scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

scholarly journals Transcriptome analysis reveal the mechanism of susceptible wheat seedlings response to Puccinia striiformis f. sp.

2020 ◽  
Author(s):  
Rong Liu ◽  
Yuwei Chen ◽  
Min Zhou ◽  
Jing Lu ◽  
Chihong Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Puccinia Striiformis ◽  
Expression Patterns ◽  
Photosynthetic Electron Transport ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Cdna Libraries ◽  
Pcr Analysis ◽  
Wheat Seedlings

Abstract Background Wheat (Triticum aestivum L.) is most widely cultivated and a major staple food crops in the world. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), which significantly reduce yield and quality of wheat. Although some resistant genes have been successfully used in wheat breeding, large of the regulating networks and the underlying molecular mechanisms of Pst response remains unknown. Therefore, to identify differentially expressed genes (DEGs) and regulate network involved in Pst resistance, we sequenced 15 cDNA libraries constructed from wheat seedlings with CYR34 infection.Results In this study, a highly susceptible cv. Chuanyu12 (CY12) were used to study the transcriptome profiles after inoculated with Pst physiological race CYR34. A total of 13892, 10195, 12268 and 14044 DEGs were investigated at 24h, 48h, 72h and 7days Pst infection, respectively. Certain key genes and pathways responsible for Pst-CYR34 in CY12 were identified. The results revealed that Pst-CYR34 inhibited the DEGs related to energy metabolism, biosynthesis, carbon fixation, phenylalanine metabolism, and plant hormone signaling pathway after Pst inoculation at 24h, 48h, 72h and 7d. These down-regulated DEGs including light-harvesting chlorophyll protein complex in photosystem I and photosystem II; cytochrome b6/f/ complex, F-type ATPase and photosynthetic electron transport; ethylene, jasmonic acid (JA) and salicylic acid (SA); lignin and flavonoids biosynthesis in CY12. Quantitative Real-time PCR analysis verified the expression patterns of these DEGs.Conclusions Our results give insights into the foundation for further exploring the molecular mechanism regulating networks of Pst response and pave the way for durable resistant breeding in bread wheat.

Comparative transcriptomic analysis of flowering induction in pitaya induced by supplementary lighting

2019 ◽  
Author(s):  
Rui Xiong ◽  
Liu Chengli ◽  
Min Xu ◽  
Shuang-Shuang Wei ◽  
Hua Tang
Keyword(s):  
Time Course ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Floral Induction ◽  
Transcriptomic Analysis ◽  
Pcr Analysis ◽  
Reverse Transcription Pcr ◽  
Transcription Factor Genes ◽  
Supplementary Lighting ◽  
Transcriptomic Level

Abstract Background Pitayas are currently attracting considerable interest as a fruit with many health benefits. However, the lack of natural light after November in Hainan, China, severely restricts the production of pitaya in winter. To further explore the molecular mechanisms regulating flowering in pitaya, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya subjected to light induction. Results We assembled 68113 unigenes in total, comprising 29782 unigenes with functional annotations in the NR database, 20716 annotations in SwissProt, 18088 annotations in KOG, and 11059 annotations in KEGG. Comparison between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormones were detected. Moreover, we discovered many CONSTANS-LIKE, FLOWERING LOCUS T and other DEGs involved in direct regulation of flowering, along with CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we confirmed 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis. Conclusions These DEGs may include some key genes that control the floral-induction network, increasing our understanding of the molecular mechanism of floral regulation in pitaya. These findings will also aid the development of biotechnologies aimed at creating a variant of pitaya that is less sensitive to light conditions and blooms throughout the year.

scholarly journals De novo Characterization of the Platycladus orientalis Transcriptome and Analysis of Photosynthesis-Related Genes during Aging

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 393
Author(s):  
Ermei Chang ◽  
Jin Zhang ◽  
Xiamei Yao ◽  
Shuo Tang ◽  
Xiulian Zhao ◽  
...  
Keyword(s):  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Age And Growth ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Old Trees

In China, Platycladus orientalis has a lifespan of thousands of years. The long lifespan of these trees may be relevant for the characterization of plant aging at the molecular level. However, the molecular mechanism of the aging process of P. orientalis is still unknown. To explore the relationship between age and growth of P. orientalis, we analyzed physiological changes during P. orientalis senescence. The malondialdehyde content was greater in 200-, 700-, and 1100-year-old ancient trees than in 20-year-old trees, whereas the peroxidase and superoxide dismutase activities, as well as the soluble protein content, exhibited the opposite trend. Furthermore, we performed a de novo transcriptome assembly using RNA-Seq and obtained 48,044 unigenes with an average length of 896 bp. A total of 418 differentially expressed genes were identified in different stages of aging of P. orientalis. Clustering analysis revealed distinct timepoints at which the oxidation–reduction and photosynthesis pathways changed. Eight clusters with distinct expression patterns were identified. The expression levels of photosynthesis-, oxidation–reduction-, and transporter-related genes were down-regulated, whereas those of transcription-, signaling-, and senescence-related genes were up-regulated during aging. In addition, consistent with the most obviously down-regulated genes of photosynthesis-related genes, the photosynthetic indexes including chlorophyll a and b levels decreased steadily during P. orientalis aging. This study combined transcriptome with physiological and biochemical data, revealing potential candidate genes influencing senescence during P. orientalis aging.

