Developmental Stage-specific Expression Research Articles

Histone H3.3 variant plays a critical role on zygote-to-oocyst development in malaria parasites

The Plasmodium life cycle involves differentiation into multiple morphologically distinct forms, a process regulated by developmental stage-specific gene expression. Histone proteins are involved in epigenetic regulation in eukaryotes, and the histone variant H3.3 plays a key role in the regulation of gene expression and maintenance of genomic integrity during embryonic development in mice. However, the function of H3.3 through multiple developmental stages in Plasmodium remains unknown. To examine the function of H3.3, h3.3-deficient mutants (Δh3.3) were generated in P. berghei. The deletion of h3.3 was not lethal in blood stage parasites, although it had a minor effect of the growth rate in blood stage; however, the in vitro ookinete conversion rate was significantly reduced, and the production of the degenerated form was increased. Regarding the mosquito stage development of Δh3.3, oocysts number was significantly reduced, and no sporozoite production was observed. The h3.3 gene complemented mutant have normal development in mosquito stage producing mature oocysts and salivary glands contained sporozoites, and interestingly, the majority of H3.3 protein was detected in female gametocytes. However, Δh3.3 male and female gametocyte production levels were comparable to the wild-type levels. Transcriptome analysis of Δh3.3 male and female gametocytes revealed the upregulation of several male-specific genes in female gametocytes, suggesting that H3.3 functions as a transcription repressor of male-specific genes to maintain sexual identity in female gametocytes. This study provides new insights into the molecular biology of histone variants H3.3 which plays a critical role on zygote-to-oocyst development in primitive unicellular eukaryotes.

Dynamic changes in LINC00458/HBL1 lncRNA expression during hiPSC differentiation to cardiomyocytes

Long non-coding RNAs (lncRNAs) constitute the largest and most diverse class of non-coding RNAs. They localize to the nucleus, cytoplasm, or both compartments, and regulate gene expression through various mechanisms at multiple levels. LncRNAs tend to evolve faster and present higher tissue- and developmental stage-specific expression than protein-coding genes. Initially considered byproducts of erroneous transcription without biological function, lncRNAs are now recognized for their involvement in numerous biological processes, such as immune response, apoptosis, pluripotency, reprogramming, and differentiation. In this study, we focused on Heart Brake lncRNA 1 (HBL1), a lncRNA recently reported to modulate the process of pluripotent stem cell differentiation toward cardiomyocytes. We employed RT-qPCR and high-resolution RNA FISH to monitor the expression and localization of HBL1 during the differentiation progression. Our findings indicate a significant increase in HBL1 expression during mesodermal and cardiac mesodermal stages, preceding an anticipated decrease in differentiated cells. We detected the RNA in discrete foci in both the nucleus and in the cytoplasm. In the latter compartment, we observed colocalization of HBL1 with Y-box binding protein 1 (YB-1), which likely results from an interaction between the RNA and the protein, as the two were found to be coimmunoprecipitated in RNP-IP experiments. Finally, we provide evidence that HBL1, initially reported as an independent lncRNA gene, is part of the LINC00458 (also known as lncRNA-ES3 or ES3) gene, forming the last exon of some LINC00458 splice isoforms.

Identification of the CONSTANS-like family in Cymbidium sinense, and their functional characterization

