Comparative Transcriptome Analysis for Understanding Predator-Induced Polyphenism in the Water Flea Daphnia pulex

The crustacean Daphnia pulex is one of the best model organisms for studying inducible defense mechanisms due to their inducible morphology in response to the predator Chaoborus larvae. In this study, multiple developmental stages of D. pulex were exposed to C. flavicans larvae and transcriptome profiles of samples from late embryo to fifth instar were sequenced by the RNA-seq technique to investigate the genetic background underlying inducible defenses. In comparison, differentially expressed genes between defensive and normal morphs were identified, including 908 genes in late embryo, 1383 genes in the first-third (1–3) instar, and 1042 genes in fourth-fifth (4–5) instar. Gene ontology enrichment analysis showed that structural constituents of the cuticle and structural molecule activity genes were prominent up-regulated genes in late embryos. Down-regulated genes in late embryos and 1–3 instar comprised metabolic process, hydrolase activity, and peptidase activity gene classes. Pathway analysis indicated that small molecule neurotransmitter pathways were potentially involved in the development of inducible defenses. The characterization of genes and pathways in multiple developmental stages can improve our understanding of inducible defense responses of D. pulex to predation at the molecular level.

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Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

Bulletin of Entomological Research ◽

10.1017/s0007485321000171 ◽

2021 ◽

pp. 1-14

Author(s):

Peirong Li ◽

Xinru Li ◽

Wei Wang ◽

Xiaoling Tan ◽

Xiaoqi Wang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Metabolic Pathways ◽

Developmental Stages ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Mythimna Separata ◽

Kegg Pathway Analysis ◽

Oriental Armyworm ◽

Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

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Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

Rice ◽

10.1186/s12284-021-00461-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kieu Thi Xuan Vo ◽

Md Mizanor Rahman ◽

Md Mustafizur Rahman ◽

Kieu Thi Thuy Trinh ◽

Sun Tae Kim ◽

...

Keyword(s):

Stress Responses ◽

Biotic Stress ◽

Defense Mechanisms ◽

Defense Responses ◽

Global Changes ◽

Biotic Stresses ◽

Novel Proteins ◽

Stress Agent ◽

Global Food ◽

Shed Light

AbstractBiotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.

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Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

Scientific Reports ◽

10.1038/s41598-021-88055-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hangxia Jin ◽

Xiaomin Yu ◽

Qinghua Yang ◽

Xujun Fu ◽

Fengjie Yuan

Keyword(s):

Developmental Stage ◽

Phytic Acid ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Defense Mechanisms ◽

Developmental Stages ◽

Sucrose Metabolism ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

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Transcriptome Analysis of Eggplant Root in Response to Root-Knot Nematode Infection

Pathogens ◽

10.3390/pathogens10040470 ◽

2021 ◽

Vol 10 (4) ◽

pp. 470

Author(s):

Min Zhang ◽

Hongyuan Zhang ◽

Jie Tan ◽

Shuping Huang ◽

Xia Chen ◽

...

Keyword(s):

Defense Mechanisms ◽

Expression Profiles ◽

Resistance Mechanism ◽

Solanum Melongena ◽

Enrichment Analysis ◽

Nematode Resistance ◽

Differentially Expressed ◽

Root Knot Nematode ◽

Solanum Torvum ◽

Plant Nematode

Eggplant (Solanum melongena L.), which belongs to the Solanaceae family, is an important vegetable crop. However, its production is severely threatened by root-knot nematodes (RKNs) in many countries. Solanum torvum, a wild relative of eggplant, is employed worldwide as rootstock for eggplant cultivation due to its resistance to soil-borne diseases such as RKNs. In this study, to identify the RKN defense mechanisms, the transcriptomic profiles of eggplant and Solanum torvum were compared. A total of 5360 differentially expressed genes (DEGs) were identified for the response to RKN infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs are mainly involved in the processes of response to stimulus, protein phosphorylation, hormone signal transduction, and plant-pathogen interaction pathways. Many phytohormone-related genes and transcription factors (MYB, WRKY, and NAC) were differentially expressed at the four time points (ck, 7, 14, and 28 days post-infection). The abscisic acid signaling pathway might be involved in plant-nematode interactions. qRT-PCR validated the expression levels of some of the DEGs in eggplant. These findings demonstrate the nematode-induced expression profiles and provide some insights into the nematode resistance mechanism in eggplant.

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Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

BMC Genomics ◽

10.1186/s12864-021-07434-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shuo Wei ◽

Wen Zhang ◽

Rao Fu ◽

Yang Zhang

Keyword(s):

Metabolic Pathways ◽

Developmental Stages ◽

Expression Patterns ◽

Growth Cycle ◽

Model Organisms ◽

Gibberellin Biosynthesis ◽

Type I ◽

Multiple Model ◽

Genome Wide ◽

Tomato Growth

Abstract Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

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Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice

Rice ◽

10.1186/s12284-020-00437-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Lan-Lan Wang ◽

Jing-Jing Jin ◽

Li-Hua Li ◽

Shao-Hong Qu

Keyword(s):

