scholarly journals Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis

2019 ◽  
Vol 20 (18) ◽  
pp. 4387 ◽  
Author(s):  
Hongmei Zhuang ◽  
Qian Lou ◽  
Huifang Liu ◽  
Hongwei Han ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Skin Pigmentation ◽  
Anthocyanin Content ◽  
Anthocyanidin Synthase ◽  
De Novo Transcriptome ◽  
Metabolome Analysis ◽  
Transcriptional Changes ◽  
The Difference

Purple turnip Brassica rapa ssp. rapa is highly appreciated by consumers but the metabolites and molecular mechanisms underlying the root skin pigmentation remain open to study. Herein, we analyzed the anthocyanin composition in purple turnip (PT) and green turnip (GT) at five developmental stages. A total of 21 anthocyanins were detected and classified into the six major anthocynanin aglycones. Distinctly, PT contains 20 times higher levels of anthocyanins than GT, which explain the difference in the root skin pigmentation. We further sequenced the transcriptomes and analyzed the differentially expressed genes between the two turnips. We found that PT essentially diverts dihydroflavonols to the biosynthesis of anthocyanins over flavonols biosynthesis by strongly down-regulating one flavonol synthase gene, while strikingly up-regulating dihydroflavonol 4-reductase (DFR), anthocyanidin synthase and UDP-glucose: flavonoid-3-O-glucosyltransferase genes as compared to GT. Moreover, a nonsense mutation identified in the coding sequence of the DFR gene may lead to a nonfunctional protein, adding another hurdle to the accumulation of anthocyanin in GT. We also uncovered several key members of MYB, bHLH and WRKY families as the putative main drivers of transcriptional changes between the two turnips. Overall, this study provides new tools for modifying anthocyanin content and improving turnip nutritional quality.

scholarly journals Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal PathogenRhizopus delemar

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Poppy C. S. Sephton-Clark ◽  
Jose F. Muñoz ◽  
Elizabeth R. Ballou ◽  
Christina A. Cuomo ◽  
Kerstin Voelz
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Developmental Process ◽  
Fungal Spores ◽  
Hyphal Growth ◽  
Large Shift ◽  
Rhizopus Delemar ◽  
Content Type ◽  
Transcriptional Changes ◽  
Dormant Spore

ABSTRACTRhizopus delemaris an invasive fungal pathogen responsible for the frequently fatal disease mucormycosis. Germination, a crucial mechanism by which infectious spores ofRhizopus delemarcause disease, is a key developmental process that transforms the dormant spore state into a vegetative one. The molecular mechanisms that underpin this transformation may be key to controlling mucormycosis; however, the regulation of germination remains poorly understood. This study describes the phenotypic and transcriptional changes that take place over the course of germination. This process is characterized by four distinct stages: dormancy, isotropic swelling, germ tube emergence, and hyphal growth. Dormant spores are shown to be transcriptionally unique, expressing a subset of transcripts absent in later developmental stages. A large shift in the expression profile is prompted by the initiation of germination, with genes involved in respiration, chitin, cytoskeleton, and actin regulation appearing to be important for this transition. A period of transcriptional consistency can be seen throughout isotropic swelling, before the transcriptional landscape shifts again at the onset of hyphal growth. This study provides a greater understanding of the regulation of germination and highlights processes involved in transformingRhizopus delemarfrom a single-cellular to multicellular organism.IMPORTANCEGermination is key to the growth of many organisms, including fungal spores. Mucormycete spores exist abundantly within the environment and germinate to form hyphae. These spores are capable of infecting immunocompromised individuals, causing the disease mucormycosis. Germination from spore to hyphae within patients leads to angioinvasion, tissue necrosis, and often fatal infections. This study advances our understanding of how spore germination occurs in the mucormycetes, identifying processes we may be able to inhibit to help prevent or treat mucormycosis.

scholarly journals Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Ma ◽  
Rongyan Wang ◽  
Xiuhua Li ◽  
Bo Gao ◽  
Shulong Chen
Keyword(s):  
Sweet Potato ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cylas Formicarius ◽  
Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

scholarly journals The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

2022 ◽  
Author(s):  
Shinichi Morita ◽  
Tomoko F. Shibata ◽  
Tomoaki Nishiyama ◽  
Yuuki Kobayashi ◽  
Katsushi Yamaguchi ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Genetic Regulation ◽  
Draft Genome ◽  
Evolutionary Developmental Biology ◽  
Rhinoceros Beetle ◽  
Insect Order ◽  
Trypoxylus Dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

scholarly journals Transcriptomic analyses reveal molecular mechanisms underlying regulation of floral attributes in Lonicera japonica Thunb.

