Aphis glycines
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA551277 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| VYZN01.dat.gz | Other | |||
| VYZN01.fasta.gz | Fasta.gz | |||
| VYZN01.master.dat | Other | |||
| SRR10158900_1.fastq.gz | Fastqsanger.gz |
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Project description:Soybean aphid is one of the major limiting factors for soybean production. However, the mechanism for aphid resistance in soybean is remain enigmatic, very little information is available about the different mechanisms between antibiosis and antixenosis genotypes. Here we dissected aphid infestation into three stages and used genome-wide gene expression profiling to investigate the underlying aphid-plant interaction mechanisms. Approximately 990 million raw reads in total were obtained, the high expression correlation in each genotype between infestation and non-infestation indicated that the response to aphid was controlled by a small subset of important genes. Moreover, plant response to aphid infestation was more rapid in resistant genotypes. Among the differentially expressed genes (DEGs), a total of 901 transcription factor (TF) genes categorized to 40 families were identified with distinct expression patterns, of which AP2/ERF, MYB and WRKY families were proposed to playing dominated roles. Gene expression profiling demonstrated that these genes had either similar or distinct expression patterns in genotypes. Besides, JA-responsive pathway was domination in aphid-soybean interaction compared to SA pathway, which was not involved plant response to aphid in susceptible and antixenotic genotypes but played an important role in antibiosis one. Throughout, callose were deposited in all genotypes but it was more rapidly and efficiently in antibiotic one. However, reactive oxygen species were not involved in response to aphid attack in resistant genotypes during aphid infestation. Our study helps uncover important genes associated with aphid-attack response in antibiosis and antixenotic genotypes of soybean.
2020-08-26 | GSE141720 | GEO
Project description:Gene expression profiles in resistant (cv. Dowling) and susceptible (Williams 82) soybean genotypes [Glycine max (L.) Merrill] were compared at 6 and 12 h with and without aphid (Aphis glycines Matsumura) infestation using cDNA microarrays consisting of approximately 18,000 soybean-expressed sequence tags. More genes were induced in Dowling than Williams 82 at 6 h after infestation. Genes that were differentially expressed between aphid and control treatments were selected as aphid-response genes. Eighty-four genes showed specific responses in Dowling and included genes related to defense and other processes. Expression of three defense-related genes was examined at 6, 12, 24, 48, and 72 h after infestation in both genotypes by quantitative real-time PCR. The increases in the transcripts of three defense-related genes were earlier and stronger at 6, 12 and 24 h after infestation in Dowling compared to Williams 82. The differential gene expression between the two genotypes without aphids was determined, and five genes with constitutively higher expression levels were found in Dowling. Keywords = genomic Keywords = Defense Responses Keywords = plant Keywords = DNA-binding protein Keywords = PR proteins Keywords = plant resistance Keywords = signal transduction keywords = insect Keywords: susceptible vs resistant
2008-10-13 | GSE3070 | GEO
Project description:Sequencing of the genome of Aphis glycines (soybean aphid) a pest of Glycine max (soybean)
| PRJNA336353 | ENA
Project description:Purpose: Soybean aphid (Aphis glycines Matsumura; SBA) is major pest of soybean (Glycine max) in the United States of America. One previous study on soybean, soybean-aphid interactions showed that avirulent (biotype 1) and virulent (biotype 2) biotypes can co-occur and potentially interact on resistant and susceptible soybean resulting induced susceptibility. The main objective of this research was to employ RNA sequencing technique to characterize the induced susceptibility effect in which initial feeding by virulent aphids can increase the suitability of avirulent aphids in both susceptible and resistant cultivars. Methods: The data in this submission come from the green house experiment using two genotypes of soybean: susceptible soybean cultivar was LD12-15838R and the resistant cultivar was LD12-15813Ra (with Rag1 gene) and two aphid populations: biotype 1 (avirulent) and biotype 2 (virulent biotype 2). RNA was extracted from the leave samples from resistant and susceptible cultivars treated with no aphids, biotype 2: biotype1 collected at day 1 and no aphids, biotype 2: biotype1 and no aphids: biotype1 at day 11 using PureLink RNA mini kit (Invitrogen, USA). RNA samples were treated with TURBOTM DNase (Invitrogen, USA) to remove any DNA contamination following the manufacturer’s instructions. Assessment of the isolated RNA integrity was performed by 1% agarose gel electrophoresis, and RNA concentration was measured by Nanodrop 2000 (Thermo Fisher Scientific, USA). Three replicates from these treatments in resistant and susceptible cultivars were pooled in equimolar