scholarly journals RNA Sequencing Analysis of Metopolophium dirhodum (Walker) (Hemiptera: Aphididae) Reveals the Mechanism Underlying Insecticide Resistance

2021 ◽  
Vol 5 ◽  
Author(s):  
Haifeng Gao ◽  
Xun Zhu ◽  
Guangkuo Li ◽  
Enliang Liu ◽  
Yuyang Shen ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Transcriptome Sequencing ◽  
Western China ◽  
Sequencing Analysis ◽  
Transcriptome Data ◽  
Metopolophium Dirhodum ◽  
Gene Characterization ◽  
Agricultural Regions ◽  
Phloem Feeding ◽  
Aphid Development

Xinjiang (XJ) and Ningxia (NX) provinces are important agricultural regions in western China. Aphids are one kind of the most devastating pests in both the provinces. Aphids are typical phloem-feeding insects distributed worldwide and can severely damage crops. In this study, two representative Metopolophium dirhodum (Walker) (Hemiptera: Aphididae) populations were collected from the typical agricultural regions of XJ and NX, respectively for a high-throughput transcriptome sequencing analysis. A total of 5,265 differentially expressed genes (DEGs) were identified. The functional annotation of DEGs and the identification of enriched pathways indicated many of the DEGs are involved in processes related to energy metabolism, development, and insecticide resistance. Furthermore, an investigation of insecticide toxicity revealed the NX population is more resistant to insecticide treatments than the XJ population. Thus, the transcriptome data generated in present study can be used for functional gene characterization relevant to aphid development, metabolism, environmental adaptation, and insecticide resistance.

scholarly journals Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.)

2021 ◽  
Vol 22 (13) ◽  
pp. 6641
Author(s):  
Chen Li ◽  
Meng Kou ◽  
Mohamed Hamed Arisha ◽  
Wei Tang ◽  
Meng Ma ◽  
...  
Keyword(s):  
High Temperature ◽  
Metabolic Pathways ◽  
Transcriptome Sequencing ◽  
Ipomoea Batatas ◽  
Sequencing Analysis ◽  
Storage Roots ◽  
Metabolic Analysis ◽  
Cooking Process

The saccharification of sweetpotato storage roots is a common phenomenon in the cooking process, which determines the edible quality of table use sweetpotato. In the present study, two high saccharified sweetpotato cultivars (Y25, Z13) and one low saccharified cultivar (X27) in two growth periods (S1, S2) were selected as materials to reveal the molecular mechanism of sweetpotato saccharification treated at high temperature by transcriptome sequencing and non-targeted metabolome determination. The results showed that the comprehensive taste score, sweetness, maltose content and starch change of X27 after steaming were significantly lower than those of Y25 and Z13. Through transcriptome sequencing analysis, 1918 and 1520 differentially expressed genes were obtained in the two periods of S1 and S2, respectively. Some saccharification-related transcription factors including MYB families, WRKY families, bHLH families and inhibitors were screened. Metabolic analysis showed that 162 differentially abundant metabolites related to carbohydrate metabolism were significantly enriched in starch and sucrose capitalization pathways. The correlation analysis between transcriptome and metabolome confirmed that the starch and sucrose metabolic pathways were significantly co-annotated, indicating that it is a vitally important metabolic pathway in the process of sweetpotato saccharification. The data obtained in this study can provide valuable resources for follow-up research on sweetpotato saccharification and will provide new insights and theoretical basis for table use sweetpotato breeding in the future.

scholarly journals Studies on trans-sutural distraction osteogenesis-related genes based on transcriptome sequencing

2020 ◽  
Author(s):  
Baicheng Wang ◽  
Hongyu Xue ◽  
Haizhou Tong ◽  
Peiyang Zhang ◽  
Mei Wang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Distraction Osteogenesis ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
Sequencing Analysis ◽  
Sprague Dawley ◽  
Down Regulation ◽  
Important Approach ◽  
Immune Pathways ◽  
Experimental Group

