catalogs (i.e., eclosion hormone, corazonin, and bursicon) are found in most arachnids, and these ERNs in A. americanum have high evolutionary relatedness with other tick species. Protein modeling analysis indicates that ERNs primarily consist of secondary structures and protein stabilizing forces (i.e., hydrophobic clusters, hydrogen bond networks, and salt bridges). Gene functional analysis shows that ENRs are involved in many ecdysis-related functions, including ecdysis-triggering hormone activity, neuropeptide signaling pathway, and corazonin receptor binding. Bursicon proteins have functions in chitin binding and G protein-coupled receptor activity and strong interactions with leucine-rich repeat-containing G-protein coupled receptor 5. ERNs were expressed in higher levels in newly molted adults and synganglia. RNAi-mediated knockdown of burs α and burs β expression led to a significant decrease in the expression of an antimicrobial peptide, defensin, suggesting they might act in signaling or regulatory pathways that control the expression of immune-related genes. Arthropods are vulnerable immediately after molting because new cuticles are soft and susceptible to injury and pathogen infections. Bursicon homodimers act in prophylactic immunity during this vulnerable period by increasing the synthesis of transcripts encoding antimicrobial peptides to protect them from microbial invasion. Collectively, the expression pattern and characterization of ERNs in this study contribute to a deeper understanding of the physiological processes in A. americanum.

Increased Slc34a2 expression and paracellular phosphate permeability contribute to high intestinal phosphate absorption in young mice.

Phosphorus is a critical constituent of bone as a component of hydroxyapatite. Bone mineral content accrues rapidly early in life necessitating a positive phosphorus balance, which could be established by a combination of increased renal reabsorption and intestinal absorption. Intestinal absorption can occur via a transcellular pathway mediated by the apical sodium-phosphate cotransporter, Slc34a2/NaPiIIb or via the paracellular pathway. We sought to determine how young mammals increase dietary phosphorus absorption from the small intestine to establish a positive phosphorus balance, a prerequisite for rapid bone growth. The developmental expression profile of genes mediating phosphate absorption from the small intestine was determined in mice by qPCR and immunohistochemistry. Additionally, Ussing chamber studies were performed on small bowel of young (p7-p14) and older (8- to 17-week-old) mice to examine developmental changes in paracellular Pi permeability and transcellular Pi transport. Blood and urinary Pi levels were higher in young mice. Intestinal paracellular phosphate permeability of young mice was significantly increased relative to older mice across all intestinal segments. NaPiIIb expression was markedly increased in juvenile mice, in comparison to adult animals. Consistent with this, young mice had increased transcellular phosphate flux across the jejunum and ileum relative to older animals. Moreover, transcellular phosphate transport was attenuated by the NaPiIIb inhibitor NTX1942 in the jejunum and ileum of young mice. Our results are consistent with young mice increasing phosphate absorption via increasing paracellular permeability and the NaPiIIb-mediated transcellular pathway.

Transcriptome analysis reveals the role of Zelda in the regulation of embryonic and wing development of Tribolium castaneum.

Zinc finger protein (Zelda) of Tribolium castaneum (TcZelda) has been showed to play pivotal roles in embryonic development and metamorphosis. However, the regulatory mechanism of TcZelda associated with these physiology processes is unclear. Herein, the developmental expression profile showed that Zelda of T. castaneum was highly expressed in early eggs. Tissue expression profiling revealed that TcZelda was mainly expressed in the larval head and adult ovary of late adults and late larvae. TcZelda knockdown led to a 95% mortality rate in adults. These results suggested that TcZelda is related to the activation of the zygote genome in early embryonic development. Furthermore, 592 differentially expressed genes were identified from the dsZelda treated group. Compared with the control group, altered disjunction (ALD) and AGAP005368-PA (GAP) in the dsZelda group were significantly down-regulated, while TGF-beta, propeptide (TGF) was significantly up-regulated, suggesting that TcZelda may be involved in insect embryonic development. In addition, the expression of Ubx ultrabithorax (UBX), Cx cephalothorax (CX), En engrailed (EN), and two Endocuticle structural glycoprotein sgabd (ABD) genes were significantly down-regulated, suggesting that they may cooperate with TcZelda to regulate the development of insect wings. Additionally, Elongation (ELO), fatty acid synthase (FAS), and fatty acyl-CoA desaturase (FAD) expression was inhibited in dsZelda insects, which could disturb the lipase signaling pathways, thus, disrupting the insect reproductive system and pheromone synthesis. These results may help reveal the function of TcZelda in insects and the role of certain genes in the gene regulatory network and provide new ideas for the prevention and control of T. castaneum.