BackgroundCymbidium sinense is an orchid that is typically used as a potted plant, given its high-grade ornamental characteristics, and is most frequently distributed in China and SE Asia. The inability to strictly regulate flowering in this economically important potted and cut-flower orchid is a bottleneck that limits its industrial development. Studies on C. sinense flowering time genes would help to elucidate the mechanism regulating flowering. There are very few studies on the genetic regulation of flowering pathways in C. sinense. Photoperiod significantly affects the flowering of C. sinense, but it was unknown how the CONSTANS gene family is involved in regulating flowering.ResultsIn this study, eight CONSTANS-like genes were identified and cloned. They were divided into three groups based on a phylogenetic analysis. Five representative CsCOL genes (CsCOL3/4/6/8/9) were selected from the three groups to perform expression characterization and functional study. CsCOL3/4/6/8/9 are nucleus-localized proteins, and all five CsCOL genes were expressed in all organs, mainly in leaves followed by sepals. The expression levels of CsCOL3/4 (group I) were higher in all organs than other CsCOL genes. Developmental stage specific expression revealed that the expression of CsCOL3/4/9 peaked at the initial flowering stage. In contrast, the transcript level of CsCOL6/8 was highest at the pedicel development stage. Photoperiodic experiments demonstrated that the transcripts of the five CsCOL genes exhibited distinct diurnal rhythms. Under LD conditions, the overexpression of CsCOL3/4 promoted early flowering, and CsCOL6 had little effect on flowering time, whereas CsCOL8 delayed flowering of Arabidopsis thaliana. However, under SD conditions, overexpression of CsCOL4/6/8 promoted early flowering and the rosette leaves growth, and CsCOL3 induced flower bud formation in transgenic Arabidopsis.ConclusionThe phylogenetic analysis, temporal and spatial expression patterns, photoperiodic rhythms and functional study indicate that CsCOL family members in C. sinense were involved in growth, development and flowering regulation through different photoperiodic pathway. The results will be useful for future research on mechanisms pertaining to photoperiod-dependent flowering, and will also facilitate genetic engineering-based research that uses Cymbidium flowering time genes.

Transcriptomic profiles reveal the characteristics of oocytes and cumulus cells at GV, MI, and MII in follicles before ovulation

BackgroundThe oocyte and its surrounding cumulus cells (CCs) exist as an inseparable entity. The maturation of the oocyte relies on communication between the oocyte and the surrounding CCs. However, oocyte evaluation is primarily based on morphological parameters currently, which offer limited insight into the quality and competence of the oocyte. Here, we conducted transcriptomic profiling of oocytes and their CCs from 47 patients undergoing preimplantation genetic testing for aneuploidy (PGT-A). We aimed to investigate the molecular events occurring between oocytes and CCs at different stages of oocyte maturation (germinal vesicle [GV], metaphase I [MI], and metaphase II [MII]). Our goal is to provide new insights into in vitro oocyte maturation (IVM).ResultsOur findings indicate that oocyte maturation is a complex and dynamic process and that MI oocytes can be further classified into two distinct subtypes: GV-like-MI oocytes and MII-like-MI oocytes. Human oocytes and cumulus cells at three different stages of maturation were analyzed using RNA-seq, which revealed unique transcriptional machinery, stage-specific genes and pathways, and transcription factor networks that displayed developmental stage-specific expression patterns. We have also identified that both lipid and cholesterol metabolism in cumulus cells is active during the late stage of oocyte maturation. Lipids may serve as a more efficient energy source for oocytes and even embryogenesis.ConclusionsOverall, our study provides a relatively comprehensive overview of the transcriptional characteristics and potential interactions between human oocytes and cumulus cells at various stages of maturation before ovulation. This study may offer novel perspectives on IVM and provide a reliable reference data set for understanding the transcriptional regulation of follicular maturation.

The trehalose 6-phosphate phosphatase family in plants.

Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signalling metabolite linking plant growth and development to carbon metabolism. While recent work has focused predominantly on the enzymes that produce Tre6P, little is known about the proteins that catalyse its degradation, the trehalose 6-phosphate phosphatases (TPPs). Often occurring in large protein families, TPPs exhibit cell-, tissue- and developmental stage-specific expression patterns, suggesting important regulatory functions in controlling local levels of Tre6P and trehalose as well as Tre6P signalling. Furthermore, growing evidence through gene expression studies and transgenic approaches shows that TPPs play an important role in integrating environmental signals with plant metabolism. This review highlights the large diversity of TPP isoforms in model and crop plants and identifies how modulating Tre6P metabolism in certain cell types, tissues, and at different developmental stages may promote stress tolerance, resilience and increased crop yield.