AbstractTrans-sutural distraction osteogenesis (TSDO) is an important approach to improve mid-face hypoplasia. In recent years, many studies have been carried out on physical mechanisms of TSDO; however, it’s specific cytological and molecular mechanisms are still unclear. In this study, we performed transcriptome sequencing analysis in Sprague Dawley rats at 1 and 2 weeks after suture osteogenesis and compared RNA expression levels between experimental and control groups. At one week, enrichment pathways were mainly up-regulated in muscle- and bone-related pathways. By contrast, pathways of the immune system showed a state of inhibition and down-regulation, especially for B cells; the main immune pathways showed significant down-regulation. However, two weeks later, the experimental group showed positive up-regulation of the pathways related to DNA synthesis and replication, cell cycle, and chromosome replication. At the same time, the immune pathways that were down-regulated in the first week were up-regulated in the second week. In other words, the up-regulated muscle- and bone-related pathways show opposite trends. The expression of bone- and myogenesis-related transcriptome was up-regulated and the immune-related pathways were down-regulated in the experimental group at 1 week. At 2 weeks, the pathways related to bone- and muscle were down-regulated, while those related to cell cycle regulation and DNA replication were up-regulated. These results suggest that musculoskeletal-related molecules may play an important role during suture osteogenesis at 1 week, and immune regulation may be involved in this process; however, at 2 weeks, molecules related to cell proliferation and replication may be a major role.

scholarly journals Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiaoling Zhang ◽  
Yanli Wang ◽  
Yuanyuan Yan ◽  
Hua Peng ◽  
Yun Long ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Sequencing Analysis ◽  
Embryonic Callus

Application of the FAO-recommended method for detecting insecticide resistance in Aphis jabae Scopoli, Sitobion avenae (F.), Metopolophium dirhodum (Walker) and Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

1983 ◽  
Vol 73 (1) ◽  
pp. 107-115 ◽  
Author(s):  
M. F. Stribley ◽  
G. D. MOORES ◽  
A. L. DEVONSHIRE ◽  
R. M. SAWICKI
Keyword(s):  
Insecticide Resistance ◽  
Rhopalosiphum Padi ◽  
Sitobion Avenae ◽  
Aphis Fabae ◽  
Cereal Aphids ◽  
Metopolophium Dirhodum ◽  
Large Numbers ◽  
The Uk ◽  
Dip Test

AbstractBaseline toxicity measurements established discriminating concentrations of pirimicarb and demeton-S-methyl guaranteed to kill susceptible examples of Aphis fabae Scop., Sitobion avenae (F.), Metopolophium dirhodum (Wlk.) and Rhopalosiphum padi (L.) in the dip-test, the FAO-recommended method for detecting resistance in aphids. There was no evidence for resistance to either insecticide in field-collected populations of aphids from various parts of the UK or amongst variants of S. avenae characterised by staining their esterases after electrophoresis. New, simple techniques for rearing large numbers of colonies of cereal aphids are described.

scholarly journals Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis

2016 ◽  
pp. E1-E1
Author(s):  
Sarah Djebali ◽  
Valentin Wucher ◽  
Sylvain Foissac ◽  
Christophe Hitte ◽  
Erwan Corre ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Sequencing Analysis ◽  
Bioinformatics Pipeline

scholarly journals Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hongju Jian ◽  
Aoxiang Zhang ◽  
Jinqi Ma ◽  
Tengyue Wang ◽  
Bo Yang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Qtl Mapping ◽  
Flowering Time ◽  
Transcriptome Sequencing ◽  
Sequencing Analysis ◽  
Brassica Napus L

scholarly journals Long-read transcriptome sequencing analysis with IsoTools

2021 ◽  
Author(s):  
Matthias Lienhard ◽  
Twan van den Beucken ◽  
Florian Claiment ◽  
Stefan Boerno ◽  
Myriam Hochradel ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transcriptome Sequencing ◽  
Sequencing Analysis ◽  
Differential Splicing ◽  
Accurate Analysis ◽  
Extensive Documentation ◽  
Long Read ◽  
Potential Applications ◽  
Transcriptional Changes ◽  
Analysis Package

Long-read transcriptome sequencing (LRTS) holds the promise to boost our understanding of alternative splicing. Recent advances in accuracy and throughput have diminished the major limitations and enabled the direct quantification of isoforms. Considering the complexity of the data and the broad range of potential applications, it is clear that highly flexible, accurate analysis tools are crucial. Here, we present IsoTools, a comprehensive Python-based analysis package, for the improvement of alternative and differential splicing analysis. IsoTools provides a comprehensive data structure that integrates genomic information from LRTS transcripts together with the reference annotation, and enables broad functionality to quality control, visualize and analyze the data. Additionally, we implemented a graph-based method for the identification of alternative splicing events and a statistical approach based on the beta binomial distribution for the detection of differential events. To demonstrate our methods, we generated PacBio Iso-Seq data of human hepatocytes treated with the HDAC inhibitor valproic acid, a compound known to induce widespread transcriptional changes. Contrasted with short read RNA-Seq of the same samples, this analysis shows that LRTS provides valuable additional insights for a better understanding of alternative splicing, in particular with respect to complex novel and differential splicing events. IsoTools is made available for the community along with extensive documentation at https://github.com/MatthiasLienhard/isotools.

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