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 C. elegans PVD Neurons: A Platform for Functionally Validating and Characterizing Neuropsychiatric Risk Genes

2016 ◽  
Author(s):  
Cristina Aguirre-Chen ◽  
Nuri Kim ◽  
Olivia Mendivil Ramos ◽  
Melissa Kramer ◽  
W. Richard McCombie ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
De Novo ◽  
Genetic Interaction ◽  
Cost Effective ◽  
Chromatin Remodelers ◽  
C Elegans ◽  
Effective Manner

AbstractOne of the primary challenges in the field of psychiatric genetics is the lack of an in vivo model system in which to functionally validate candidate neuropsychiatric risk genes (NRGs) in a rapid and cost-effective manner1−3. To overcome this obstacle, we performed a candidate-based RNAi screen in which C. elegans orthologs of human NRGs were assayed for dendritic arborization and cell specification defects using C. elegans PVD neurons. Of 66 NRGs, identified via exome sequencing of autism (ASD)4 or schizophrenia (SCZ)5−9 probands and whose mutations are de novo and predicted to result in a complete or partial loss of protein function, the C. elegans orthologs of 7 NRGs were found to be required for proper neuronal development and represent a variety of functional classes, including transcriptional regulators and chromatin remodelers, molecular chaperones, and cytoskeleton-related proteins. Notably, the positive hit rate, when selectively assaying C. elegans orthologs of ASD and SCZ NRGs, is enriched >14-fold as compared to unbiased RNAi screening10. Furthermore, we find that RNAi phenotypes associated with the depletion of NRG orthologs is recapitulated in genetic mutant animals, and, via genetic interaction studies, we show that the NRG ortholog of ANK2, unc-44, is required for SAX-7/MNR-1/DMA-1 signaling. Collectively, our studies demonstrate that C. elegans PVD neurons are a tractable model in which to discover and dissect the fundamental molecular mechanisms underlying neuropsychiatric disease pathogenesis.

scholarly journals Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during MT-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)

2019 ◽  
Author(s):  
Xiaochun Liu ◽  
Xi Wu ◽  
Yang Yang ◽  
Chaoyue Zhong ◽  
Yin Guo ◽  
...  
Keyword(s):  
Germ Cells ◽  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Transcriptome Profiling ◽  
Sex Reversal ◽  
Epinephelus Coioides ◽  
Isolated Cells ◽  
Male Germ Cells

Abstract Background: Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the process of its spermatogenesis is not well-understood. In the present study, transcriptome sequencing of the male germ cells from orange-spotted grouper was performed to explore the molecular mechanisms underlying spermatogenesis. Results: In this study, the orange-spotted grouper was induced to change sex from female to male by 17alpha-methyltestosterone implantation. During the artificial spermatogenesis, different cell types from cysts containing spermatogonia, spermatocytes, spermatids, and spermatozoa were isolated by laser capture microdissection. Subsequently, transcriptomic analysis for the isolated cells were performed. A series of genes was used to verify and investigate the expression patterns in spermatogenesis. Furthermore, we also analyzed the expression of the same set of genes involved with steroid metabolism and sex throughout spermatogenesis (early-mid, late, and maturing stages) in the orange-spotted grouper. Several generally female-related genes took significantly changes in sex reversal hinted that the female-related genes in previously recognized may also play vital roles in spermatogenesis and sex reversal. In the transcriptomic data, we focused on zbtb family genes, which may be related to the process of spermatogenesis. Their expression patterns and cellular localization were examined, and the location of Eczbtb40 in different gonadal stages was investigated. We found that Eczbtb40 was expressed throughout spermatogenesis. These preliminary findings suggest that Eczbtb40 is highly conserved during vertebrate evolution and plays roles in spermatogenesis. Besides, the expression of Eczbtb40 and Eccyp17a1a overlapped in male germ cells, especially spermatogonium and spermatocyte, which suggested that Eczbtb40 might interact with Eccyp17a1a participant in spermatogenesis and sex reversal. Conclusions: The present study first depicted RNA sequencing of the male germ cells from orange-spotted grouper, and identified many important functional genes and pathways involved in spermatogenesis. The Eczbtb40 gene was subjected to molecular characterization and expression pattern analysis. These results will contribute to future studies of the molecular mechanism of spermatogenesis and sex reversal.

scholarly journals De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Marisa E. Miller ◽  
Ying Zhang ◽  
Vahid Omidvar ◽  
Jana Sperschneider ◽  
Benjamin Schwessinger ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Rust Fungus ◽  
Expression Patterns ◽  
Haplotype Diversity ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
Oat Crown Rust

ABSTRACT Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae. IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of P. coronata f. sp. avenae.

scholarly journals Comparative Transcriptome Analysis of a Fan-shaped Inflorescence in Pineapple Using RNA-seq

