Functional Groups Of Genes Research Articles

Shallow groundwater table fluctuations affect bacterial communities and nitrogen functional genes along the soil profile in a vegetable field

Fluctuations in the shallow groundwater table change the biochemical environment and nitrogen cycling processes along the soil profile and cause the loss of nitrogen from the soil profile and nitrogen pollution in shallow groundwater. With a microcosm experiment, this study aimed to examine the effects of variations in soil properties caused by water table fluctuations on the bacterial communities and the nitrogen transformation functional genes along the soil profile in a vegetable field. The results showed that Proteobacteria and Acidobacteria were the dominant phyla in the samples. With the lowering of the water table and continuous drying of the soil profile, the abundances of the narG, nirK, nirS and nosZ genes gradually decreased, and the abundances of the AOA-amoA and AOB-amoA genes gradually increased. The functional genes gradually decreased with increasing soil depth. Water table fluctuations had obvious effects on the bacterial communities in the C and D layers, but the soil physicochemical properties had greater impacts in the A and B layers. The soil water content (W), TN, TOC, NH4+-N, pH and NO3−-N were significantly related to the soil bacterial communities. The two key functional gene groups directly driving the major processes for NH4+-N and NO3--N transformation were nosZ/narG and nosZ/(nirK+nirS). This study provides insights into the relative importance of variations in soil properties and the microbial community in the soil profile caused by water table fluctuations in driving the transformation of soil nitrogen.

557. Impact of Heavy Metal Exposure in the Transcriptional Response of Methicillin--Resistant Staphylococcus aureus (MRSA)-USA300 Latin-American Variant (USA300-LV)

BackgroundUSA 300-LV is the predominant MRSA clone in Colombia and contains a genomic island designated “COMER” with genes for copper (Cu) and mercury (Hg) resistance. HM environmental contamination is a serious threat to public health in Colombia and could also influence the selection and evolution of HM resistance genes in MRSA. Here, we investigate the global transcriptomic responses of USA300-LV after exposure to HM under the hypothesis that USA300-LV strains are highly capable of sustaining higher HM concentrationsMethodsWe performed comparative RNAseq experiments in USA300-LV clinical strain (CA-MRSA12). Total RNA was isolated in exponential phase in the absence and presence of sub-inhibitory concentrations of Cu and Hg (3 replicates). cDNA libraries were prepared and sequenced on an Illumina platform. Differentially expressed genes (DEG) were calculated by DeSeq2 (p-adjusted value ˂ 0.01) and results on 19 selected genes were confirmed by qRT-PCR.ResultsUS300-LV exhibited a larger number of differentially expressed genes when exposed to Hg (n = 114) compared with Cu treatment (n = 16). The most common functional groups of genes upregulated after Hg exposure included those involved in amino acid metabolism (n = 18). In contrast, 45 genes were downregulated after Hg exposure, mostly associated to host immune system defense (n = 11). qRT-PCR confirmed that the most upregulated genes were those involved in murein hydrolase activity, Hg resistance and the transcriptional regulator Cro/CI. Of 9 genes that were downregulated, functional groups included ype VII secretion system, immune modulators and leucocidins. Copper treatment resulted in only 12 genes that were upregulated including those in the COMER element (n = 6), aminoacid metabolism (n = 3), ROS response (n = 1), host immune system defense (n = 1) and unknown function (n = 1). Downregulated genes were those associated to host immune system defense (n = 2), energy generation (n = 1) and unknown function (n = 1).ConclusionDifferential adaptive responses after exposure to HM in USA300-LV suggest a role in the evolution of antimicrobial resistance and successful spread in the region. Metabolic adaptations involving amino acid metabolism seem to play a role in the evolution of HM resistance in MRSA.Disclosures All authors: No reported disclosures.

