Paranosema locustae is an environmentally friendly parasitic predator with promising applications in locust control. In this study, transcriptome sequencing was conducted on gonadal tissues of Locusta migratoria males and females infected and uninfected with P. locustae at different developmental stages. A total of 18,635 differentially expressed genes (DEGs) were identified in female ovary tissue transcriptomes, with the highest number of DEGs observed at 1 day post-eclosion (7141). In male testis tissue transcriptomes, a total of 32,954 DEGs were identified, with the highest number observed at 9 days post-eclosion (11,245). Venn analysis revealed 25 common DEGs among female groups and 205 common DEGs among male groups. Gene ontology and Kyoto Encyclopaedia of Genes and Genome analyses indicated that DEGs were mainly enriched in basic metabolism such as amino acid metabolism, carbohydrate metabolism, lipid metabolism, and immune response processes. Protein–protein interaction analysis results indicated that L. migratoria regulates the expression of immune- and reproductive-related genes to meet the body's demands in different developmental stages after P. locustae infection. Immune- and reproductive-related genes in L. migratoria gonadal tissue were screened based on database annotation information and relevant literature. Genes such as Tsf, Hex1, Apolp-III, Serpin, Defense, Hsp70, Hsp90, JHBP, JHE, JHEH1, JHAMT, and VgR play important roles in the balance between immune response and reproduction in gonadal tissues. For transcriptome validation, Tsf, Hex1, and ApoLp-III were selected and verified by quantitative real-time polymerase chain reaction (qRT-PCR). Correlation analysis revealed that the qRT-PCR expression patterns were consistent with the RNA-Seq results. These findings contribute to further understanding the interaction mechanisms between locusts and P. locustae.

Sperm infertility or subfertility is detrimental to the precious highland germplasm like yak whose population has been gradually declining in India. Understanding the ‘omic’ landscape of infertile or subfertile yak sperm can reveal some interesting insights. In an attempt to do the same, this study considered the semen of infertile or subfertile yak bulls for whole-genome and transcriptome evaluations. DNA sequencing revealed that the yak sperm genome contains the necessary genes to carry out all the important biological processes related to the growth, development, survival and multiplication of an organism. Interestingly, RNA Seq results highlighted that genes like VAMP7, MYLK, ARAP2 and MARCH6 showed increased expression, while biological processes related to immune response (GO:0043308, GO:0002447, GO:0002278, GO:0043307, GO:0043312, GO:0002283, GO:0043299 and GO:0002446) were significantly overrepresented. These findings hint at a possible role played by immune system in regulating infertility or subfertility in yaks. Further, in-depth studies can validate these findings and help in improving our biological understanding in this area.

Confronting environments with low relative humidity is one of the main challenges faced by insects with expanding distribution ranges. Anastrepha ludens (the Mexican fruit fly) has evolved to cope with the variable conditions encountered during its lifetime, which allows it to colonise a wide range of environments. However, our understanding of the mechanisms underpinning the ability of this species to confront environments with low relative humidity is incomplete. In this sense, omic approaches such as transcriptomics can be helpful for advancing our knowledge on how this species copes with desiccation stress. Considering this, in this study, we performed transcriptomic analyses to compare the molecular responses of laboratory-reared A. ludens exposed and unexposed to desiccation. Data from the transcriptome analyses indicated that the responses to desiccation are shared by both sexes. We identified the up-regulation of transcripts encoding proteins involved in lipid metabolism and membrane remodelling, as well as proteases and cuticular proteins. Our results provide a framework for understanding the response to desiccation stress in one of the most invasive fruit fly species in the world.

Cruznema velatum isolated from soil in a chestnut orchard located at Guangdong province, China, is redescribed with morphology, molecular barcoding sequences, and transcriptome data. The morphological comparison for C. velatum and six other valid species is provided. Phylogeny analysis suggests genus Cruznema is monophyletic. The species is amphimix, can be cultured with Escherichia coli in 7–9 days from egg to egg-laying adult, and has a lifespan of 11 to 14 days at 20°C. The transcription data generated 45,366 unigenes; 29.9%, 31.3%, 24.8%, and 18.6% of unigenes were annotated in KOG, SwissProt, GO, and KEGG, respectively. Further gene function analysis demonstrated that C. velatum share the same riboflavin, lipoic acid, and vitamin B6 metabolic pathways with Caenorhabditis elegans and Pristionchus pacificus.