Comprehensive characterization and expression analysis of enzymatic antioxidant gene families in passion fruit (Passiflora edulis)

Passion fruit, a valuable tropical fruit, faces climate-related growth challenges. Antioxidant enzymes are vital for both stress protection and growth regulation in plants. We first provided systemic analysis of enzymatic antioxidant gene families in passion fruit, identifying 90 members including 11 PeSODs, 45 PeAPXs, 8 PeCATs, 7 PeGPXs, 6 PeMDHARs, 8 PeDHARs, and 5 PeGRs. Gene members in each gene family with same subcellular localization showed closer phylogenetic relationship. Many antioxidant genes exhibited tissue- or developmental stage-specific expression patterns during floral and fruit development, with some widely expressed. Their co-expressed genes were linked to photosynthesis and energy metabolism, suggesting roles in protecting highly proliferating tissues from oxidative damage. Potential genes for enhancing temperature stress resistance were identified. The involvement of diverse regulatory factors including miRNAs, transcription factors, and CREs might contribute to the complex roles of antioxidant genes. This study informs future research on antioxidant genes and passion fruit breeding.

P-221 Single-cell transcriptomic profiles reveal the characteristics of oocytes and CCs at GV, MI, and MII in oocytes before ovulation

Abstract Study question what is the mechanism of the interaction between oocytes and CCs supporting oocyte development during oocyte maturation? Summary answer Cumulus cells are responsible for the accumulation of lipids and fatty acids to ensure oocytes have enough energy available for later embryogenesis. What is known already The oocyte and its surrounding cumulus cells (CCs) exist as an inseparable entity. The maturation of the oocyte is reliant on the materials and energy provided by CCs Although several reports have addressed the transcriptome of oocytes and granulosa cells during human folliculogenesis, many questions remain unanswered regarding the interaction between oocytes and CCs during the final stages of folliculogenesis before ovulation. Therefore, the mechanism of the interaction between oocytes and CCs supporting oocyte development during oocyte maturation is needed to be studied. Study design, size, duration We collected a total of 139 samples from 47 preimplantation genetic testing (PGT) patients for RNA sequencing , including 97 CCs (GV: 35; MI: 30; MII: 32) and 42 oocytes (GV: 22; MI: 11; MII: 9).10 cells were randomly selected from individually cumulus-oocyte complex per CC sample to avoid bias due to the different number of CCs in each follicle. The samples were collected within a time frame of 3 months. Participants/materials, setting, methods The oocytes removed from CGCs were quickly transferred to the operating dish for marking, the maturation stage was assessed and recorded by observing the nucleus of oocytes, the CCs were mechanically isolated. Isolated RNA from oocytes and CCs underwent library preparation using an oligo deoxy-thymidine(dT) priming approach followed by deep sequencing. Data processing and bioinformatics analysis were performed using software, mainly including FASTP, STAR, String Tie, ARCANE and DESeq2 along with functional annotation analysis. Main results and the role of chance We found that oocyte maturation is a dynamic process and MI oocytes can be subdivided into GV-like-MI oocytes and MII-like-MI oocytes. we revealed unique transcriptional machinery, transcription factor networks, and crosstalk, displaying developmental stage-specific expression patterns at the three stages of oocyte maturation. We also identified that both lipid and cholesterol metabolism in cumulus cells are active during the late stage of oocyte maturation, and lipids may serve as a more efficient energy source for oocytes and even embryogenesis. Moreover, we also found that the metabolic profile of MII CCs, particularly those associated with the synthesis pathway of heparan sulfate synthesis, predicts the quality of DAY 3 blastomeres（P = 0.0001）. Limitations, reasons for caution The transcriptional profile of mural granulosa cells during the final stages of follicle maturation has not been fully explored. Wider implications of the findings This study provides a relatively systematic and comprehensive overview of the transcriptional features and interactions between oocytes and CCs at different stages of maturation before ovulation and may provide insights into developing a non-invasive method for the clinical assessment of oocyte quality and prediction of DAY3 blastomere quality in ART. Trial registration number not applicable

Functional characterization of Cinnamate 4-hydroxylase gene family in soybean (Glycine max).

