scholarly journals Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

2021 ◽  
Vol 22 (13) ◽  
pp. 6909
Author(s):  
Gang Li ◽  
Xunyan Liu ◽  
Guy Smagghe ◽  
Jinzhi Niu ◽  
Jinjun Wang
Keyword(s):  
Spider Mite ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Spider Mites ◽  
Mite Species ◽  
Differentially Expressed ◽  
Regulatory Function ◽  
Panonychus Citri ◽  
Molting Process ◽  
Non Coding Rnas

Molting is essential for arthropods to grow. As one of the important arthropod pests in agriculture, key spider mite species (Tetranychus and Panonychus) can normally molt three times from the larva to adult stage within a week. This physiological strategy results in the short lifecycle of spider mites and difficulties in their control in the field. Long non-coding RNAs (lncRNAs) regulate transcriptional editing, cellular function, and biological processes. Thus, analysis of the lncRNAs in the spider mite molting process may provide new insights into their roles in the molting mechanism. For this purpose, we used high-throughput RNA-seq to examine the expression dynamics of lncRNAs and mRNAs in the molting process of different development stages in Panonychus citri. We identified 9199 lncRNAs from 18 transcriptomes. Analysis of the lncRNAs suggested that they were shorter and had fewer exons and transcripts than mRNAs. Among these, 356 lncRNAs were differentially expressed during three molting processes: late larva to early protonymph, late protonymph to early deutonymph, and late deutonymph to early adult. A time series profile analysis of differentially expressed lncRNAs showed that 77 lncRNAs were clustered into two dynamic expression profiles (Pattern a and Pattern c), implying that lncRNAs were involved in the molting process of spider mites. Furthermore, the lncRNA–mRNA co-expression networks showed that several differentially expressed hub lncRNAs were predicted to be functionally associated with typical molting-related proteins, such as cuticle protein and chitin biosynthesis. These data reveal the potential regulatory function of lncRNAs in the molting process and provide datasets for further analysis of lncRNAs and mRNAs in spider mites.

scholarly journals Biodiversity of spider mites (Acari: Tetranychidae) in Serbia: a review, new records and key to all known species

Acarologia ◽  
2017 ◽  
Vol 58 (1) ◽  
pp. 3-14
Author(s):  
Ivana Marić ◽  
Dejean Marčić ◽  
Radmila Petanović ◽  
Philippe Auger
Keyword(s):  
Host Plant ◽  
Plant Species ◽  
Spider Mite ◽  
New Records ◽  
Spider Mites ◽  
Mite Species ◽  
Cultivated Plants ◽  
Panonychus Citri ◽  
Tetranychus Evansi ◽  
Host Plant Species

Despite the economic importance of spider mites (Acari: Tetranychidae), data on their biodiversity are scarce in some regions of Europe, such as Balkan Peninsula and particularly in Serbia. In this country, according to the Spider Mites Web database, only 17 spider mite species belonging to seven genera have been reported. This study provides a review of the Serbian literature dealing with spider mites species recorded in Serbia and presents results of a four-year faunistic survey in which spider mites were collected on cultivated plants and native vegetation throughout the country. In the survey, a total of 23 species were recorded, including six species new to Serbian acarofauna: Bryobia praetiosa, Eotetranychus aceri, E. fraxini, E. pruni, Panonychus citri and Tetranychus evansi. Together with previously reported data, it raises the number of known spider mite species in Serbia to 36. A total of 90 host plant species from 21 families that are favorable to spider mites were recorded in this study; there were 62 new host records for 20 spider mite species with 11 records of new plant species as hosts of spider mites. There were 63 new records for Serbia among host plant species, raising the number of Serbian hosts for tetranychid mites to 137. The spider mite species new to Serbian acarofauna were found on 17 newly recorded host plants from 11 families. A key to all known spider mites species from Serbia is provided.