The protein kinases of Dictyostelia and their incorporation into a signalome

Protein kinases are major regulators of cellular processes, but the roles of most kinases remain unresolved. Dictyostelid social amoebas have been useful in identifying functions for 30% of its kinases in cell migration, cytokinesis, vesicle trafficking, gene regulation and other processes but their upstream regulators and downstream effectors are mostly unknown. Comparative genomics can assist to distinguish between genes involved in deeply conserved core processes and those involved in species-specific innovations, while co-expression of genes as evident from comparative transcriptomics can provide cues to the protein complement of regulatory networks. Genomes and developmental and cell-type specific transcriptomes are available for species that span the 0.5 billion years of evolution of Dictyostelia from their unicellular ancestors. In this work we analysed conservation and change in the abundance, functional domain architecture and developmental regulation of protein kinases across the 4 major taxon groups of Dictyostelia. All data are summarized in annotated phylogenetic trees of the kinase subtypes and accompanied by functional information of all kinases that were experimentally studied. We detected 393 different protein kinase domains across the five studied genomes, of which 212 were fully conserved. Conservation was highest (71%) in the previously defined AGC, CAMK, CK1, CMCG, STE and TKL groups and lowest (26%) in the “other” group of typical protein kinases. This was mostly due to species-specific single gene amplification of “other” kinases. Apart from the AFK and α-kinases, the atypical protein kinases, such as the PIKK and histidine kinases were also almost fully conserved. The phylogeny-wide developmental and cell-type specific expression profiles of the protein kinase genes were combined with profiles from the same transcriptomic experiments for the families of G-protein coupled receptors, small GTPases and their GEFs and GAPs, the transcription factors and for all genes that upon lesion generate a developmental defect. This dataset was subjected to hierarchical clustering to identify clusters of co-expressed genes that potentially act together in a signalling network. The work provides a valuable resource that allows researchers to identify protein kinases and other regulatory proteins that are likely to act as intermediates in a network of interest.

A Highly Expressed Antennae Odorant-Binding Protein Involved in Recognition of Herbivore-Induced Plant Volatiles in Dastarcus helophoroides

Natural enemies such as parasitoids and parasites depend on sensitive olfactory to search for their specific hosts. Herbivore-induced plant volatiles (HIPVs) are vital components in providing host information for many natural enemies of herbivores. However, the olfactory-related proteins involved in the recognition of HIPVs are rarely reported. In this study, we established an exhaustive tissue and developmental expression profile of odorant-binding proteins (OBPs) from Dastarcus helophoroides, an essential natural enemy in the forestry ecosystem. Twenty DhelOBPs displayed various expression patterns in different organs and adult physiological states, suggesting a potential involvement in olfactory perception. In silico AlphaFold2-based modeling and molecular docking showed similar binding energies between six DhelOBPs (DhelOBP4, 5, 6, 14, 18, and 20) and HIPVs from Pinus massoniana. While in vitro fluorescence competitive binding assays showed only recombinant DhelOBP4, the most highly expressed in the antennae of emerging adults could bind to HIPVs with high binding affinities. RNAi-mediated behavioral assays indicated that DhelOBP4 was an essential functional protein for D. helophoroides adults recognizing two behaviorally attractive substances: p-cymene and γ-terpinene. Further binding conformation analyses revealed that Phe 54, Val 56, and Phe 71 might be the key binding sites for DhelOBP4 interacting with HIPVs. In conclusion, our results provide an essential molecular basis for the olfactory perception of D. helophoroides and reliable evidence for recognizing the HIPVs of natural enemies from insect OBPs' perspective.

Cytochrome P450 gene CYP6BQ8 mediates terpinen-4-ol susceptibility in the red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae).

Cytochrome P450 proteins (CYPs) in insects can encode various detoxification enzymes and catabolize heterologous substances, conferring tolerance to insecticides. This study describes the identification of a P450 gene (CYP6BQ8) from Tribolium castaneum (Herbst) and investigation of its spatiotemporal expression profile and potential role in the detoxification of terpinen-4-ol, a component of plant essential oils. The developmental expression profile showed that TcCYP6BQ8 expression was relatively higher in early- and late-larval stages of T. castaneum compared with other developmental stages. Tissue expression profiles showed that TcCYP6BQ8 was mainly expressed in the head and integument of both larvae and adults. The expression profiling of TcCYP6BQ8 in developmental stages and tissues is closely related to the detoxification of heterologous substances. TcCYP6BQ8 expression was significantly induced after exposure to terpinen-4-ol, and RNA interference against TcCYP6BQ8 increased terpinen-4-ol-induced larval mortality from 47.78 to 66.67%. This indicates that TcCYP6BQ8 may be involved in T. castaneum's metabolism of terpinen-4-ol. Correlation investigation between the CYP6BQ8 gene and terpinen-4-ol resistance in T. castaneum revealed that the TcCYP6BQ8 gene was one of the factors behind T. castaneum's resistance to terpinen-4-ol. This discovery may provide a new theoretical foundation for future regulation of T. castaneum.

Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

BackgroundChromosomal aneuploidy is the most common birth defect. However, the developmental mechanism and gene expression profile of fetuses with chromosomal aneuploidy are relatively unknown, and the maternal immune changes induced by fetal aneuploidy remain unclear. The inability to obtain the placenta multiple times in real-time is a bottleneck in research on aneuploid pregnancies. Plasma cell-free DNA (cfDNA) carries the gene expression profile information of its source cells and may be used to evaluate the development of fetuses with aneuploidy and the immune changes induced in the mother owing to fetal aneuploidy.MethodsHere, we carried out whole-genome sequencing of the plasma cfDNA of 101 pregnant women carrying a fetus with trisomy (trisomy 21, n = 42; trisomy 18, n = 28; trisomy 13, n = 31) based on non-invasive prenatal testing (NIPT) screening and 140 normal pregnant women to identify differential genes according to the cfDNA nucleosome profile in the region around the transcription start sites (TSSs).ResultsThe plasma cfDNA promoter profiles were found to differ between aneuploid and euploid pregnancies. A total of 158 genes with significant differences were identified, of which 43 genes were upregulated and 98 genes were downregulated. Functional enrichment and signaling pathway analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases found that these signal pathways were mainly related to the coordination of developmental signals during embryonic development, the control of cell growth and development, regulation of neuronal survival, and immune regulation, such as the MAPK, Hippo, TGF-β, and Rap1 signaling pathways, which play important roles in the development of embryonic tissues and organs. Furthermore, based on the results of differential gene analysis, a total of 14 immune-related genes with significant differences from the ImmPort database were collected and analyzed. These significantly different immune genes were mainly associated with the maintenance of embryonic homeostasis and normal development.ConclusionsThese results suggest that the distribution characteristics of cfDNA nucleosomes in maternal plasma can be used to reflect the status of fetal development and changes of the immune responses in trisomic pregnancies. Overall, our findings may provide research ideas for non-invasive detection of the physiological and pathological states of other diseases.

Molecular characterization of six heat shock protein 70 genes from Arma chinensis and their expression patterns in response to temperature stress.

Arma chinensis is an important predatory enemy of many agricultural and forest pests. Heat shock protein 70 (Hsp70) plays an essential role in insect adaptation to various stress factors. To explore the functions of Hsp70s in relation to thermal tolerance of A. chinensis, full-length cDNAs of six Hsp70 genes (AcHsp70Ba, AcHsp70-4, AcHsp68a, AcHsp68b, AcHsp70-2, and AcHsc70-4) were cloned. Their open reading frames (ORFs) were 1902, 2454, 1884, 1905, 1872, and 1947bp, respectively. Developmental expression profiles showed that AcHsp70Ba, AcHsp70-4, and AcHsc70-4 were extremely highly expressed in adult stages. AcHsp68a and AcHsp70-2 showed the highest level of expression in nymph stages, and AcHsp68b was mainly expressed in male adults. Tissue distribution analysis demonstrated that the AcHsp70s were ubiquitously expressed but showing gene-specific and sex-driven patterns of expression. High temperature induced the expression of the six AcHsp70s. Among them, AcHsp70Ba, AcHsp70-4, AcHsp68a, and AcHsc70-4 were significantly induced at 38°C for 6h, while all six AcHsp70s were significantly induced at 38°C for 24h. There were differences in responses of the six AcHsp70s to low-temperature stress. The expressions of AcHsp70-4, AcHsp68a, and AcHsp68b in male adults were significantly repressed at 4°C for 6h, whereas AcHsp70Ba and AcHsp70-2 were significantly induced. The levels of AcHsp70Ba, AcHsp68b, and AcHsp70-2 in female adults were significantly repressed at 4°C for 24h, whereas AcHsc70-4 was significantly induced. These results suggested that AcHsp70s play important roles in various developmental stages and tissue function, and contribute to the tolerance of A. chinensis to extreme temperatures.