Despite the importance of secondary dormancy for plant life cycle timing and survival, there is insufficient knowledge about the (epigenetic) regulation of this trait at the molecular level. Our aim was to determine the role of (epi)genetic processes in the regulation of secondary seed dormancy using natural genotypes of the widely distributed Capsella bursa-pastoris. Seeds of nine ecotypes were exposed to control conditions or histone deacetylase inhibitors [trichostatin A (TSA), valproic acid] during imbibition to study the effects of hyper-acetylation on secondary seed dormancy induction and germination. Valproic acid increased secondary dormancy and both compounds caused a delay of t50 for germination (radicle emergence) but not of t50 for testa rupture, demonstrating that they reduced speed of germination. Transcriptome analysis of one accession exposed to valproic acid versus water showed mixed regulation of ABA, negative regulation of GAs, BRs and auxins, as well as up-regulation of SNL genes, which might explain the observed delay in germination and increase in secondary dormancy. In addition, two accessions differing in secondary dormancy depth (deep vs non-deep) were studied using RNA-seq to reveal the potential regulatory processes underlying this trait. Phytohormone synthesis or signalling was generally up-regulated for ABA (e.g. NCED6, NCED2, ABCG40, ABI3) and down-regulated for GAs (GA20ox1, GA20ox2, bHLH93), ethylene (ACO1, ERF4-LIKE, ERF105, ERF109-LIKE), BRs (BIA1, CYP708A2-LIKE, probable WRKY46, BAK1, BEN1, BES1, BRI1) and auxin (GH3.3, GH3.6, ABCB19, TGG4, AUX1, PIN6, WAT1). Epigenetic candidates for variation in secondary dormancy depth include SNL genes, histone deacetylases and associated genes (HDA14, HDA6-LIKE, HDA-LIKE, ING2, JMJ30), as well as sequences linked to histone acetyltransferases (bZIP11, ARID1A-LIKE), or to gene silencing through histone methylation (SUVH7, SUVH9, CLF). Together, these results show that phytohormones and epigenetic regulation play an important role in controlling differences in secondary dormancy depth between accessions.

Temperature strongly impacts the rates of physiological and biochemical processes, which in turn can determine the survival and population size of insects. At low temperatures performance is limited, however, cold tolerance and performance at low temperature can be improved after short- or long-term acclimation in many insect species. To understand mechanisms underlying acclimation, we sequenced and compared the transcriptome of the blowfly Chrysomya megacephala under rapid cold hardening (RCH) and long-term cold acclimation (LCA) conditions. The RCH response was dominated by genes related to immune response, spliceosome, and protein processing in endoplasmic reticulum with up-regulation during recovery from RCH. In contrast, LCA was associated with genes related to carbohydrate metabolism and cytoskeleton branching and stabilizing. Meanwhile, mRNA levels of genes related to glycerophospholipid metabolism, and some heat shock proteins (Hsps) were collectively up-regulated by both RCH and LCA. There were more genes and pathway adjustments associated with LCA than RCH. Overall, the transcriptome data provide basic information of molecular mechanisms underpinning the RCH and LCA response. The partly independent molecular responses to RCH and LCA suggest that several avenues for manipulating cold performance exist and RCH might be more effective as it only triggers fewer genes and affects the general metabolisms less. These observations provide some appropriate methods to improve cold tolerance of C. megacephala, and hold promise for developing an extended use of mass-reared C. megacephala with better cold performance as a pollinator of crops at low temperatures.