Cinnamate 4-hydroxylase (C4H) is the first key cytochrome P450 monooxygenase (P450) enzyme in the phenylpropanoid pathway. It belongs to the CYP73 family of P450 superfamily, and catalyzes the conversion of trans-cinnamic acid to p-coumaric acid. Since p-coumaric acid serves as the precursor for the synthesis of a wide variety of metabolites involved in plant development and stress resistance, alteration in the expression of soybean C4H genes is expected to affect the downstream metabolite levels, and its ability to respond to stress. In this study, we identified four C4H genes in the soybean genome that are distributed into both class I and class II CYP73 family. GmC4H2, GmC4H14 and GmC4H20 displayed tissue- and developmental stage-specific gene expression patterns with their transcript accumulation at the highest level in root tissues. GmC4H10 appears to be a pseudogene as its transcript was not detected in any soybean tissues. Furthermore, protein homology modelling revealed substrate docking only for GmC4H2, GmC4H14 and GmC4H20. To demonstrate the function of GmC4Hs, we modified a cloning vector for the heterologous expression of P450s in yeast, and used it for microsomal protein production and enzyme assay. Our results confirmed that GmC4H2, GmC4H14 and GmC4H20 contain the ability to hydroxylate trans-cinnamic acid with varying efficiencies.

Functional analysis of two mitogen-activated protein kinases involved in thermal resistance of the predatory mite Neoseiulus californicus (Acari: Phytoseiidae).

Predatory mites are important biological control agents used against phytophagous mites and small insects. They face various environmental pressures, especially fluctuating climate factors. Neoseiulus californicus, a commercially available phytoseiid mite, is adapted to a wide range of temperature conditions. We investigated the regulatory mechanisms governing the plastic response of N. californicus for coping with environmental temperature variations. The mitogen-activated protein kinase (MAPK) signaling pathway is a highly conserved pathway of cell signal transduction that responds to environmental stress. We isolated two MAPKK genes (NcMAPKK4 and NcMAPKK6) from N. californicus and studied their functions. Developmental stage-specific expression level analysis showed that in adults, particularly females, NcMAPKK4 and NcMAPKK6 levels were higher than in other developmental stages. The expression level analysis at extremely high and low temperature conditions demonstrated that NcMAPKK4 could be induced significantly by adverse thermal stresses, whereas NcMAPKK6 distinctly responded to heat shock, indicating their different roles in thermal stress responses. After silencing of NcMAPKK4, both heat and cold resistance decreased significantly, whereas NcMAPKK6 knockdown had a greater influence on heat resistance. Knockdown of NcMAPKKs also reduced the activities of antioxidant enzymes, suggesting the regulation of NcMAPKKs was closely related to the antioxidant process in oxidative stress caused by external stimuli. These results indicate an important role of NcMAPKKs in the response to thermal stress and provide insight into the MAPK cascade pathway in the environmental adaptation mechanisms of phytoseiid mites.

Developmental Transcriptome Analysis of Red-Spotted Apollo Butterfly, Parnassius bremeri.

Parnassius bremeri (P. bremeri), a member of the genus Snow Apollo in the swallowtail family (Papilionidae), is a high alpine butterfly that lives in Russia, Korea, and China. It is an endangered wildlife (Class I) in South Korea and is a globally endangered species. The lack of transcriptomic and genomic resources of P. bremeri significantly hinders the study of its population genetics and conservation. The detailed information of the developmental stage-specific gene expression patterns of P. bremeri is of great demand for its conservation. However, the molecular mechanism underlying the metamorphic development of P. bremeri is still unknown. In the present study, the differentially expressed genes (DEGs) across the metamorphic developmental stages were compared using high-throughput transcriptome sequencing. We identified a total of 72,161 DEGs from eight comparisons. GO enrichment analysis showed that a range of DEGs were responsible for cuticle development and the melanin biosynthetic pathway during larval development. Pathway analysis suggested that the signaling pathways, such as the Wnt signaling pathway, hedgehog signaling pathway and Notch signaling pathway, are regulated during the developmental stages of P. bremeri. Furthermore, sensory receptors were also activated, especially during the larval to adult transition stage. Collectively, the results of this study provide a preliminary foundation and understanding of the molecular mechanism in their transcriptomes for further research on the metamorphic development of P. bremeri.

