Trehalose-6-phosphate synthase (TPS) is essential for plant growth and development, linking trehalose-6-phosphate (T6P) to carbon metabolism. However, little is known about the TPS gene family in peaches and their potential roles in regulating carbohydrates in peach fruit. In this study, nine TPS genes were identified in the peach genome and named according to the homologous genes in Arabidopsis. Phylogenetic analysis showed that three subfamilies were identified, including TPSI, TPSII-1, and TPSII-2, which were also consistent with gene structure analysis. Considerable cis-elements were enriched in the promoters, including plant hormone-related elements. Tissue-specific analysis showed that these TPS genes were mainly expressed in leaves, stems, and fruit, showing different expression patterns for each gene. In addition, during fruit development, the content of trehalose-6-phosphate (T6P) was positively correlated with the expression of PpTPS7a and negatively with sucrose non-fermenting-1-related kinase 1 (SnRK1) activity. Transient overexpression and silencing of PpTPS7a in peach fruit validated its function in regulating T6P content and SnRK1 activity.

Ganoderma lucidum spores (GLS), the mature germ cells ejected from the abaxial side of the pileus, have diverse pharmacological effects. However, the genetic regulation of sporulation in this fungus remains unknown. Here, samples corresponding to the abaxial side of the pileus were collected from strain YW-1 at three sequential developmental stages and were then subjected to a transcriptome assay. We identified 1598 differentially expressed genes (DEGs) and found that the genes related to carbohydrate metabolism were strongly expressed during spore morphogenesis. In particular, genes involved in trehalose and malate synthesis were upregulated, implying the accumulation of specific carbohydrates in mature G. lucidum spores. Furthermore, the expression of genes involved in triterpenoid and ergosterol biosynthesis was high in the young fruiting body but gradually decreased with sporulation. Finally, spore development-related regulatory pathways were explored by analyzing the DNA binding motifs of 24 transcription factors that are considered to participate in the control of sporulation. Our results provide a dataset of dynamic gene expression during sporulation in G. lucidum. They also shed light on genes potentially involved in transcriptional regulation of the meiotic process, metabolism pathways in energy provision, and ganoderic acids and ergosterol biosynthesis.

Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.

Wheat grain development after anthesis is an important biological process, in which major components of seeds are synthesised, and these components are further required for germination and seed vigour. We have made a comparative RNA-Seq analysis between hexaploid wheat and its individual diploid progenitors to know the major differentially expressed genes (DEGs) involved during grain development. Two libraries from each species were generated with an average of 55.63, 55.23, 68.13, and 103.81 million reads, resulting in 79.3K, 113.7K, 90.6K, and 121.3K numbers of transcripts in AA, BB, DD, and AABBDD genome species respectively. Number of expressed genes in hexaploid wheat was not proportional to its genome size, but marginally higher than that of its diploid progenitors. However, to capture all the transcripts in hexaploid wheat, sufficiently higher number of reads was required. Functional analysis of DEGs, in all the three comparisons, showed their predominance in three major classes of genes during grain development, i.e., nutrient reservoirs, carbohydrate metabolism, and defence proteins; some of them were subsequently validated through real time quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Further, developmental stage-specific gene expression showed most of the defence protein genes expressed during initial developmental stages in hexaploid contrary to the diploids at later stages. Genes related to carbohydrates anabolism expressed during early stages, whereas catabolism genes expressed at later stages in all the species. However, no trend was observed in case of different nutrient reservoirs gene expression. This data could be used to study the comparative gene expression among the three diploid species and homeologue-specific expression in hexaploid.

Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts' dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts' feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts' dietary pattern is the key determinant of the distribution and evolution of GH genes.

Inverted cuttings of Populus yunnanensis remain alive by rooting from the original morphological apex and sprouting from the base, but the lateral branches exhibit less vigorous growth than those of the upright plant. In this study, we examined the changes in hormone contents, oxidase activities, and transcriptome profiles between upright and inverted cuttings of P. yunnanensis. The results showed that the indole-3-acetic acid (IAA) and gibberellic acid (GA₃) contents were significantly lower in inverted cuttings than in upright cuttings only in the late growth period (September and October), while the abscisic acid (ABA) level was always similar between the two direction types. The biosynthesis of these hormones was surprisingly unrelated to the inversion of P. yunnanensis during the vegetative growth stage (July and August). Increased levels of peroxidases (PODs) encoded by 13 differentially expressed genes (DEGs) served as lignification promoters that protected plants against oxidative stress. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that most DEGs (107) were related to carbohydrate metabolism. Furthermore, altered activities of uridine diphosphate (UDP)-sugar pyrophosphorylase (USP, 15 DEGs) for nucleotide sugars, pectin methylesterase (PME, 7 DEGs) for pectin, and POD (13 DEGs) for lignin were important factors in the response of the trees to inversion, and these enzymes are all involved cell wall metabolism.

Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.

Nonalcoholic fatty liver disease (NAFLD) is the leading liver chronic disease featuring hepatic steatosis. Mitochondrial β-oxidation participates in the derangement of lipid metabolism at the basis of NAFLD, and mitochondrial oxidative stress contributes to the onset of the disease. We evaluated the presence and effects of mitochondrial oxidative stress in the liver from rats fed a high-fat plus fructose (HF-F) diet inducing NAFLD. Supplementation with dehydroepiandrosterone (DHEA), a multitarget antioxidant, was tested for efficacy in delaying NAFLD. A marked mitochondrial oxidative stress was originated by all diets, as demonstrated by the decrease in Superoxide Dismutase 2 (SOD2) and Peroxiredoxin III (PrxIII) amounts. All diets induced a decrease in mitochondrial DNA content and an increase in its oxidative damage. The diets negatively affected mitochondrial biogenesis as shown by decreased peroxisome proliferator-activated receptor-γ co-activator-1α (PGC-1α), mitochondrial transcription factor A (TFAM), and the COX-IV subunit from the cytochrome c oxidase complex. The reduced amounts of Beclin-1 and lipidated LC3 II form of the microtubule-associated protein 1 light chain 3 (LC3) unveiled the diet-related autophagy's decrease. The DHEA supplementation did not prevent the diet-induced changes. These results demonstrate the relevance of mitochondrial oxidative stress and the sequential dysfunction of the organelles in an obesogenic diet animal model of NAFLD.

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

As the chick transitions from embryonic to post-hatching life, its metabolism must quickly undergo a dramatic switch in its major energy source. The chick embryo derives most of its energy from the yolk, a lipid-rich/carbohydrate-poor source. Upon hatching, the chick's metabolism must then be able to utilize a lipid-poor/carbohydrate-rich source (feed) as its main form of energy. We recently found that a number of hepatically-expressed microRNAs (miRNAs) help facilitate this shift in metabolic processes in the chick liver, the main site of lipogenesis. While adipose tissue was initially thought to mainly serve as a lipid storage site, it is now known to carry many metabolic, endocrine, and immunological functions. Therefore, it would be expected that adipose tissue is also an important factor in the metabolic switch. To that end, we used next generation sequencing (NGS) and real-time quantitative PCR (RT-qPCR) to generate miRNome and transcriptome signatures of the adipose tissue during the transition from late embryonic to early post-hatch development. As adipose tissue is well known to produce inflammatory and other immune factors, we used SPF white leghorns to generate the initial miRNome and transcriptome signatures to minimize complications from external factors (e.g., pathogenic infections) and ensure the identification of bona fide switch-associated miRNAs and transcripts. We then examined their expression signatures in the adipose tissue of broilers (Ross 708). Using E18 embryos as representative of pre-switching metabolism and D3 chicks as a representative of post-switching metabolism, we identified a group of miRNAs which work concordantly to regulate a diverse but interconnected group of developmental, immune and metabolic processes in the adipose tissue during the metabolic switch. Network mapping suggests that during the first days post-hatch, despite the consumption of feed, the chick is still heavily reliant upon adipose tissue lipid stores for energy production, and is not yet efficiently using their new energy source for de novo lipid storage. A number of core master regulatory pathways including, circadian rhythm transcriptional regulation and growth hormone (GH) signaling, likely work in concert with miRNAs to maintain an essential balance between adipogenic, lipolytic, developmental, and immunological processes in the adipose tissue during the metabolic switch.