P6589Genetic risks for arrhythmia phenotypes in dilated cardiomyopathy

Abstract Background Genotype-phenotype correlations in dilated cardiomyopathy (DCM) and in particular the effects of gene variants on clinical outcomes remain poorly understood. Purpose To investigate the prognostic role of genetic variant carrier status in a large cohort of DCM patients. Methods We analyzed 487 DCM patients by next-generation sequencing and categorized the disease genes into functional gene groups. The following composite outcome measures were assessed: 1) all-cause mortality, heart transplantation or left ventricular assist device (D/HTx/VAD); 2) sudden cardiac death or malignant ventricular arrhythmias (SCD/MVAs); 3) heart failure related death, heart transplantation or left ventricular assist device implantation (DHF/HTx/VAD). Results A total of 187 pathogenic/likely pathogenic variants were found in 180 patients (37%): 55 (11%) TTN; 19 (4%) LMNA; 24 (5%) structural cytoskeleton-Z disk genes; 16 (3%) desmosomal genes; 47 (10%) sarcomeric genes; 8 (2%) ion channels genes; 11 (2%) other genes. The occurrence of D/HTx/VAD was no different between variant carriers and non-carriers (p=0.17). However, carriers of desmosomal and LMNA variants experienced the highest rate of SCD/MVA, which was independent of the left ventricular ejection fraction. Conclusions Desmosomal and LMNA gene variants identify the subset of DCM patients at greatest risk for SCD and life-threatening ventricular arrhythmias, regardless the left ventricular ejection fraction. Acknowledgement/Funding National Institutes of Health grants R01 HL69071, HL116906, and AHA17GRNT33670495

Nitrogen metabolism in photosynthetic bacteria wastewater treatment: A novel nitrogen transformation pathway

Nitrogen removal from wastewater is a worldwide environmental problem. Photosynthetic bacteria (PSB) were reported to have a great potential in treating varieties of nitrogen-contaminated wastewater. However, their nitrogen metabolic mechanism is still unclear, which was further explored in this work. The results showed that PSB can efficiently utilize NH4+-N, NO3−-N and NO2−-N. Over 90% nitrogen removal efficiencies were obtained under suitable condition. 35 ~ 51% of removed nitrogen was transformed to N2 and N2O. In addition, basically no mutual transformation occurred between NH4+-N, NO3−-N and NO2−-N in PSB, which is different from other biological technologies. Combining with the analysis of functional gene groups, it indicated that there might be a new direct nitrogen transformation pathway, i.e. NH4+ might be directly oxidized to N2/N2O in nitrogen metabolism of PSB, which breaks the limitations of existing technologies, and proposed a new understanding of nitrogen metabolism in PSB.

Genetic Risk of Arrhythmic Phenotypes in Patients With Dilated Cardiomyopathy

BackgroundGenotype-phenotype correlations in dilated cardiomyopathy (DCM) and, in particular, the effects of gene variants on clinical outcomes remain poorly understood. ObjectivesThe purpose of this study was to investigate the prognostic role of genetic variant carrier status in a large cohort of DCM patients. MethodsA total of 487 DCM patients were analyzed by next-generation sequencing and categorized the disease genes into functional gene groups. The following composite outcome measures were assessed: 1) all-cause mortality; 2) heart failure–related death, heart transplantation, or destination left ventricular assist device implantation (DHF/HTx/VAD); and 3) sudden cardiac death/sustained ventricular tachycardia/ventricular fibrillation (SCD/VT/VF). ResultsA total of 183 pathogenic/likely pathogenic variants were found in 178 patients (37%): 54 (11%) Titin; 19 (4%) Lamin A/C (LMNA); 24 (5%) structural cytoskeleton-Z disk genes; 16 (3.5%) desmosomal genes; 46 (9.5%) sarcomeric genes; 8 (1.6%) ion channel genes; and 11 (2.5%) other genes. All-cause mortality was no different between variant carriers and noncarriers (p = 0.99). A trend toward worse SCD/VT/VF (p = 0.062) and DHF/HTx/VAD (p = 0.061) was found in carriers. Carriers of desmosomal and LMNA variants experienced the highest rate of SCD/VT/VF, which was independent of the left ventricular ejection fraction. ConclusionsDesmosomal and LMNA gene variants identify the subset of DCM patients who are at greatest risk for SCD and life-threatening ventricular arrhythmias, regardless of the left ventricular ejection fraction.

Long-term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil.