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

Spider mites (Acari: Tetranychidae) in protected natural areas of Serbia

2018 ◽  
Vol 23 (10) ◽  
pp. 2033
Author(s):  
Ivana Marić ◽  
Irena Međo ◽  
Slobodan Jovanović ◽  
Radmila Petanović ◽  
Dejan Marčić
Keyword(s):  
Plant Species ◽  
Host Plants ◽  
Spider Mite ◽  
Spider Mites ◽  
Mite Species ◽  
Southeast Europe ◽  
Natural Areas ◽  
Relict Species ◽  
Protected Natural Areas ◽  
New Hosts

Despite economic importance of Tetranychidae, knowledge regarding diversity of spider mites in the Balkan Peninsula and Southeast Europe is incomplete, especially in protected natural areas. This study presents diversity of spider mites (Acari: Tetranychidae) collected over five growing seasons at 296 locations in 38 protected natural areas of Serbia. A total of 31 spider mite species were found, 10 from Bryobiinae and 21 from Tetranychinae. The species Eotetranychus fagi Zacher was recorded as new to Serbia and this record was also the first one for Southeast Europe. Spider mites were found on host plants in five basic types as well as many subtypes of terrestrial habitats, with woodland as the most dominant one. A total of 151 plant species from 44 families were recorded as hosts for spider mites including new world records: 60 new hosts for family Tetranychidae and 41 new hosts for 21 spider mite species. Host plants from Rosaceae family harbored the highest number of spider mite species (16). A considerable number of species was found on host plants from the families Betulaceae (11), Asteraceae (10) and Sapindaceae (10). Two cosmopolitan spider mites, Tetranychus urticae Koch and Tetranychus turkestani Ugarov & Nikolskii, were clearly distinguished with 67 (7 new) and 43 (13 new) recorded host species, respectively; among newly recorded hosts for Tetranychidae family, these two mite species were found on 27 and 12 hosts, respectively. After the two most common species, the most striking was the presence of Bryobia praetiosa Koch with 24 (4 new) recorded host plants, followed by Amphitetranychus viennensis (Zacher), Eotetranychus carpini (Oudemans) and Bryobia rubrioculus (Scheuten), with 21 (7 new), 20 (6 new) and 16 (2 new) hosts, respectively. The remaining tetranychids were found on 1–9 host plant species. This study provided the first insight into diversity of tetranychids in Serbian protected areas. Further research in this field should focus on mites from host plants representative of specific areas and habitats, including endangered, endemic and relict species.

scholarly journals Maize inbred line B96 is the source of large-effect loci for resistance to generalist but not specialist spider mites

2021 ◽  
Author(s):  
Huyen Bui ◽  
Robert Greenhalgh ◽  
Gunbharpur S. Gill ◽  
Meiyuan Ji ◽  
Andre H. Kurlovs ◽  
...  
Keyword(s):  
Zea Mays ◽  
Tetranychus Urticae ◽  
European Corn Borer ◽  
Spider Mite ◽  
Insect Pests ◽  
Spider Mites ◽  
Mite Species ◽  
Chromosome 1 ◽  
Corn Borer ◽  
Oligonychus Pratensis

AbstractMaize (Zea mays subsp. mays) yield loss from arthropod herbivory is substantial. While the basis of resistance to major insect herbivores has been comparatively well-studied in maize, less is known about resistance to spider mite herbivores, which are distantly related to insects and feed by a different mechanism. Two spider mites, the generalist Tetranychus urticae, and the grass-specialist Oligonychus pratensis, are notable pests of maize, especially during drought conditions. We assessed the resistance to both mite species of 38 highly diverse maize lines, including several previously reported to be resistant to one or the other mite species. We found that line B96, as well as its derivatives B49 and B75, were highly resistant to T. urticae. In contrast, neither these three lines, nor any others included in our study, were notably resistant to O. pratensis. Quantitative trait locus (QTL) mapping with F2 populations from crosses of B49, B75, and B96 to susceptible B73 identified a large-effect QTL on chromosome 6 as underlying T. urticae resistance in each line, with an additional QTL on chromosome 1 in B96. Genome sequencing and haplotype analyses identified B96 as the apparent sole source of resistance haplotypes. Our study identifies loci for use in maize breeding programs for T. urticae resistance, as well as to assess if the molecular-genetic basis of spider mite resistance is shared with insect pests of maize, as B96 is also among the most resistant known maize lines to several insects, including the European corn borer, Ostrinia nubilalis.Key message Maize(Zea mays subsp. mays) inbred lines B49, B75, and B96 harbor large-effect loci for resistance to the generalist spider mite Tetranychus urticae, but not the specialist Oligonychus pratensis.