The TGF-β Receptor Gene Saxophone Influences Larval-Pupal-Adult Development in Tribolium castaneum.

The transforming growth factor-β (TGF-β) superfamily encodes a large group of proteins, including TGF-β isoforms, bone morphogenetic proteins and activins that act through conserved cell-surface receptors and signaling co-receptors. TGF-β signaling in insects controls physiological events, including growth, development, diapause, caste determination and metamorphosis. In this study, we used the red flour beetle, Tribolium castaneum, as a model species to investigate the role of the type I TGF-β receptor, saxophone (Sax), in mediating development. Developmental and tissue-specific expression profiles indicated Sax is constitutively expressed during development with lower expression in 19- and 20-day (6th instar) larvae. RNAi knockdown of Sax in 19-day larvae prolonged developmental duration from larvae to pupae and significantly decreased pupation and adult eclosion in a dose-dependent manner. At 50 ng dsSax/larva, Sax knockdown led to an 84.4% pupation rate and 46.3% adult emergence rate. At 100 ng and 200 ng dsSax/larva, pupation was down to 75.6% and 50%, respectively, with 0% adult emergence following treatments with both doses. These phenotypes were similar to those following knockdowns of 20-hydroxyecdysone (20E) receptor genes, ecdysone receptor (EcR) or ultraspiracle protein (USP). Expression of 20E biosynthesis genes disembodied and spookier, 20E receptor genes EcR and USP, and 20E downstream genes BrC and E75, were suppressed after the Sax knockdown. Topical application of 20E on larvae treated with dsSax partially rescued the dsSax-driven defects. We can infer that the TGF-β receptor gene Sax influences larval-pupal-adult development via 20E signaling in T. castaneum.

Genome-wide analysis of histone acetyltransferase and histone deacetylase families and their expression in fruit development and ripening stage of pepper (Capsicum annuum).

The fruit development and ripening process involve a series of changes regulated by fine-tune gene expression at the transcriptional level. Acetylation levels of histones on lysine residues are dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), which play an essential role in the control of gene expression. However, their role in regulating fruit development and ripening process, especially in pepper (Capsicum annuum), a typical non-climacteric fruit, remains to understand. Herein, we performed genome-wide analyses of the HDAC and HAT family in the pepper, including phylogenetic analysis, gene structure, encoding protein conserved domain, and expression assays. A total of 30 HAT and 15 HDAC were identified from the pepper genome and the number of gene differentiation among species. The sequence and phylogenetic analysis of CaHDACs and CaHATs compared with other plant HDAC and HAT proteins revealed gene conserved and potential genus-specialized genes. Furthermore, fruit developmental trajectory expression profiles showed that CaHDAC and CaHAT genes were differentially expressed, suggesting that some are functionally divergent. The integrative analysis allowed us to propose CaHDAC and CaHAT candidates to be regulating fruit development and ripening-related phytohormone metabolism and signaling, which also accompanied capsaicinoid and carotenoid biosynthesis. This study provides new insights into the role of histone modification mediate development and ripening in non-climacteric fruits.

Genomic and transcriptomic analyses of chitin metabolism enzymes in Tenebrio molitor.

Chitin is of great importance in the cuticle and inner cuticular linings of insects. Chitin synthases (CHSs), chitin deacetylases (CDAs), chitinases (CHTs), and β-N-acetylhexosaminidases (HEXs) are important enzymes required for chitin metabolism, and playessential roles in development and metamorphosis. Although chitin metabolism genes have been well characterized in limited insects, the information in the yellow mealworm, Tenebrio molitor, a model insect, is presently still unavailable. With the help of bioinformatics, we identified 54 genes that encode putative chitin metabolism enzymes, including 2 CHSs, 10 CDAs, 32 CHTs, and 10 HEXs in the genome of T. molitor. All these genes have the conserved domains and motifs of their corresponding protein family. Phylogenetic analyses indicated that CHS genes were divided into two groups. CDA genes were clustered into five groups. CHT genes were phylogenetically grouped into 11 clades, among which 1in the endo-β-N-acetylglucosaminidases group and the others were classified in the glycoside hydrolase family 18 groups. HEX genes were assorted into six groups. Developmental and tissue-specific expression profiling indicated that the identified chitin metabolism genes showed dynamical expression patterns concurrent with specific instar during molting period, suggesting their significant roles in molting and development. They were predominantly expressed in different tissues or body parts, implying their functional specialization and diversity. The results provide important information for further clarifying their biological functions using the yellow mealworm as an ideal experimental insect.