2021 ◽  
Author(s):  
Lei Shi ◽  
Yuan Shen ◽  
Yuhao Chi
Keyword(s):  
Flower Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Floral Scent ◽  
Expression Profiles ◽  
Lonicera Japonica ◽  
Biosynthesis Pathway ◽  
Terpenoid Biosynthesis ◽  
Genes Encoding

Abstract Background Lonicera Japonica Thunb. is a perennial, semi-evergreen and twining vine in the family of Caprifoliaceae, which is widely cultivated in Asia. Thus far, L. japonica is often used to treat some human diseases including COVID-19, H1N1 influenza and hand-foot-and-mouth diseases, however, the regulatory mechanism of intrinsic physiological processes during different floral developmental stages of L. japonica remain largely unknown. Results The complete transcriptome of L. japonica was de novo-assembled and annotated, generating a total of 195850 unigenes, of which 84657 could be functionally annotated. 70 candidate genes involved in flowering transition were identified and the flowering regulatory network of five pathways was constructed in L. japonica. The mRNA transcripts of AGL24 and SOC1 exhibited a downward trend during flowering transition and followed by a gradual increase during the flower development. The transcripts of AP1 was only detected during the floral development, whereas the transcript level of FLC was high during the vegetative stages. The expression profiles of AGL24, SOC1, AP1 and FLC genes indicate that these key integrators might play the essential and evolutionarily conserved roles in control of flowering switch across the plant kingdom. We also identified 54 L. japonica genes encoding enzymes involved in terpenoid biosynthesis pathway. Most highly expressed genes centered on the MEP pathway, suggesting that this plastid pathway might represent the major pathway for terpenoid biosynthesis in L. japonica. In addition, 33 and 31 key genes encoding enzymes involved in the carotenogenesis and anthocyanin biosynthesis pathway were identified, respectively. PSY transcripts gradually increased during the flower development, supporting its role as the first rate-limiting enzyme in carotenoid skeleton production. The expression level of most anthocyanin biosynthetic genes was dramatically decreased during the flower developmental stages, consistent with the decline in the contents of anthocyanin. Conclusion These results identified a large number of potential key regulators controlling flowering time, flower color and floral scent formation in L. japonica, which improves our understanding of the molecular mechanisms underlying the flower traits and flower metabolism, as well as sets the groundwork for quality improvement and molecular breeding of L. japonica.

scholarly journals Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco

DNA Research ◽  
2020 ◽  
Vol 27 (2) ◽  
Author(s):  
Pingping Liu ◽  
Jie Luo ◽  
Qingxia Zheng ◽  
Qiansi Chen ◽  
Niu Zhai ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Developmental Process ◽  
Pearson Correlation ◽  
Molecular Networks ◽  
Environmental Perturbations ◽  
Carotenoid Metabolism ◽  
Gene Modules

Abstract Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene–metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

scholarly journals Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs

2021 ◽  
Vol 12 ◽  
Author(s):  
Anna V. Shchennikova ◽  
Alexey V. Beletsky ◽  
Mikhail A. Filyushin ◽  
Maria A. Slugina ◽  
Eugeny V. Gruzdev ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Mads Box ◽  
Mads Box Genes ◽  
Evolutionary Origins ◽  
Novel Structure ◽  
Genes Encoding

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.

scholarly journals Transcriptome profiling of anthocyanin-related genes reveals effects of light intensity on anthocyanin biosynthesis in red leaf lettuce

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4607 ◽  
Author(s):  
Yanzhao Zhang ◽  
Shuzhen Xu ◽  
Yanwei Cheng ◽  
Zhengfeng Peng ◽  
Jianming Han
Keyword(s):  
Light Intensity ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Anthocyanin Biosynthesis ◽  
Gene Annotation ◽  
High Irradiance ◽  
High Light ◽  
Anthocyanin Content ◽  
Structural Genes ◽  
Leaf Lettuce