Integrated analysis profiles of long non–coding RNAs reveal potential biomarkers across brain regions in post–traumatic stress disorder

2020 ◽  
Author(s):  
Yaoyao Bian ◽  
Lili Yang ◽  
Zhongli Wang ◽  
Wen Li ◽  
Qing Wang ◽  
...  
Keyword(s):  
Post Traumatic Stress Disorder ◽  
Traumatic Stress ◽  
Stress Disorder ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Post Traumatic Stress ◽  
Post Traumatic ◽  
Non Coding Rnas ◽  
Potential Biomarkers

Abstract Background Post–traumatic stress disorder (PTSD) is characterized by impaired fear extinction, excessive anxiety and depression. However, underlying mechanisms, especially the function roles of long non–coding RNAs (lncRNAs) involved in PTSD is still unclear. We argued that the lncRNAs, co–expressed mRNAs, as well as the associated pathways, are altered and may thus serve as potential biomarkers and key pathways related to PTSD.Methods The gene expression profiles of GSE68077 was downloaded from the GEO database, and the differentially expressed lncRNAs and mRNAs were identified. Gene ontology (GO) and Kyto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis were performed. Subsequently, protein–protein interaction (PPI) network was analyzed, and module analysis of the differentially expressed mRNAs was performed with Cytoscape software. Finally, lncRNAs–mRNAs co–expression network was constructed and core pair lncRNAs involved in PTSD were mapped.Results A total of 45 differentially expressed lncRNAs and 726 differentially expressed mRNAs were obtained. Among of which, 17 lncRNAs and 86 mRNAs were inter–regulated, and most of the lncRNAs–mRNAs co–expression showed positive correlations. The lncRNAs–mRNAs co–expressed network suggested the potentially functional roles of lncRNAs, regulated mRNAs and related pathways in PTSD. By implication of the core pair network, lncRNA–NONMMUT010120.2 synergistically up–regulated Ppargc1a and down–regulated Cir1, Slc38a9, Atp6v0a2. Moreover, lncRNA–NONMMUT023440.2, NONMMUT034155.2, NONMMUT105407.1 and NONMMUT149972.1 were co–expressed with 10 co–expressed mRNAs, which indicated that lncRNAs involved in PTSD might work by regulating the co–expressed mRNAs.

scholarly journals RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1565
Author(s):  
Zhiyun Hao ◽  
Yuzhu Luo ◽  
Jiqing Wang ◽  
Jiang Hu ◽  
Xiu Liu ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Signaling Pathway ◽  
Target Genes ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Wnt Signaling Pathway ◽  
Mammary Epithelial ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA with >200 nucleotides in length. Some lncRNAs have been proven to have clear regulatory functions in many biological processes of mammals. However, there have been no reports on the roles of lncRNAs in ovine mammary gland tissues. In the study, the expression profiles of lncRNAs were studied using RNA-Seq in mammary gland tissues from lactating Small-Tailed Han (STH) ewes and Gansu Alpine Merino (GAM) ewes with different milk yield and ingredients. A total of 1894 lncRNAs were found to be expressed. Compared with the GAM ewes, the expression levels of 31 lncRNAs were significantly up-regulated in the mammary gland tissues of STH ewes, while 37 lncRNAs were remarkably down-regulated. Gene Ontogeny (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the target genes of differentially expressed lncRNAs were enriched in the development and proliferation of mammary epithelial cells, morphogenesis of mammary gland, ErbB signaling pathway, and Wnt signaling pathway. Some miRNA sponges of differentially expressed lncRNAs, reported to be associated with lactation and mammary gland morphogenesis, were found in a lncRNA-miRNA network. This study reveals comprehensive lncRNAs expression profiles in ovine mammary gland tissues, thereby providing a further understanding of the functions of lncRNAs in the lactation and mammary gland development of sheep.