Rice Blast ◽

Blast Resistance ◽

Enrichment Analysis ◽

Defense Responses ◽

Pathogen Resistance ◽

Blast Disease ◽

Fungus Infection ◽

Blast Fungus ◽

Gene Transcription Level ◽

Non Coding Rnas

Abstract Background Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice. However, M. oryzae-induced LncRNAs in rice is yet to be studied. Findings We investigated rice LncRNAs that were associated with the rice blast fungus. Totally 83 LncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some LncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) LncRNAs and genes co-expression analysis revealed some LncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that LncRNA may be involved in JA-mediated rice resistance to blast fungus. Conclusions This study identified blast fungus-responsive LncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

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How Can Satellite DNA Divergence Cause Reproductive Isolation? Let Us Count the Chromosomal Ways

Genetics Research International ◽

10.1155/2012/430136 ◽

2012 ◽

Vol 2012 ◽

pp. 1-11 ◽

Cited By ~ 16

Author(s):

Patrick M. Ferree ◽

Satyaki Prasad

Keyword(s):

Reproductive Isolation ◽

Developmental Stages ◽

Rapid Evolution ◽

Model Organisms ◽

Cellular Mechanisms ◽

Closely Related Species ◽

Heterochromatin Formation ◽

Interspecies Hybrids ◽

Postzygotic Reproductive Isolation ◽

And Function

Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed.

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Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-02-15-0023-r ◽

2015 ◽

Vol 28 (10) ◽

pp. 1102-1116 ◽

Cited By ~ 14

Author(s):

M. C. Magno-Pérez-Bryan ◽

P. M. Martínez-García ◽

J. Hierrezuelo ◽

P. Rodríguez-Palenzuela ◽

E. Arrebola ◽

...

Keyword(s):

Secondary Metabolites ◽

Biofilm Formation ◽

Bacillus Amyloliquefaciens ◽

Communication Systems ◽

Defense Mechanisms ◽

Ad Hoc ◽

Cell Communication ◽

Defense Responses ◽

Microbial Pathogens ◽

Stimulate Plant Growth

Bacillus amyloliquefaciens CECT 8237 and CECT 8238, formerly known as Bacillus subtilis UMAF6639 and UMAF6614, respectively, contribute to plant health by facing microbial pathogens or inducing the plant’s defense mechanisms. We sequenced their genomes and developed a set of ad hoc scripts that allowed us to search for the features implicated in their beneficial interaction with plants. We define a core set of genes that should ideally be found in any beneficial Bacillus strain, including the production of secondary metabolites, volatile compounds, metabolic plasticity, cell-to-cell communication systems, and biofilm formation. We experimentally prove that some of these genetic elements are active, such as i) the production of known secondary metabolites or ii) acetoin and 2-3-butanediol, compounds that stimulate plant growth and host defense responses. A comparison with other Bacillus genomes permits us to find differences in the cell-to-cell communication system and biofilm formation and to hypothesize variations in their persistence and resistance ability in diverse environmental conditions. In addition, the major protection provided by CECT 8237 and CECT 8238, which is different from other Bacillus strains against bacterial and fungal melon diseases, permits us to propose a correlation with their singular genetic background and determine the need to search for additional blind biocontrol-related features.

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A Faster and a Stronger Defense Response: One of the Key Elements in Grapevine Explaining Its Lower Level of Susceptibility to Esca?

Phytopathology ◽

10.1094/phyto-11-12-0305-r ◽

2013 ◽

Vol 103 (10) ◽

pp. 1028-1034 ◽

Cited By ~ 17

Author(s):

Carole Lambert ◽

Ian Li Kim Khiook ◽

Sylvia Lucas ◽

Nadège Télef-Micouleau ◽

Jean-Michel Mérillon ◽

...

Keyword(s):

Defense Response ◽

Defense Mechanisms ◽

Defense Responses ◽

Cabernet Sauvignon ◽

Susceptible Cultivar ◽

Pathogenesis Related ◽

Leaf Level ◽

Plant Pathogen Interaction ◽

Related Proteins ◽

Stilbene Compounds

Wood diseases like Esca are among the most damaging afflictions in grapevine. The defense mechanisms in this plant–pathogen interaction are not well understood. As some grapevine cultivars have been observed to be less susceptible to Esca than others, understanding the factors involved in this potentially stronger defense response can be of great interest. To lift part of this veil, we elicited Vitis vinifera plants of two cultivars less susceptible to Esca (‘Merlot’ and ‘Carignan’) and of one susceptible cultivar (‘Cabernet Sauvignon’), and monitored their defense responses at the leaf level. Our model of elicitation consisted in grapevine cuttings absorbing a culture filtrate of one causal agent of Esca, Phaemoniella chlamydospora. This model might reflect the early events occurring in Esca-affected grapevines. The two least susceptible cultivars showed an earlier and stronger defense response than the susceptible one, particularly with regard to induction of the PAL and STS genes, and a higher accumulation of stilbene compounds and some pathogenesis-related proteins.

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A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

PeerJ ◽

10.7717/peerj.3702 ◽

2017 ◽

Vol 5 ◽

pp. e3702 ◽

Cited By ~ 5

Author(s):

Santiago Montero-Mendieta ◽

Manfred Grabherr ◽

Henrik Lantz ◽

Ignacio De la Riva ◽

Jennifer A. Leonard ◽

...

Keyword(s):

Defense Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Cost Effective ◽

Model Organisms ◽

Rna Seq ◽

Assembly Pipeline ◽

Wide Variability ◽

History Of ◽

Inexperienced User

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

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