Red leaf lettuce (Lactuca sativaL.) is popular due to its high anthocyanin content, but poor leaf coloring often occurs under low light intensity. In order to reveal the mechanisms of anthocyanins affected by light intensity, we compared the transcriptome ofL. sativaL. var.capitataunder light intensities of 40 and 100 μmol m−2s−1. A total of 62,111 unigenes were de novo assembled with an N50 of 1,681 bp, and 48,435 unigenes were functionally annotated in public databases. A total of 3,899 differentially expressed genes (DEGs) were detected, of which 1,377 unigenes were up-regulated and 2,552 unigenes were down-regulated in the high light samples. By Kyoto Encyclopedia of Genes and Genomes enrichment analysis, the DEGs were significantly enriched in 14 pathways. Using gene annotation and phylogenetic analysis, we identified seven anthocyanin structural genes, includingCHS,CHI,F3H,F3′H,DFR,ANS, and3GT, and two anthocyanin transport genes,GSTandMATE. In terms of anthocyanin regulatory genes, five MYBs and one bHLH gene were identified. AnHY5gene was discovered, which may respond to light-signaling and regulate anthocyanin structural genes. These genes showed a log2FC of 2.7–9.0 under high irradiance, and were validated using quantitative real-time-PCR. In conclusion, our results indicated transcriptome variance in red leaf lettuce under low and high light intensity, and observed a anthocyanin biosynthesis and regulation pattern. The data should further help to unravel the molecular mechanisms of anthocyanins influenced by light intensity.

scholarly journals De novo Sequencing and Comparative Transcriptome Analyses Provide First Insights Into Polysaccharide Biosynthesis During Fruiting Body Development of Lentinula edodes

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiaozhen Li ◽  
Jing Chen ◽  
Jianyu Liu ◽  
Hailong Yu ◽  
Lujun Zhang ◽  
...  
Keyword(s):  
Fruiting Body ◽  
Biosynthetic Pathway ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Developmental Stages ◽  
De Novo ◽  
Hot Water ◽  
Growth Stages ◽  
Fruiting Bodies ◽  
Polysaccharide Biosynthesis

Polysaccharides separated from Lentinula edodes are well known for their medicinal properties. However, the precise molecular mechanisms of polysaccharide biosynthesis in L. edodes remain unclear. In this study, the fruiting bodies of L. edodes in four developmental stages with significant differences in polysaccharide yield were collected, and the characteristics of polysaccharides were studied. De novo sequencing and comparative transcriptomic analysis were performed by using high-throughput Illumina RNA-sequencing. KS1P30, KS2P30, KS3P30, and KS4P30 were obtained from the four developmental stages, respectively, by hot water extraction and 30% ethanol precipitation. These four polysaccharides had good immune activity in vitro; all of them were β-glucopyranose with a high molecular weight. Glucose was the main monosaccharide component of these polysaccharides. High-quality clean reads (57.88, 53.17, 53.28, and 47.56 million for different growth stages) and mapping ratios ranging from 84.75 to 90.11% were obtained. In total, 11,493 (96.56%) unigenes and 18,924 (97.46%) transcripts were successfully annotated in five public databases. The biosynthetic pathway and related genes of LEFP30 were mined. The molecular mechanism of LEFP30 yield change in the different developmental stages was predicted. The results provide some insights into the possible mechanisms involved in the biosynthetic pathway of this kind of polysaccharide in L. edodes fruiting bodies. They also indicate that candidate genes can be used as important resources for biotechnology and molecular breeding to regulate L. edodes fruiting body polysaccharide biosynthesis.

scholarly journals Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Marisol Salgado-Albarrán ◽  
Erick I. Navarro-Delgado ◽  
Aylin Del Moral-Morales ◽  
Nicolas Alcaraz ◽  
Jan Baumbach ◽  
...  
Keyword(s):  
Viral Infection ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Therapeutic Potential ◽  
Cell Responses ◽  
Epigenetic Machinery ◽  
Integrative Analyses ◽  
Transcriptional Changes ◽  
Feasible Alternative ◽  
Gene Modules

AbstractCOVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in SARS-CoV-2 infection in order to propose drug-based therapeutic options. Transcriptional changes due to epigenetic regulation are key host cell responses to viral infection and have been studied in SARS-CoV and MERS-CoV; however, such changes are not fully described for SARS-CoV-2. In this study, we analyzed multiple transcriptomes obtained from cell lines infected with MERS-CoV, SARS-CoV, and SARS-CoV-2, and from COVID-19 patient-derived samples. Using integrative analyses of gene co-expression networks and de-novo pathway enrichment, we characterize different gene modules and protein pathways enriched with Transcription Factors or Epifactors relevant for SARS-CoV-2 infection. We identified EP300, MOV10, RELA, and TRIM25 as top candidates, and more than 60 additional proteins involved in the epigenetic response during viral infection that has therapeutic potential. Our results show that targeting the epigenetic machinery could be a feasible alternative to treat COVID-19.

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