Gene expression variation can be partitioned into different components (regulatory, genetic and acclimatory effects) but for lichen-forming fungi, the relative importance of each of these effects is unclear. Here, we studied gene expression in the lichen-forming fungus Lobaria pulmonaria in response to thermal stress and parasitism by the lichenicolous fungus Plectocarpon lichenum. Our experimental procedure was to acclimate lichen thalli to 4 °C over three weeks and then expose them to 15 °C and 25 °C for 2 hours each, sampling infected and visually asymptomatic thalli at each temperature. Quantitative Real-Time PCR was utilized to quantify gene expression of six candidate genes, normalizing expression values with two reference genes. We found that two genes encoding heat shock proteins (hsp88 and hsp98), two polyketide synthase genes (rPKS1, nrPKS3) and elongation factor 1-1-α (efa) were upregulated at higher temperatures. Moreover, we observed higher expression of hsp98 at 25 °C in samples infected by P. lichenum than in uninfected samples. Finally, in partial redundancy analyses, most of the explained variation in gene expression was related to temperature treatment; genetic variation and long-term acclimatization to sites contributed far less. Hence, regulatory effects (i.e. direct adjustments of gene expression in response to the temperature change) dominated over genetic and acclimatory effects in the gene expression variability of L. pulmonaria. This study suggests that L. pulmonaria could become a valuable lichen model for studying heat shock protein responses in vivo.

Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

The structure and organization of cells within organs is essential to their function, but nowhere in the body is this more spectacular than the brain. There, sprawling, snowflake-like neurons have grown into a precise arrangement, reaching out to neighboring cells to form neural circuits. Communication within neural circuits, made possible by spatial positioning, forms the basis of our physiology. Recently, a high-resolution cell atlas generated by MERFISH (multiplex error-robust fluorescence in situ hybridization) technology has mapped this spectacular organ with unmatched resolution, depth, and scale. The atlas catalogs cells as they exist in the intact biological system and will allow us to learn more about rare cell types and sparsely expressed cell signaling receptors fundamental to health and disease.

Microbiome, the study of microbial communities in specific environments, has developed significantly since the Human Microbiome Project began. Microbiomes have been associated with changes within environmental niches and the development of various diseases. The development of high-throughput technology such as next-generation sequencing has also allowed us to perform transcriptome studies, which provide accurate functional profiling data. Metabolome studies, which analyse the metabolites found in the environment, are the most direct environmental condition indicator. Although each dataset provides valuable information on its own, the integration of multiple datasets provides a deeper understanding of the relationship between the host, agent and environment. Therefore, network analysis using multiple datasets might give a clearer understanding of disease pathogenesis.

The brain, a lung, a tumor: each contains a complex array of cell types arranged in an intricate spatial pattern that is critical to their role within the tissue. While work is underway to create an atlas of cellular diversity across tissues, traditional methods either have sufficiently high multiplexing capacity but lack spatial context, or they provide spatial information but lack the multiplexing capacity to identify subtle variations in cell type or state. This limitation precludes a comprehensive view across a whole tissue, including rare cells, as they exist within a tissue of interest. Since understanding how the molecular and cellular organization of a biological tissue contributes to its functionality is fundamental to developing treatments that target the cell biology underlying diseased states, improved tools that map biological systems with both high spatial resolution and high multiplexing capacity promise to deliver new, clinically relevant insights into the functional composition of biological systems. The recently developed multiplexed error-robust fluorescence in situ hybridization (MERFISH) method provides information about gene expression at subcellular resolution and reveals cell type, state, and cell-cell interaction by quantifying the expression and exact location of hundreds to thousands of transcripts within intact tissues. MERFISH represents a major advancement toward directly interrogating rich cellular heterogeneity and is being applied to gain insight into the biological complexity within and around us.

In order to better understand the molecular mechanisms associated with salinity tolerance, transcriptome analysis of a local salt-tolerant wheat landrace (i.e. Roshan) was performed under salt stress. Transcriptome sequencing yielded 137,508,542 clean reads using the Illumina HiSeq 2000 platform. The results of two alignment programs, i.e. STAR and HISAT2, were used separately to perform the analysis of differentially expressed genes (DEGs) using DESeq2. Finally, a total of 17,897 DEGs were identified by DESeq2. Moreover, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses identified 108 GO terms and 62 significant KEGG pathways, of which ‘metabolic process’ and ‘metabolic pathways’ were the most abundant enriched term and pathway, respectively. Additionally, key salinity-tolerant genes, including asparagine synthetase, were also identified in the present study. Out of 87 identified families of transcription factors, GAI‐RGA ‐ and ‐SCR (GRAS) was one of the most important, which participates in signal transduction, and meristem maintenance and development. Eventually, to validate the gene expression levels, six DEGs were selected for a quantitative real-time polymerase chain reaction, and the results were in line with those of RNA-Seq. The findings of the current study can guide future genetic and molecular studies and allow a better understanding and improvement of salt tolerance in wheat.