Rapeseed (Brassica napus L.) meal is an important source of protein, but the presence of anti-nutritional compounds, such as fibre and glucosinolates, still limits its use as a livestock feed. Understanding the genetic basis of seed fibre biosynthesis would help to manipulate its content in seeds of oilseed rape. Here, we applied high-resolution skim genotyping by sequencing (SkimGBS) and characterised 187,835 single-nucleotide polymorphism (SNP) markers across a mapping population subsequently used for a genetic mapping study (R/qtl). This approach allowed the identification of 11 stable QTL related to seed quality traits and led to the identification of potential functional genes underlying these traits. Among these, key genes with a known role in carbohydrate metabolic process, cell wall, lignin, and flavonoid biosynthesis, including cellulase GH5, TT10/LAC15, TT4, and SUC2, were found. This study furthers the understanding of the molecular mechanisms underlying seed fibre content and provides new markers for molecular breeding in B. napus.

The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.

Sterol regulatory element-binding proteins (SREBPs) play vital roles in fatty acid metabolism and other metabolic processes in mammals. However, in penaeid shrimp, the repertoire of genes modulated by SREBP is unknown. Here, RNA interference-mediated knockdown followed by transcriptome sequencing on the Illumina Novaseq 6000 platform was used to explore the genes modulated by SREBP in Penaeus vannamei hepatopancreas. A total of 706 differentially expressed genes (DEGs) were identified, out of which 282 were upregulated and 424 downregulated. Although gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that most of the downregulated DEGs were involved in physiological processes related to immunity, metabolism, and cellular signaling pathways, many of the dysregulated genes have uncharacterized functions. While most of the dysregulated genes were annotated in metabolic processes, such as carbohydrate metabolism, lipid metabolism, signal transduction, and immune system, a large number (42.21%) are uncharacterized. Collectively, our current data revealed that SREBP modulates many genes involved in crucial physiological processes, such as energy metabolism, immune response, and cellular signaling pathways, as well as numerous genes with unannotated functions, in penaeid shrimp. These findings indicated that our knowledge of the repertoire of genes modulated by SREBP in shrimp lags behind that of mammals, probably due to limited research or because the complete genome of P. vannamei has just been sequenced.

Probiotic bacteria are receiving increased attention due to the potential benefits to their hosts. Plateau yaks have resistance against diseases and stress, which is potentially related to their inner probiotics. To uncover the potential functional genes of yak probiotics, we sequenced the whole genome of Lactobacillus sakei (L. sakei). The results showed that the genome length of L. sakei was 1.99 Mbp, with 1943 protein coding genes (21 rRNA, 65 tRNA, and 1 tmRNA). There were three plasmids found in this bacteria, with 88 protein coding genes. EggNOG annotation uncovered that the L. sakei genes were found to belong to J (translation, ribosomal structure, and biogenesis), L (replication, recombination, and repair), G (carbohydrate transport and metabolism), and K (transcription). GO annotation showed that most of the L. sakei genes were related to cellular processes, metabolic processes, biological regulation, localization, response to stimulus, and organization or biogenesis of cellular components. CAZy annotation found that there were 123 CAZys in the L. sakei genome, with glycosyl transferases and glycoside hydrolases. Our results revealed the genome characteristics of L. sakei, which may give insight into the future employment of this probiotic bacterium for its functional benefits.

Productivity of wheat (Triticumaestivum) is markedly affected by high temperature and nitrogen deficiency. Identifying the functional proteins produced in response to these multiple stresses acting in a coordinated manner can help in developing tolerance in the crop. In this study, two wheat cultivars with contrasting nitrogen efficiencies (N-efficient VL616 and N-inefficient UP2382) were grown in control conditions, and under a combined stress of high temperature (32 °C) and low nitrogen (4 mM), and their leaf proteins were analysed in order to identify the responsive proteins. Two-dimensional electrophoresis unravelled sixty-one proteins, which varied in their expression in wheat, and were homologous to known functional proteins involved in biosynthesis, carbohydrate metabolism, energy metabolism, photosynthesis, protein folding, transcription, signalling, oxidative stress, water stress, lipid metabolism, heat stress tolerance, nitrogen metabolism, and protein synthesis. When exposed to high temperature in combination with low nitrogen, wheat plants altered their protein expression as an adaptive means to maintain growth. This response varied with cultivars. Nitrogen-efficient cultivars showed a higher potential of redox homeostasis, protein stability, osmoprotection, and regulation of nitrogen levels. The identified stress-responsive proteins can pave the way for enhancing the multiple-stress tolerance in wheat and developing a better understanding of its mechanism.