RNAi of the nuclear receptor HR3 suggests a role in the molting process of the spider mite Panonychus citri

2020 ◽  
Vol 81 (1) ◽  
pp. 75-83
Author(s):  
Gang Li ◽  
Xun-Yan Liu ◽  
Xi Han ◽  
Jin-zhi Niu ◽  
Jin-Jun Wang
Keyword(s):  
Nuclear Receptor ◽  
Spider Mite ◽  
Panonychus Citri ◽  
Molting Process

PADGE: analysis of heterogeneous patterns of differential gene expression

2007 ◽  
Vol 32 (1) ◽  
pp. 154-159 ◽  
Author(s):  
Li Li ◽  
Amitabha Chaudhuri ◽  
John Chant ◽  
Zhijun Tang
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Statistical Power ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Cancer Genes ◽  
Data Set ◽  
Differential Gene

We have devised a novel analysis approach, percentile analysis for differential gene expression (PADGE), for identifying genes differentially expressed between two groups of heterogeneous samples. PADGE was designed to compare expression profiles of sample subgroups at a series of percentile cutoffs and to examine the trend of relative expression between sample groups as expression level increases. Simulation studies showed that PADGE has more statistical power than t-statistics, cancer outlier profile analysis (COPA) (Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM. Science 310: 644–648, 2005), and kurtosis (Teschendorff AE, Naderi A, Barbosa-Morais NL, Caldas C. Bioinformatics 22: 2269–2275, 2006). Application of PADGE to microarray data sets in tumor tissues demonstrated its utility in prioritizing cancer genes encoding potential therapeutic targets or diagnostic markers. A web application was developed for researchers to analyze a large gene expression data set from heterogeneous biological samples and identify differentially expressed genes between subsets of sample classes using PADGE and other available approaches. Availability: http://www.cgl.ucsf.edu/Research/genentech/padge/ .

scholarly journals Updated and annotated review of Tetranychidae occurring in mainland Portugal, the Azores, and Madeira Archipelagos

Acarologia ◽  
2021 ◽  
Vol 61 (2) ◽  
pp. 380-393
Author(s):  
Pedro Naves ◽  
Filomena Nóbrega ◽  
Philippe Auger
Keyword(s):  
Scientific Information ◽  
National Level ◽  
First Record ◽  
Relevant Information ◽  
Spider Mites ◽  
Mite Species ◽  
Tetranychus Kanzawai ◽  
Panonychus Citri ◽  
New Host ◽  
Mainland Portugal

Data on the diversity, distribution, and main hosts of spider mites (Acari: Tetranychidae) are scarce in the Iberian Peninsula, particularly for Portugal, where only 21 species are recorded on the mainland and in the Azores and Madeira archipelagos. Moreover, the scientific information is mainly available in national publications, and difficult to access for international researchers. In this paper, we review the literature dealing with spider mites in mainland Portugal and the archipelagos of the Azores and Madeira, compiling and synthesizing the most relevant information on their distribution, hosts and pest potential. Further information was obtained by verifying slides in the acarological collection of the Instituto Nacional de Investigação Agrária e Veterinária (INIAV), the most important national collection, and by verifying mites collected on different plant hosts during the period 2018-2020. In total, we found records for 28 spider mite species in Portugal, comprising nine Bryobiinae and 19 Tetranychinae, and including new national records for Stigmaeopsis nanjingensis and Eotetranychus tiliarium. Additionally, we record a new exotic mite species for the mainland, Eotetranychus lewisi, which was found in two localities in the Algarve District on leaves of Euphorbia pulcherrima. This is the first record for continental Europe of an established population in outdoor conditions of this regulated quarantine pest. We also comment on the presence of seven species not reported by international taxonomic databases but already recorded from Portugal: Aplonobia histricina, Eotetranychus rubiphilus, Schizonobia sycophanta, Tetranychus kanzawai and Tetranycopsis horridus (at a national level), and Oligonychus perseae and Panonychus citri (for the mainland). New host records are given for Bryobia praetiosa, Petrobia (Tetranychina) harti, S. sycophanta, E. coryli, E. rubiphilus, Tetranychus kanzawai, Tetranychus lintearius, Tetranychus ludeni and Tetranychus turkestani.

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