Fluorescent proteins (FPs) are reported to play an important role as photoprotectants and antioxidants in corals subjected to stressful conditions. Identifying the various FP genes expressed and FP gene expression patterns under stress in diverse coral species can provide insight into FP function. In this study, we identified 16 putative FP homologues from the transcriptomes of corals with varying susceptibility to elevated temperature, including Acropora digitifera, Favites colemani, Montipora digitata and Seriatopora caliendrum. Each coral expressed a different complement of FP transcripts, which were predicted to have distinct spectral properties. The most diverse and abundant repertoire of FP transcripts, including at least 6 green FPs, were expressed in the temperature-tolerant coral, F. colemani. In comparison, the other corals expressed fewer FP types. Specific FP transcripts exhibited variable expression profiles in coral fragments subjected to 32 ± 1 °C (treatment) or 28 ± 1 °C (control) for up to 72 h, suggesting that distinct FPs may have different roles. Further studies on the expression of the proteins encoded by these FP transcripts, their fluorescence activity, tissue localization, and possible antioxidant properties, are needed to reveal their contribution to thermal stress tolerance in certain species of corals.

Oxygen concentration influences oocyte quality and subsequent embryo development, but it remains unclear whether oxygen concentrations affect the developmental competence and transcriptomic profile of yak oocytes. In this study, we investigated the effects of different oxygen concentrations (5% versus 20%) on the developmental competence, reactive oxygen species (ROS) levels, glutathione (GSH) content, and transcriptomic profile of yak oocytes. The results showed that a low oxygen concentration significantly increased the maturation rate of yak oocytes (81.2 ± 2.2% vs 75.9 ± 1.3%) and the blastocyst quality of yak in vitro fertilized embryos. Analysis of ROS and GSH showed that a low oxygen concentration reduced ROS levels and increased the content of GSH (75.05 ± 7.1 ng/oocyte vs 50.63 ± 5.6 ng/oocyte). Furthermore, transcriptomic analysis identified 120 differentially expressed genes (DEGs) between the two groups of oocytes. Gene enrichment analysis of the DEGs indicated multiple cellular processes, including oxidative phosphorylation, transcription regulation, mitochondrial regulation, oestrogen signalling pathway, HIF-1 signalling pathway, TNF signalling pathway, were involved in the response to oxygen concentration alterations. Taken together, these results indicated that a low oxygen concentration improved the developmental competence of yak oocytes.

Bien que le lithium soit le traitement de première ligne pour la prévention des rechutes dans le trouble bipolaire seuls 30 % des patients sont de bons répondeurs. Ainsi, un sous-groupe important des patients, traités avec du lithium, présente des taux élevés de rechute. En l’absence de marqueurs cliniques prédictifs de réponse il reste difficile de prédire avec précision quels patients répondront en évitant de les soumettre à de longues périodes de traitements au lithium. L’identification de biomarqueurs prédictifs est donc un enjeu majeur pour améliorer la prise en charge des patients bipolaires. Le mécanisme d’action du lithium est complexe car il exerce une action inhibitrice ou activatrice sur plusieurs voies de signalisation cellulaires. L’ensemble de ces cibles et effecteurs contribuent aux effets neuroprotecteurs dans le cerveau et de stabilisation de l’humeur et complexifient la compréhension de la réponse prophylactique au lithium. Les études visant à identifier une corrélation entre la réponse au lithium et des mutations de gènes ont produit des résultats controversés. Afin de mieux comprendre la variabilité de la réponse au lithium, une approche complémentaire aux études génétiques, consiste à étudier les effets moléculaires induits par un traitement aigu ou chronique au lithium. Il a ainsi été montré que le lithium module les niveaux d’expression de gènes au niveau des ARN messagers, des protéines aussi des miRNA dans plusieurs modèles in vivo et in vitro. Ces études ouvrent de nouvelles voies de recherche pour identifier des biomarqueurs de la réponse prophylactique au lithium pouvant être transférés en clinique afin d’éviter de longues périodes de traitement inefficace au lithium et élaborer des stratégies de traitement plus personnalisées.