Nitrate (NO3-) and ammonium (NH4+) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of two oilseed rape cultivars, Xiangyou 15 (high N efficiency, denoted "15") and 814 (low N efficiency, denoted "814"), were inhibited under NH4+ nutrition, though both cultivars grew normally under NO3- nutrition. To gain insight into the underlying molecular mechanisms, transcriptomic changes were investigated in the roots of 15 and 814 plants subjected to nitrogen-free (control, CK), NO3- (NT), and NH4+ (AT) treatments at the seedling stage. A total of 14,355 differentially expressed genes (DEGs) were identified. Among the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway categories of these DEGs, carbohydrate metabolism, lipid metabolism, protein metabolism, and cell wall biogenesis were inhibited by AT treatment. Interestingly, DEGs such as N transporters, genes involved in N assimilation and CESA genes related to cellulose synthase were also mostly downregulated in the AT treatment group. This downregulation of genes related to crucial metabolic pathways resulted in inhibition of oilseed rape growth after AT treatment.

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

SPX (spexin) and its receptors GalR2 and GalR3 (galanin receptor subtype 2 and galanin receptor subtype 3) play an important role in the regulation of lipid and carbohydrate metabolism in human and animal fat tissue. However, little is still known about the role of this peptide in the metabolism of muscle. The aim of this study was to determine the impact of SPX on the metabolism, proliferation and differentiation of the skeletal muscle cell line C2C12. Moreover, we determined the effect of exercise on the SPX transduction pathway in mice skeletal muscle. We found that increased SPX, acting via GalR2 and GalR3 receptors, and ERK1/2 phosphorylation stimulated the proliferation of C2C12 cells (p < 0.01). We also noted that SPX stimulated the differentiation of C2C12 by increasing mRNA and protein levels of differentiation markers Myh, myogenin and MyoD (p < 0.01). SPX consequently promoted myoblast fusion into the myotubule (p < 0.01). Moreover, we found that, in the first stage (after 2 days) of myocyte differentiation, GalR2 and GalR3 were involved, whereas in the last stage (day six), the effect of SPX was mediated by the GalR3 isoform. We also noted that exercise stimulated SPX and GalR2 expression in mice skeletal muscle as well as an increase in SPX concentration in blood serum. These new insights may contribute to a better understanding of the role of SPX in the metabolism of skeletal muscle.

The potential probiotic benefits of Bifidobacterium bifidum have received increasing attention recently. We used comparative genomic analysis to explore the differences in the genome and the physiological characteristics of B. bifidum isolated from the fecal samples of Chinese adults and infants. The relationships between genotypes and phenotypes were analyzed to assess the effects of isolation sources on the genetic variation of B. bifidum. The phylogenetic tree results indicated that the phylogeny of B. bifidum may be related to the geographical features of its isolation source. B. bifidum was found to have an open pan-genome and a conserved core genome. The genetic diversity of B. bifidum is mainly reflected in carbohydrate metabolism- and immune/competition-related factors, such as the glycoside hydrolase gene family, bacteriocin operons, antibiotic resistance genes, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. Additionally, the type III A CRISPR-Cas system was discovered in B. bifidum for the first time. B. bifidum strains exhibited niche-specific characteristics, and the results of this study provide an improved understanding of the genetics of this species.

Thrips (Thysanoptera: Thripidae) is a major insect pest for alfalfa which can result in decreased plant nutrients, low yields, and even plant death. To identify the differentially expressed genes and metabolites in response to thrips in alfalfa, a combination of metabolomics and transcriptomics was employed using alfalfa (Caoyuan No. 2) with and without thrips infestation. The results showed that the flavonoid biosynthesis and isoflavonoid biosynthesis pathways were the most significantly enriched pathways in response to thrips infection, as shown by the combined transcriptome and metabolome analysis. The transcriptome results showed that SA and JA signal transduction and PAPM-triggered immunity and the MAPK signaling pathway-plant pathways played a crucial role in thrips-induced plant resistance in alfalfa. In addition, we found that thrips infestation could also induce numerous changes in plant primary metabolism, such as carbohydrate and amino acid metabolism as compared to the control. Overall, our results described here should improve fundamental knowledge of molecular responses to herbivore-inducible plant defenses and contribute to the design of strategies against thrips in alfalfa.