Circular RNAs: Biomarkers of cancer

AbstractCircular RNAs (circRNAs) are a class of single‐stranded closed RNAs that are produced by the back splicing of precursor mRNAs. The formation of circRNAs mainly involves intron‐pairing‐driven circularization, RNA‐binding protein (RBP)‐driven circularization, and lariat‐driven circularization. The vast majority of circRNAs are found in the cytoplasm, and some intron‐containing circRNAs are localized in the nucleus. CircRNAs have been found to function as microRNA (miRNA) sponges, interact with RBPs and translate proteins, and play an important regulatory role in the development and progression of cancer. CircRNAs exhibit tissue‐ and developmental stage–specific expression and are stable, with longer half‐lives than linear RNAs. CircRNAs have great potential as biomarkers for cancer diagnosis and prognosis, which is highlighted by their detectability in tissues, especially in fluid biopsy samples such as plasma, saliva, and urine. Here, we review the current studies on the properties and functions of circRNAs and their clinical application value.

Emerging roles of circular RNAs in tuberculosis.

Tuberculosis (TB) remains a major global health issue, resulting in around 1.5 million people deaths each year. Better diagnostic and therapeutic tools are urgently needed. Circular RNAs (circRNAs) are a new class of noncoding RNAs with a covalently closed structure, and exhibit a tissue-, cell-, and developmental stage-specific expression pattern. Recently, circRNAs were thought to be regulatory molecules implicated in the onset and progression of a series of human diseases including tuberculosis. In tuberculosis, circRNAs have been shown to regulate host anti-TB immune responses, such as decreasing monocyte apoptosis, enhancing autophagy and promoting macrophage polarization. Importantly, circRNAs are physically stable and abundant in several types of body fluids. Therefore they are considered as promising minimally-invasive biomarkers. In this review, we focus on the recent advances in the immune regulatory roles of circRNAs, as well as their potential diagnostic value in TB.

Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Cross-Linking†.

Interactions of DNA with structural proteins such as histones, regulatory proteins and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The invivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved, little progress has been achieved in the cross-linking step. Because of its low efficiency, the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" cross-linking agent. Efficient biphotonic cross-linking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein cross-links invitro model systems and cells.

The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids.

Intestinal organoids are innovative in vitro tools to study the digestive epithelium. The objective of this study was to generate jejunum and colon organoids from suckling and weaned piglets in order to determine the extent to which organoids retain a location-specific and a developmental stage-specific phenotype. Organoids were studied at three time points by gene expression profiling for comparison with the transcriptomic patterns observed in crypts in vivo. In addition, the gut microbiota and the metabolome were analyzed to characterize the luminal environment of epithelial cells at the origin of organoids. The location-specific expression of 60 genes differentially expressed between jejunum and colon crypts from suckling piglets was partially retained (48%) in the derived organoids at all time point. The regional expression of these genes was independent of luminal signals since the major differences in microbiota and metabolome observed in vivo between the jejunum and the colon were not reproduced in vitro. In contrast, the regional expression of other genes was erased in organoids. Moreover, the developmental stage-specific expression of 30 genes differentially expressed between the jejunum crypts of suckling and weaned piglets was not stably retained in the derived organoids. Differentiation of organoids was necessary to observe the regional expression of certain genes while it was not sufficient to reproduce developmental stage-specific expression patterns. In conclusion, piglet intestinal organoids retained a location-specific phenotype while the characteristics of developmental stage were erased in vitro. Reproducing more closely the luminal environment might help to increase the physiological relevance of intestinal organoids.

Evolutionary history of the NLR gene families across lophotrochozoans

NOD-like receptor (NLR) genes are critical innate immune receptors in animals and plants. Lophotrochozoans represent one of the most species-rich superphyla that includes molluscs, segmented worms, flatworms, bryozoans, and other invertebrates, which is crucial to our understanding of immune system evolution in bilaterians. However, NLRs have not been systematically described in lophotrochozoans. We annotated 185 NLRs in 29 lophotrochozoan genomes, and analyzed their domain organization, phylogenetic distribution, molecular evolution, and gene expression. We found that all the 24 molluscan genomes studied encoded no more than three NLRs. None of these molluscan NLRs represented an inducible expression pattern under the infection of eight pathogens; some molluscan NLRs showed developmental stage-specific expression patterns. Instead, 29 molluscan incomplete NLR (incNLR) genes, encoding for proteins absent in the NACHT domain were upregulated under pathogen infection. We also documented the species-specific expansion of NLRs in the clades Polychaeta and Pteriidae. Our study revealed that gene duplication, domain shuffling, gene loss, and novel expression pattern played important roles in the molecular evolution of NLRs.

