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 Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

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.

Rhizopogon roseolus basidiospore germination decreases as the fruiting bodies mature and the spore wall becomes more complex

Botany ◽  
2016 ◽  
Vol 94 (4) ◽  
pp. 311-320 ◽  
Author(s):  
Shota Nakano ◽  
Qi Gao ◽  
Tadanori Aimi ◽  
Norihiro Shimomura
Keyword(s):  
Fruiting Body ◽  
Spore Germination ◽  
Developmental Stages ◽  
Germination Rate ◽  
Spore Wall ◽  
Ultrastructural Changes ◽  
Fruiting Bodies ◽  
Rhizopogon Roseolus ◽  
Germination Success ◽  
Spore Walls

Rhizopogon roseolus (Corda) Th. Fr. is a basidiomycete truffle that is considered edible. Its gleba changes color from white to beige to brown as it matures. Although ultrastructural changes in the spore wall have been linked to the maturation of the fruiting body, little is known regarding the relationship between spore germination success and the ultrastructure of the spore wall. We examined spore germination on agar plates and analyzed the spore wall ultrastructure using transmission electron microscopy (TEM). Fruiting bodies, collected from a pine forest, were classified into three developmental stages based on gleba color, and the germination success was evaluated at each stage. Variability in the spore germination rate was observed between individual fruiting bodies. The peak germination rate was recorded for the spores from the fruiting bodies in the beige glebal stage, and the rate was lower in the brown glebal stage. When spore wall structures were studied using TEM, the spore wall was found to be multilayered upon maturation of the fruiting body. The spores of the beige glebal stage showed three types of spore walls, namely two-layered, three-layered, and four-layered spore walls. On the other hand, the spores of the brown glebal stage showed predominantly four-layered spore walls. These results indicate that spore germination of R. roseolus decreases as the fruiting body matures and the spore wall becomes more complex.

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 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.

Bacterial community dynamics across developmental stages of fungal fruiting bodies

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Daniyal Gohar ◽  
Mari Pent ◽  
Kadri Põldmaa ◽  
Mohammad Bahram
Keyword(s):  
Bacterial Community ◽  
Fruiting Body ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Developmental Stages ◽  
Body Parts ◽  
Fruiting Bodies ◽  
Bacterial Community Dynamics ◽  
Host Development

ABSTRACT Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

scholarly journals Vessel Enlargement in Development and Pathophysiology

2021 ◽  
Vol 12 ◽  
Author(s):  
Laia Gifre-Renom ◽  
Elizabeth A. V. Jones
Keyword(s):  
Endothelial Cells ◽  
Blood Flow ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Circulatory System ◽  
Vascular Diseases ◽  
High Plasticity ◽  
Developmental Models ◽  
Downstream Signaling

From developmental stages until adulthood, the circulatory system remodels in response to changes in blood flow in order to maintain vascular homeostasis. Remodeling processes can be driven by de novo formation of vessels or angiogenesis, and by the restructuration of already existing vessels, such as vessel enlargement and regression. Notably, vessel enlargement can occur as fast as in few hours in response to changes in flow and pressure. The high plasticity and responsiveness of blood vessels rely on endothelial cells. Changes within the bloodstream, such as increasing shear stress in a narrowing vessel or lowering blood flow in redundant vessels, are sensed by endothelial cells and activate downstream signaling cascades, promoting behavioral changes in the involved cells. This way, endothelial cells can reorganize themselves to restore normal circulation levels within the vessel. However, the dysregulation of such processes can entail severe pathological circumstances with disturbances affecting diverse organs, such as human hereditary telangiectasias. There are different pathways through which endothelial cells react to promote vessel enlargement and mechanisms may differ depending on whether remodeling occurs in the adult or in developmental models. Understanding the molecular mechanisms involved in the fast-adapting processes governing vessel enlargement can open the door to a new set of therapeutical approaches to be applied in occlusive vascular diseases. Therefore, we have outlined here the latest advances in the study of vessel enlargement in physiology and pathology, with a special insight in the pathways involved in its regulation.

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