Nitrogen (N) deposition is a component of global change that has considerable impact on belowground carbon (C) dynamics. Plant growth stimulation and alterations of fungal community composition and functions are the main mechanisms driving soil C gains following N deposition in N-limited temperate forests. In N-rich tropical forests, however, N deposition generally has minor effects on plant growth; consequently, C storage in soil may strongly depend on the microbial processes that drive litter and soil organic matter decomposition. Here, we investigated how microbial functions in old-growth tropical forest soil responded to 13years of N addition at four rates: 0 (Control), 50 (Low-N), 100 (Medium-N), and 150 (High-N) kgNha-1 year-1 . Soil organic carbon (SOC) content increased under High-N, corresponding to a 33% decrease in CO2 efflux, and reductions in relative abundances of bacteria as well as genes responsible for cellulose and chitin degradation. A 113% increase in N2 O emission was positively correlated with soil acidification and an increase in the relative abundances of denitrification genes (narG and norB). Soil acidification induced by N addition decreased available P concentrations, and was associated with reductions in the relative abundance of phytase. The decreased relative abundance of bacteria and key functional gene groups for C degradation were related to slower SOC decomposition, indicating the key mechanisms driving SOC accumulation in the tropical forest soil subjected to High-N addition. However, changes in microbial functional groups associated with N and P cycling led to coincidentally large increases in N2 O emissions, and exacerbated soil P deficiency. These two factors partially offset the perceived beneficial effects of N addition on SOC storage in tropical forest soils. These findings suggest a potential to incorporate microbial community and functions into Earth system models considering their effects on greenhouse gas emission, biogeochemical processes, and biodiversity of tropical ecosystems.

Antifibrotic Potential of MiR-335-3p in Hereditary Gingival Fibromatosis

Hereditary gingival fibromatosis (HGF) is a highly genetically heterogeneous disease, and current therapeutic method is limited to surgical resection with a high recurrence rate. MicroRNAs (miRNAs) are able to fine-tune large-scale target genes. Here we established a simple but effective computational strategy based on available miRNA target prediction algorithms to pinpoint the most potent miRNA that could negatively regulate a group of functional genes. Based on this rationale, miR-335-3p was top ranked by putatively targeting 85 verified profibrotic genes and 79 upregulated genes in HGF patients. Experimentally, downregulation of miR-355-3p was demonstrated in HGF-derived gingival fibroblasts as well as in transforming growth factor β–stimulated normal human gingival fibroblasts (NHGFs) compared to normal control. Ectopic miR-335-3p attenuated, whereas knockdown of miR-335-3p promoted, the fibrogenic activity of human gingival fibroblasts. Mechanically, miR-335-3p directly targeted SOS1, SMAD2/3, and CTNNB1 by canonical and noncanonical base paring. In particular, different portfolios of fibrotic markers were suppressed by silencing SOS1, SMAD2/3, or CTNNB1, respectively. Thus, our study first proposes a novel miRNA screening approach targeting a functionally related gene set and identifies miR-335-3p as a novel target for HGF treatment. Mechanically, miR-335-3p suppresses the fibrogenic activity of human gingival fibroblasts by repressing multiple core molecules in profibrotic networks. Our strategy provides a new paradigm in the treatment for HGF as well as other diseases.

Genetic associations as indices for assessing nitrogen transformation processes in co-composting of cattle manure and rice straw

In this study, mechanism of nitrogen transformation was investigated in terms of genetic associations (nitrogen-related gene groups) in co-composting of cattle manure and rice straw. Mutual validation among KEGG, Pearson correlation, stepwise regression, and Path analyses indicated that the functional genes synergistically affected on nitrogen transformation in composting process. NxrA/qnorB (0.9419 ± 0.0334) and (amoA + anammox)/Bacteria (0.7187 ± 0.0334) were the key functional gene groups mediating NH4+-N transformation. AmoA/(narG + napA) (−0.8400 ± 0.0129), amoA/bacteria (0.8692 ± 0.0273), and (nirK + nirS)/nosZ (1.1652 ± 0.0089) determined NO3−-N, NO2−-N and N2O transformation, respectively. AmoA/(napA + narG) mediated both NO3−-N and NO2−-N transformation. AmoA/anammox (−0.7172 ± 0.0591) and (nirK + nirS)/nosZ (−0.6626 ± 0.0825) served as predominant factors for total nitrogen removal. These results provided a molecular-level insight that nitrification, anaerobic ammonia oxidation and denitrification (SNAD) might simultaneously contribute to nitrogen transformation during composting, rather than sequentially.