Expression patterns and functional analysis of porcine lnc-34015

Long noncoding RNAs (lncRNAs) play important roles in immune regulation in humans and animals. The lnc-34015 was discovered to be critical for the development of muscles, based on the muscle transcriptome of pigs; however, the underlying molecular mechanism requires better understanding. Here, the sequence characteristics of lnc-34015 were analyzed and a competitive endogenous RNA regulatory network of lncRNA was predicted. The developmental expression trend and tissue expression profiles of lnc-34015 were investigated using quantitative polymerase chain reaction. The lnc-34015 sequence is overlapped with introns 11 and 12 of CWF19L1, while CWF19L1, PKD2L1, and CHUK were identified as cis-regulatory genes of lnc-34015. Bioinformatics analyses revealed that lnc-34015 binds to 15 microRNAs (miRNAs), including miR-3646, miR-377-3p, and miR-190b-3p, to regulate downstream gene expression. GO and KEGG enrichment results show that lnc-34015 was mainly involved in cell proliferation, stress response, transcriptional regulation, and alternative splicing. The expression trend of lnc-34015 in muscle was similar to that of target genes and opposite to that of miRNAs. The expression of lnc-34015 was significantly higher in the porcine small intestine and IPEC-J2 cells. Our findings suggest that lnc-34015 regulates CHUK, ZBTB20, and XIAP gene expression by competing with endogenous RNAs to regulate porcine inflammatory responses.

Knockout of the EgriBLOS2 gene results in the transparent integuments of Ectropis grisescens larvae

• CRISPR/Cas9-mediated EgriBLOS2 knockout resulted in larval transparent integuments of Ectropis grisescens . • As many as 70% of the transparent larvae were obtained in G0 generation. • EgriBLOS2 was involved in the formation of larval interment colors. The body colors of insects have evolved specialized roles in body protection, signaling and physiology. In some case, the larvae can camouflage their body colors to adapt the habitants and protect themselves. However, the genetic and molecular basis on larval body colors of the tea geometrid, Ectropis grisescens , remains poorly known. Here, we reported an effect of the lysosome-related organelles complex-1, subunit 2 ( EgriBLOS2 ) gene knockout on larval integuments of E. grisescens , by using a clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system. Combining transcriptomic data and PCR approaches, we first identified the EgriBLOS2 gene from E. grisescens , which encoded 137 amino acids and comprised 3 introns. In the phylogenetic analysis, EgriBLOS2 clustered in the Lepidoptera clade with high conservation to members in other lepidopteran species. Developmental expression profiles revealed that EgriBLOS2 was constantly transcribed at each stage, in which its expression was significantly lower in 2nd instar larvae than that of other instars. After injecting EgriBLOS2 -specific guide RNA and Cas9 messenger RNA into eggs, 70% of larvae showed the translucent integuments in G0 generation, with an emphasis on black splayed patterns in the 2nd and 8th segments of abdomens. However, some typical characteristics of larvae were not obviously changed in mutant instars, such as ocelli, mouthparts and other appendants. This study has unraveled the roles of EgriBLOS2 in the formation of larval integument colors, and provides an alternative strategy for pest management based on the colors in this species .

Functional analysis of a cytochrome P450 gene CYP9Z6 responding to terpinen-4-ol in the red flour beetle, Tribolium castaneum

Tribolium castaneum is an agricultural and stored pest found throughout the world. The cytochrome P450 genes of T. castaneum can encode various detoxification enzymes and catabolize heterologous substances, conferring tolerance to insecticides. Herein, we describe the identification of a P450 gene (CYP9Z6) from T. castaneum and investigated its expression profile and potential role in the detoxification of terpinen-4-ol. TcCYP9Z6 expression was significantly induced after exposure to terpinen-4-ol, and RNA-mediated silencing of TcCYP9Z6 increased terpinen-4-ol-induced larval mortality from 47.75% to 63.92%, showing that TcCYP9Z6 is closely related to the detoxification of terpinen-4-ol. The developmental expression profile revealed that TcCYP9Z6 was mainly expressed in late adults and late larvae. Tissue expression profiling revealed that the highest TcCYP9Z6 expression occurred in the head, in both the adult and the larval tissues, followed by the gut in larvae and the antennae in adults. These developmental stages and tissues with high TcCYP9Z6 expression are closely related to the detoxification of heterologous substances. These results indicated that TcCYP9Z6 may play a pivotal role in the detoxification of terpinen-4-ol, which provides support for using TcCYP9Z6 a potential gene for the RNAi-mediated prevention and control of T. castaneum.