Helminth parasitology is an important discipline, which poses often unique technical challenges. One challenge is that helminth parasites, particularly those in humans, are often difficult to obtain alive and in sufficient quantities for study; another is the challenge of studying these organisms in vitro – no helminth parasite life cycle has been fully recapitulated outside of a host. Arguably, the key issue retarding progress in helminth parasitology has been a lack of experimental tools and resources, certainly relative to the riches that have driven many parasitologists to adopt free-living model organisms as surrogate systems. In response to these needs, the past 10–12 years have seen the beginnings of helminth parasitology's journey into the ‘omics’ era, with the release of abundant sequencing resources, and the functional genomics tools with which to test biological hypotheses. To reflect this progress, the 2019 Autumn Symposium of the British Society for Parasitology was held in Queen's University Belfast on the topic of ‘post-genomic progress in helminth parasitology’. This issue presents examples of the current state of play in the field, while this editorial summarizes how genomic datasets and functional genomic tools have stimulated impressive recent progress in our understanding of parasite biology.

Ascarid parasites infect a variety of hosts and regular anthelmintic treatment is recommended for all species. Parascaris spp. is the only ascarid species with widespread anthelmintic resistance, which allows for the study of resistance mechanisms. The purpose of this study was to establish an in vitro drug exposure protocol for adult anthelmintic-naïve Parascaris spp. and report a preliminary transcriptomic analysis in response to drug exposure. Live worms were harvested from foal necropsies and maintained in RPMI-1640 at 37 °C. Serial dilutions of oxibendazole (OBZ) and ivermectin (IVM) were prepared for in vitro drug exposure, and worm viability was monitored over time. In a second drug trial, worms were used for transcriptomic analysis. The final drug concentrations employed were OBZ at 40.1 μm (10 μg mL−1) and IVM at 1.1 μm (1 μg mL−1) for 24 and 3 h, respectively. The RNA-seq analysis revealed numerous differentially expressed genes, with some being potentially related to drug detoxification and regulatory mechanisms. This report provides a method for in vitro drug exposure and the phenotypic responses for Parascaris spp., which could be extrapolated to other ascarid parasites. Finally, it also provides preliminary transcriptomic data following drug exposure as a reference point for future studies of Parascaris spp.

Adipogenesis, myogenesis and fibrogenesis are related processes that can contribute to meat quality. Therefore, extending the knowledge of these processes would facilitate the identification of molecular markers that predict intramuscular fat accretion. The main purpose of this work, based on previous results, was to further study the expression of key genes related to adipogenic, myogenic, fibrogenic processes and some cytokines in Longissimus thoracis (LT) and Masseter (MS) muscles of Pirenaica and Holstein young bulls. Longissimus thoracis and MS muscles from Pirenaica (n = 4) and Spanish Holstein (n = 4) were sampled for proximate analysis, determination of adipocyte size distribution and expression of key candidate genes. Fat percentage was lower in LT than in MS muscle in Pirenaica young bulls (P = 0.023) and was higher in LT muscle in Holstein than in Pirenaica young bulls (P = 0.007). Gene expression analysis revealed that the mRNA level of myogenic differentiation 1 (MYOD) was higher in LT than in MS muscles in both groups of animals (P < 0.001) and that myostatin (MSTN) expression was also higher in LT than in MS muscle in Holstein bulls (P = 0.001). On the other hand, MSTN and PPARG showed higher expression in LT and MS in Pirenaica young bulls (P = 0.026), while the expression of fatty acid-binding protein 4 (FABP4) was higher in Holstein young bulls, also in both muscles (P < 0.001). The results suggested that the development of intramuscular adipose depot was directly related to the expression of adipogenic genes, such as FABP4, but inversely related to the expression of the cytokine MSTN and the myogenic gene MYOD, genes which showed a muscle-specific expression.