Quantitative response of nitrogen dynamic processes to functional gene abundances in a pond-ditch circulation system for rural wastewater treatment

The pond-ditch circulation system (PDCS) is a promising solution for the restoration of rural wastewater. However, the underlying nitrogen removal mechanisms and roles of functional genes in nitrogen transformation processes have not yet been quantified at the molecular level. In this study, PDCSs have been found to have high removal efficiencies when the chemical oxygen demand (COD) and total nitrogen (TN) was high (>70%; 62.7–93.9%, respectively). Meanwhile, the presence of simultaneous nitrification, anaerobic ammonium oxidation (anammox), and denitrification processes were the primary nitrogen removal mechanisms in the PDCSs. According to the stepwise regression analysis and path analysis, two key functional gene groups, nosZ/(nirS + nirK) and (nxrA/amoA), were driving these major processes for TN and ammonia nitrogen (NH4+-N), respectively. Moreover, the key functional gene group narG/nxrA was affecting processes related to nitrate-nitrogen (NO3−-N) and nitrite-nitrogen (NO2−-N) conversion. Furthermore, results from the 15N isotope pairing technique suggested that for PDCSs, anammox was mainly responsible for nitrogen removal due to its high contribution to total N2 production (50.3%) in the ditch; denitrification, on the other hand, was primarily attributed to nitrogen removal, rather than the anammox process, in two ponds (41.3–43.1%).

Transcriptome profiling reveals male- and female-specific gene expression pattern and novel gene candidates for the control of sex determination and gonad development in Xenopus laevis

Xenopus laevis is an amphibian (frog) species widely used in developmental biology and genetics. To unravel the molecular machinery regulating sex differentiation of Xenopus gonads, we analyzed for the first time the transcriptome of developing amphibian gonads covering sex determination period. We applied microarray at four developmental stages: (i) NF50 (undifferentiated gonad during sex determination), (ii) NF53 (the onset of sexual differentiation of the gonads), (iii) NF56 (sexual differentiation of the gonads), and (iv) NF62 (developmental progression of differentiated gonads). Our analysis showed that during the NF50, the genetic female (ZW) gonads expressed more sex-specific genes than genetic male (ZZ) gonads, which suggests that a robust genetic program is realized during female sex determination in Xenopus. However, a contrasting expression pattern was observed at later stages (NF56 and NF62), when the ZW gonads expressed less sex-specific genes than ZZ gonads, i.e., more genes may be involved in further development of the male gonads (ZZ). We identified sexual dimorphism in the expression of several functional groups of genes, including signaling factors, proteases, protease inhibitors, transcription factors, extracellular matrix components, extracellular matrix enzymes, cell adhesion molecules, and epithelium-specific intermediate filaments. In addition, our analysis detected a sexually dimorphic expression of many uncharacterized genes of unknown function, which should be studied further to reveal their identity and if/how they regulate gonad development, sex determination, and sexual differentiation. Comparison between genes sex-specifically expressed in developing gonads of Xenopus and available transcriptome data from zebrafish, two reptile species, chicken, and mouse revealed significant differences in the genetic control of sex determination and gonad development. This shows that the genetic control of gonad development is evolutionarily malleable.

IntronDB: a database for eukaryotic intron features.