2020 ◽  
Author(s):  
Tao Xie ◽  
Zhiquan Cai ◽  
Aiping Luan ◽  
Wei Zhang ◽  
Jing Wu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Soluble Sugar ◽  
Differentially Expressed ◽  
Soluble Solids ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Stem Apex ◽  
Inflorescence Axis ◽  
Flower Stem

Abstract Background: Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was evolved in an exceptional material, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between a fan-shaped inflorescence (FI) and a capitulum inflorescence (CI) pineapples were analyzed in the three tissues, i.e., the flower stem apex (FIs and CIs), the base of the inflorescence (FIb and CIb), and the inflorescence axis (FIa and CIa).Results: Except for a clear differentiation of inflorescence morphology, no significant differences in the structure of inflorescence organs and the main nutritional components (soluble solids, soluble sugar, titratable acid, and VC) in fruits were found between the two pineapples. Between the fan- and capitulum-shaped inflorescences, a total of 5370 differentially expressed genes (DEGs) were identified across the three tissues; and 3142, 2526 and 2255 DEGs were found in the flower stem apex, the base of the inflorescence, and the inflorescence axis, respectively. Of these genes, there were 489 overlapping DEGs in all three tissue comparisons. In addition, 5769 DEGs were identified between different tissues within each pineapple. Functional analysis indicated between the two pineapples that 444 transcription factors (TFs) and 206 inflorescence development related genes (IDGs) were differentially expressed in at least one tissue comparison, while 45 TFs and 21 IDGs were overlapped across the 3 tissues. Among the 489 overlapping DEGs in the 3 tissue comparisons between the two pineapples, excluding the IDGs and TFs, 80 of them revealed a higher percentage of involvement in the biological processes relating to response to auxin, and reproductive processes. RNA-seq value and real-time quantitative PCR analysis exhibited the same gene expression patterns in the three tissues. Conclusions: Our result provided novel cues for understanding the molecular mechanisms of the formation of fan-shaped inflorescence in pineapple, making a valuable resource for the study of plant breeding and the speciation of the pineapples.

Differential expression of a transcription regulatory factor, the LIM domain only 4 protein Lmo4, in muscle sensory neurons

Development ◽  
2002 ◽  
Vol 129 (21) ◽  
pp. 4879-4889
Author(s):  
Hsiao-Huei Chen ◽  
Joseph W. Yip ◽  
Alexandre F. R. Stewart ◽  
Eric Frank
Keyword(s):  
Differential Expression ◽  
Sensory Neurons ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
Expression Patterns ◽  
Cdna Libraries ◽  
Homeodomain Protein ◽  
Lim Domain ◽  
Homeodomain Proteins ◽  
Lim Homeodomain

In the stretch-reflex system, proprioceptive sensory neurons make selective synaptic connections with different subsets of motoneurons, according to the peripheral muscles they supply. To examine the molecular mechanisms that may influence the selection of these synaptic targets, we constructed single-cell cDNA libraries from sensory neurons that innervate antagonist muscles. Differential screening of these libraries identified a transcription regulatory co-factor of the LIM homeodomain proteins, the LIM domain only 4 protein Lmo4, expressed in most adductor but few sartorius sensory neurons. Differential patterns of Lmo4 expression were also seen in sensory neurons supplying three other muscles. A subset of motoneurons also expresses Lmo4 but the pattern of expression is not specific for motor pools. Differential expression of Lmo4 occurs early, as neurons develop their characteristic LIM homeodomain protein expression patterns. Moreover, ablation of limb buds does not block Lmo4 expression, suggesting that an intrinsic program controls the early differential expression of Lmo4. LIM homeodomain proteins are known to regulate several aspects of sensory and motor neuronal development. Our results suggest that Lmo4 may participate in this differentiation by regulating the transcriptional activity of LIM homeodomain proteins.

scholarly journals Research Note. Transcriptomic study of the rat pinworm Syphacia muris

2015 ◽  
Vol 52 (4) ◽  
pp. 370-374 ◽  
Author(s):  
M. Okamoto ◽  
K. Taira ◽  
R. Ito ◽  
F. Asai
Keyword(s):  
Immune Response ◽  
Gene Ontology ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Innate Immune ◽  
Gene Ontology Analysis ◽  
Laboratory Rats ◽  
Syphacia Muris ◽  
Generation Sequencing

Summary Syphacia muris is a ubiquitous nematode parasite and common contaminant of laboratory rats. A lthough S. muris infection is considered symptomless, it has some effects on the host’s immunity and therefore can interfere with experimental settings and interrupt final results. However, the molecular mechanisms involved in the alteration within the host’s immunity remain unclear because of the absence of information about mRNA expressed in this parasite. In this study we performed the transcriptome profiling of S. muris by next-generation sequencing. After de novo assembly and annotation, 14,821 contigs were found to have a sequence homology with any nematode sequence. Gene ontology analysis showed that the majority of the expressed genes are involved in cellular process, binding, and catalytic activity. Although the rate of expressed genes involved in the immune system was low, we found candidate genes that might be involved in the alteration within the host’s immunity by regulating the host’s innate immune response.

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