Temporal and Isoform-Specific Expression of CTBP2 Is Evolutionarily Conserved Between the Developing Chick and Human Retina.

Complex transcriptional gene regulation allows for multifaceted isoform production during retinogenesis, and novel isoforms transcribed from a single locus can have unlimited potential to code for diverse proteins with different functions. In this study, we explored the CTBP2/RIBEYE gene locus and its unique repertoire of transcripts that are conserved among vertebrates. We studied the transcriptional coregulator (CTBP2) and ribbon synapse-specific structural protein (RIBEYE) in the chicken retina by performing comprehensive histochemical and sequencing analyses to pinpoint cell and developmental stage-specific expression of CTBP2/RIBEYE in the developing chicken retina. We demonstrated that CTBP2 is widely expressed in retinal progenitors beginning in early retinogenesis but becomes limited to GABAergic amacrine cells in the mature retina. Inversely, RIBEYE is initially epigenetically silenced in progenitors and later expressed in photoreceptor and bipolar cells where they localize to ribbon synapses. Finally, we compared CTBP2/RIBEYE regulation in the developing human retina using a pluripotent stem cell derived retinal organoid culture system. These analyses demonstrate that similar regulation of the CTBP2/RIBEYE locus during chick and human retinal development is regulated by different members of the K50 homeodomain transcription factor family.

Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

BackgroundCircular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive.ResultsTrichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration.ConclusionsOur study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens.

Single-cell transcriptomics reveals hidden information in trypanosomatids

Dixenic parasites often encounter environmental extremes during the transition from vector to host. Preadapted transmission stages overcome these challenges to promote parasites' survival and ensure life cycle progression. Recently, Vigneron et al. and Briggs et al. used single-cell transcriptomics to investigate developmental stage specific gene expression patterns during parasite differentiation.

Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control.

The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura, and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed on > 130 host plants, including several economically important crops. The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long-read data and Illumina short read), a high-quality genome assembly was achieved (N50 = 1.1 Mb). An official gene set (18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq datasets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression combined with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed four potential genes of interest (three of them Spodoptera-specific) upregulated during first- and third-instar larval stages for targeted pest-outbreak management. The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provide critical insights into the biology of this devastating polyphagous insect pest species worldwide. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.

Molecular Characterization of NDL1-AGB1 Mediated Salt Stress Signaling: Further Exploration of the Role of NDL1 Interacting Partners.

Salt stress is considered to be the most severe abiotic stress. High soil salinity leads to osmotic and ionic toxicity, resulting in reduced plant growth and crop production. The role of G-proteins during salt stresses is well established. AGB1, a G-protein subunit, not only plays an important role during regulation of Na+ fluxes in roots, but is also involved in the translocation of Na+ from roots to shoots. N-Myc Downregulated like 1 (NDL1) is an interacting partner of G protein βγ subunits and C-4 domain of RGS1 in Arabidopsis. Our recent in-planta expression analysis of NDL1 reported changes in patterns during salt stress. Based on these expression profiles, we have carried out functional characterization of the AGB1-NDL1 module during salinity stress. Using various available mutant and overexpression lines of NDL1 and AGB1, we found that NDL1 acts as a negative regulator during salt stress response at the seedling stage, an opposite response to that of AGB1. On the other hand, during the germination phase of the plant, this role is reversed, indicating developmental and tissue specific regulation. To elucidate the mechanism of the AGB1-NDL1 module, we investigated the possible role of the three NDL1 stress specific interactors, namely ANNAT1, SLT1, and IDH-V, using yeast as a model. The present study revealed that NDL1 acts as a modulator of salt stress response, wherein it can have both positive as well as negative functions during salinity stress. Our findings suggest that the NDL1 mediated stress response depends on its developmental stage-specific expression patterns as well as the differential presence and interaction of the stress-specific interactors.