The rate and extent of unbalanced eukaryotic intron changes exhibit dynamic patterns for different lineages of species or certain functional groups of genes with varied spatio-temporal expression modes affected by selective pressure. To date, only a few key conserved splicing signals or regulatory elements have been identified in introns and little is known about the remaining intronic regions. To trace the evolutionary trajectory of spliceosomal introns from available genomes under a unified framework, we present IntronDB, which catalogs ∼50000000 introns from over 1000 genomes spanning the major eukaryotic clades in the tree of life. Based on the position of introns relative to coding regions, it categorizes introns into three groups, such as 5'UTR, CDS and 3'UTR and subsequently divides CDS introns into three categories, such as phase 0, phase 1 and phase 2. It provides the quality evaluation for each sequence entry and characterizes the intronic parameters including number, size, sequence composition and positioning information as well as the features for exons and genes, making possible the comparisons between introns and exons. It reports the dinucleotides around the intron boundary and displays the consensus sequence features for all introns, small introns and large introns for each genome. By incorporating the taxonomic assignment of genomes, it performs high-level or genome-wide statistical analysis for single feature and coupled features both in a single genome and across multiple genomes. It offers functionalities to browse the data from representative protein-coding transcripts and download the data from all transcripts from protein-coding genes. http://www.nextgenbioinformatics.org/IntronDB. Supplementary data are available at Bioinformatics online.

Analysis of alternative splicing events in the root tips and nodules of Pisum sativum L

Background. Legumes establish symbioses with nitrogen-fixing bacteria from the Rhizobium group. In exchange for nutrients, bacteria provide fixed nitrogen needed to support plant growth. At the moment, information about the involvement of alternative splicing (AS) in the establishment and maintenance this symbiotic relationships is almost absent, but, as it is a powerful mechanism for the regulation of proteome diversity of the cell, it therefore may participate in cellular response to microsymbionts.
 Materials and methods. Alternative splicing was analyzed using the assembly of supertranscripts and alignment of the reads from nodules and root tips to this reference. Target genes expression levels was estimated in tips of non-inoculated roots, and in nodules (2, 4, and 6 weeks post inoculation) with use of RT-qPCR.
 Results.In this study, the analysis of AS events in the nodules and root tips of the pea was carried out. The presence of isoforms of four pea genes (PsSIP1, PsIGN, PsWRKY40, PsPR-10) was confirmed and their expression level was estimated.
 Conclusion. Pea nodules were shown to be more enriched with AS events compared to root tips. Among the functional groups of genes that demonstrate AS events, one of the most enriched functional groups is the pathogens stress response. Intron retention probably leads to degradation of the transcript via NMD-system or to change of the protein function, that modulates the activity of genes in nodules.

Field-grown soybean transcriptome shows diurnal patterns in photosynthesis-related processes.

Many plant physiological processes have diurnal patterns regulated by diurnal environmental changes and circadian rhythms, but the transcriptional underpinnings of many of these cycles have not been studied in major crop species under field conditions. Here, we monitored the transcriptome of field‐grown soybean (Glycine max) during daylight hours in the middle of the growing season with RNA‐seq. The analysis revealed 21% of soybean genes were differentially expressed over the course of the day. Expression of some circadian‐related genes in field‐grown soybean differed from previously reported expression patterns measured in controlled environments. Many genes in functional groups contributing to and/or depending on photosynthesis showed differential expression, with patterns particularly evident in the chlorophyll synthesis pathway. Gene regulatory network inference also revealed seven diurnally sensitive gene nodes involved with circadian rhythm, transcription regulation, cellular processes, and water transport. This study provides a diurnal overview of the transcriptome for an economically important field‐grown crop and a basis for identifying pathways that could eventually be tailored to optimize diurnal regulation of carbon gain.

Developing a Genomics Model to Predict Failure of Isocitrate Dehydrogenase (IDH) Inhibitors for Treatment of Patients with IDH1- or IDH2-Mutated Acute Myeloid Leukemia

Background: Small molecule drugs that target specific pathogenic gene mutations offer the possibility of treating cancers while maintaining a wide therapeutic margin. Potential mechanisms of resistance to such targeted therapies include alternate or additional mutations in the target gene, activating mutations in genes downstream in the same pathway, or mutations in genes in an alternate prosurvival pathway. Co-occurring mutations that contribute to resistance may be present at the start of therapy and lead to immediate treatment failure. Therapy planning might be optimized if one could predict failure to a specific treatment even when the target was present. Ivosidenib (IVO, Agios Pharmaceuticals, Inc.) and enasidenib (ENA, Celgene Corp.) are small molecule inhibitors of IDH1 and IDH2 gain-of-function mutant enzymes, respectively, developed for treatment of acute myeloid leukemia (AML) with such mutations. In the Phase 1 monotherapy trials of IVO and ENA for treatment of relapsed or refractory (R/R) AML, the majority of patients appeared to be resistant to treatment; 67% and 77% of the patients with the target IDH mutation, respectively, failed to achieve complete remission with full (CR) or partial (CRh) hematological recovery. IDH1- and IDH2-mutated AMLs have multiple co-occurring mutations which may impact this resistance. The purpose of this study was to determine if there is a co-occurring mutation signature at treatment baseline that can identify patients with relapsed or refractory IDH1- or IDH2-mutated AML who would be resistant to treatment with mutant IDH inhibitors. We hypothesized that since the molecular pathogenesis was the same in IDH1- and IDH2-mutated AML (overexpression of the oncometabolite 2-hydroxyglutarate ), the co-occurring mutations that contributed to resistance would also be the same.Methods: Adequate clinical and genomics data were available for 147 patients with IDH1-mutated R/R AML treated with IVO (Study AG120-C-001, NCT02074839) and 87 patients with IDH2-mutated R/R AML treated with ENA (Study AG221-C-001, NCT01915498). Only patients with the treatment-targeted IDH mutations as determined by the companion diagnostic were included in the analysis cohorts. Patients who failed to achieve an FDA-adjudicated CR or CRh within the first 6 cycles of therapy were considered nonresponders; patients without a response assessment after start of therapy were excluded from analysis. Genomics data were generated using next-generation sequencing platforms.Results: To address the hypothesis, a mutational signature or model was first generated with the data from the ENA-treated patients, and subsequently tested on the data from the IVO-treated patients. In the first step, data were fit to the model using a proprietary algorithm that implemented a Monte-Carlo simulation expansion of Fisher's regularized linear discriminant analysis. The candidate model with the minimal number of genes that can differentiate more than half of the difference between responder and nonresponder groups includes 19 genes. However, more accuracy was attained by developing a 46- or 96-gene model. By Ingenuity Pathway Analysis, nonresponders differed from responders by mutations in only a few functional groups of genes (leukemia cell proliferation, leukemia cell differentiation and leukemia cell movement). In the assessment of diagnostic accuracy, the 96-gene model had 96% sensitivity, 69% specificity and 90% accuracy for identifying patients with IDH2-mutated AML who would not respond to treatment with ENA (Table). When tested in the cohort of patients with IDH1-mutated AML treated with IVO, the model had 97% sensitivity but only 10% specificity and 65% accuracy.Conclusions: We conclude that genomics data may be useful to identify patients with co-occurring mutations that predict resistance to targeted therapies, but a predictive genomics signature may be specific to the treatment target gene rather than being generalizable across target genes that share a common mechanism of pathogenesis. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Tissue differences revealed by gene expression profiles of various cell lines.

Mechanisms through which tissues are formed and maintained remain unknown but are fundamental aspects in biology. Tissue-specific gene expression is a valuable tool to study such mechanisms. But in many biomedical studies, cell lines, rather than human body tissues, are used to investigate biological mechanisms Whether or not cell lines maintain their tissue-specific characteristics after they are isolated and cultured outside the human body remains to be explored. In this study, we applied a novel computational method to identify core genes that contribute to the differentiation of cell lines from various tissues. Several advanced computational techniques, such as Monte Carlo feature selection method, incremental feature selection method, and support vector machine (SVM) algorithm, were incorporated in the proposed method, which extensively analyzed the gene expression profiles of cell lines from different tissues. As a result, we extracted a group of functional genes that can indicate the differences of cell lines in different tissues and built an optimal SVM classifier for identifying cell lines in different tissues. In addition, a set of rules for classifying cell lines were also reported, which can give a clearer picture of cell lines in different issues although its performance was not better than the optimal SVM classifier. Finally, we compared such genes with the tissue-specific genes identified by the Genotype-tissue Expression project. Results showed that most expression patterns between tissues remained in the derived cell lines despite some uniqueness that some genes show tissue specificity.

Contributions of TaSUTs to grain weight in wheat under drought.

The homologous genes to OsSUT1-5 in wheat were identified and detailed analysed. TaSUT1 was the predominant sucrose transporter group and it illustrated the genotypic variations towards drought during grain filling. Sucrose transporters (SUT) play crucial roles in wheat stem water soluble carbohydrate (WSC) remobilization to grain. To determine the major functional SUT gene groups in shoot parts of wheat during grain development, drought tolerant varieties, Westonia and Kauz, were investigated in field drought experiments. Fourteen homologous genes to OsSUT1-5 were identified on five homeologous groups, namely TaSUT1_4A, TaSUT1_4B, TaSUT1_4D; TaSUT2_5A, TaSUT2_5B, TaSUT2_5D; TaSUT3_1A, TaSUT3_1D; TaSUT4_6A, TaSUT4_6B, TaSUT4_6D; TaSUT5_2A, TaSUT5_2B, and TaSUT5_2D, and their gene structures were analysed. Wheat plants above the ground were harvested from pre-anthesis to grain maturity and the stem, leaf sheath, rachis, lemma and developing grain were used for analysing TaSUT gene expression. Grain weight, thousand grain weight, kernel number per spike, biomass and stem WSC were characterized. The study showed that among the five TaSUT groups, TaSUT1 was the predominant sucrose transporting group in all organs sampled, and the expression was particularly high in the developing grain. In contrast to TaSUT1, the gene expression levels of TaSUT2, TaSUT3 and TaSUT4 were lower, except for TaSUT3 which showed preferential expression in the lemma before anthesis. The TaSUT5 gene group was very weakly expressed in all tissues. The upregulated gene expression of TaSUT1 Westonia type in stem and grain reveal a crucial role in stem WSC remobilization to grain under drought. The high TaSUT1 gene expression and the significant correlations with thousand grain weight (TGW) and kernel number per spike demonstrated the contribution in Kauz's high grain yield in an irrigated environment and high TGW in Westonia under drought stress. Further molecular level identification is required for gene marker development.

Understanding plastome evolution in Hemiparasitic Santalales: Complete chloroplast genomes of three species, Dendrotrophe varians, Helixanthera parasitica, and Macrosolen cochinchinensis.

Santalales is a large order, with over 2200 species, most of which are root or aerial (stem) hemiparasites. In this study, we report the newly assembled chloroplast genome of Dendrotrophe varians (140,666 bp) in the family Amphorogynaceae and the cp genomes of Helixanthera parasitica (124,881 bp) and Macrosolen cochinchinensis (122,986 bp), both in the family Loranthaceae. We compared the cp genomes of 11 Santalales including eight currently available cp genomes. Santalales cp genomes are slightly or not reduced in size (119–147 kb), similar to other hemiparasitic species, when compared with typical angiosperm cp genomes (120–170 kb). In a phylogeny examining gene content, the NADH dehydrogenase gene group is the only one among eight functional gene groups that lost complete functionally in all examined Santalales. This supports the idea that the functional loss of ndh genes is the initial stage in the evolution of the plastome of parasitic plants, but the loss has occurred independently multiple times in angiosperms, while they are not found in some parasites. This suggests that the functional loss of ndh genes is not essential for the transition from autotroph to parasite. We additionally examined the correlation between gene content and type of parasitism (obligate/facultative and stem/root parasites) of all hemiparasitic species in which cp genomes have been reported to date. Correlation was not found in any types of parasitism.

Gene expression during different periods of the handling-stress response in Pampus argenteus

Common aquaculture practices subject fish to a variety of acute and chronic stressors. Such stressors are inherent in aquaculture production but can adversely affect survival, growth, immune response, reproductive capacity, and behavior. Understanding the biological mechanisms underlying stress responses helps with methods to alleviate the negative effects through better aquaculture practices, resulting in improved animal welfare and production efficiency. In the present study, transcriptome sequencing of liver and kidney was performed in silver pomfret (Pampus argenteus) subjected to handling stress versus controls. A total of 162.19 million clean reads were assembled to 30 339 unigenes. The quality of the assembly was high, with an N50 length of 2 472 bases. For function classification and pathway assignment, the unigenes were categorized into three GO (gene ontology) categories, twenty-six clusters of eggNOG (evolutionary genealogy of genes: non-supervised orthologous groups) function categories, and thirty-eight KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Stress affected different functional groups of genes in the tissues studied. Differentially expressed genes were mainly involved in metabolic pathways (carbohydrate metabolism, lipid metabolism, amino-acid metabolism, uptake of cofactors and vitamins, and biosynthesis of other secondary metabolites), environmental information processing (signaling molecules and their interactions), organismal systems (endocrine system, digestive system), and disease (immune, neurodegenerative, endocrine and metabolic diseases). This is the first reported analysis of genome-wide transcriptome in P. argenteus, and the findings expand our understanding of the silver pomfret genome and gene expression in association with stress. The results will be useful to future analyses of functional genes and studies of healthy artificial breeding in P. argenteus and other related fish species.

Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers.

Microarray-based markers such as Diversity Arrays Technology (DArT) have become the genetic markers of choice for construction of high-density maps, quantitative trait loci (QTL) mapping and genetic diversity analysis based on their efficiency and low cost. More recently, the DArT technology was further developed in combination with high-throughput next-generation sequencing (NGS) technologies to generate the DArTseq platform representing a new sequencing tool of complexity-reduced representations. In this study, we used DArTseq markers to investigate genetic diversity and genome-wide association studies (GWAS) of grain quality traits in rice (Oryza sativa L.). The study was performed using 59 rice genotypes with 525 SNPs derived from DArTseq platform. Population structure analysis revealed only two distinct genetic clusters where genotypes were grouped based on environmental adaptation and pedigree information. Analysis of molecular variance indicated a low degree of differentiation among populations suggesting the need for broadening the genetic base of the current germplasm collection. GWAS revealed 22 significant associations between DArTseq-derived SNP markers and rice grain quality traits in the test genotypes. In general, 2 of the 22 significant associations were in chromosomal regions where the QTLs associated with the given traits had previously been reported, the other 20 significant SNP marker loci were indicative of the likelihood discovery of novel alleles associated with rice grain quality traits. DArTseq-derived SNP markers that include SNP12_100006178, SNP13_3052560 and SNP14_3057360 individually co-localised with two functional gene groups that were associated with QTLs for grain width and grain length to width ratio on chromosome 3, indicating trait dependency or pleiotropic-effect loci. This study demonstrated that DArTseq markers were useful genomic resources for genome-wide association studies of rice grain quality traits to accelerate varietal development and release.

Transcriptome Reveals Differentially Expressed Genes in Saccharum spontaneum GX83-10 Leaf Under Drought Stress

Saccharum spontaneum is the most important and widely used wild germplasm in sugarcane resistance breeding, which can improve sugarcane resistance and ratoon capacity. In order to further exploit and utilize the resistance genes in S. spontaneum, we used a new generation of sequencing technology Illumina HiSeq high-throughput platform to analyze the expression profile of transcriptome genes in S. spontaneum GX83-10 leaves under normal watering (SS_CK) and drought stress (SS_T). The sequencing data were assembled by de novo, and functional annotation, differential gene screening and enrichment analysis were done. The results showed that 54499640 and 56440692 clean reads were obtained from the drought stress group and the control group, respectively. A total of 88941 unigenes and 1325 significantly differentially expressed genes (DEGs) were obtained in this study. The 125 functional gene groups were enriched by GO enrichment analysis. Five metabolic pathways were obtained by KEGG enrichment analysis, namely ascorbate and aldarate metabolism, plant hormone signal transduction, carotenoid biosynthesis, starch and sucrose metabolism, and phenylpropanoid biosynthesis. Seven significantly up-regulated genes were selected to conduct qRT-PCR analysis, and the results confirmed that all the seven genes were significantly up-regulated at varying degrees under drought stress. This study revealed the molecular mechanism of S. spontaneum leaf in response to drought stress and provided a reference for researches on related key genes which would be beneficial to breed new drought-resistant sugarcane varieties.