concentration. RNAseq library construction was prepared using Illumina’s TruSeq Stranded mRNA Kit v1 (San Diego, CA). The libraries were quantified by QuBit dsDNA HS Assay (Life Technologies, Carlsbad, CA) and pooled in equimolar concentrations. The libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Reagent Cartridge v2 (San Diego, CA) at 75 cycles. Results: A total of 10 RNA libraries were prepared and sequenced with the sequencing depth ranging from 24,779,816 to 29,72,4913. Total reads of 266,535,654 were subjected to FastQC analysis to determine the data quality using various quality metrics such as mean quality scores, per sequence quality scores, per sequence GC content, and sequence length distribution. The phred quality scores per base for all the samples were higher than 30. The GC content ranged from 45 to 46% and followed the normal distribution. After trimming, more than 99% of the reads were retained as the clean and good quality reads. Upon mapping these reads, we obtained high mapping rate ranging from 90.4% to 92.9%. Among the mapped reads, 85.8% to 91.9% reads were uniquely mapped. Conclusions: The objective of this study is to characterize the mechanism of induced susceptibility in soybean via transcriptional response study of soybean in presence of biotype 1 and biotype 2 soybean aphids using RNA-Seq. The data resulted from this study might provide insights into the interactions between soybean and soybean aphids and identify genes, their regulation and enriched pathways that may be associated with resistance or susceptibility to A. glycines.
2019-04-26 | GSE129626 | GEO
Project description:Aphis glycines strain:Biotype 3 Transcriptome or Gene expression
| PRJNA222584 | ENA
Project description:The aim for this study was to compare the differences in the methylome of three Russian wheat aphid populations that differ in virulence and bacterial load. Differences in the methylome of US Russian wheat aphid biotype 2 (US-RWA2) that have undergone removal of their phytobiomes through isolation of newly born nymphs from their mothers compared to nymphs who stayed in close proximity to their progenitors. US-RWA1 is the least virulent biotype and US-RWA2 is the most virulent biotype. The isolated US-RWA2 population (with a reduced bacterial load) has been shown to be less virulent than the co-fed population (Luna et al., 2018). The corresponding two methylomes were then compared to the methylome of US Russian wheat aphid biotype 1 (US-RWA1 is less virulent than US-RWA2) to ascertain the contribution (or lack thereof) of the phytobiome in regards to the increased/decreased virulence of phytobiome present and absent aphids. We investigated the overall, genic, intergenic, exonic and intronic methylation - as well as genic and intergenic hemimethylation -all three available contexts ( CpG, CHG and CHH) through use of the Bismark pipeline. These findings were used to ascertain to what effect the phytobiome (bacterial load) had on methylation within the US Russian wheat aphid biotypes.
2022-06-30 | GSE185975 | GEO
Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. Aphids do not normally kill their host and colonize plants for long periods of time, up to several months in soybean. However, our knowledge of plant responses to long-term aphid colonization is very limited. We used microarrays to characterize the soybean plant's transcriptional response against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured transcript levels in leaves after 21 days of aphid infestation.
2018-06-15 | GSE115790 | GEO
Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. We used microarrays to characterize the soybean plant's transcriptional defense against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured trancript levels in leaves after one and seven days of aphid infestation.
2012-01-31 | GSE35427 | GEO
Project description:The cotton - melon aphid Aphis gossypii is an extremely polyphagous sap feeding insect which infests more than 900 crops worldwide and posing a severe threat to farmers. The salivary proteins acts as interface between aphid and their host plant.However, the cotton aphid salivary proteome was not studied yet. Identifying the salivary proteins helps in better understanding of aphid adaptation to their host plant which aids us to search for novel plant genetic source.
2024-09-09 | PXD045238 | JPOST Repository
Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. We used microarrays to characterize the soybean plant's transcriptional defense against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured trancript levels in leaves after one and seven days of aphid infestation. This was a full-factorial experiment with three factors: soybean variety (susceptible SD01-76R,resistant LD05-16060), aphid treatment (control, aphids), and infestation duration (1 day, 7 days). There were three replicates per treatment, for a total of 24 samples. The experiment was carried out in a growth chamber. At the V3 growth stage, thirty aphids were added to the third trifoliate leaves of the aphid-treated plants. Each plant had a net to prevent aphid movement among different plants. The aphids were removed prior to sampling.
2012-01-31 | E-GEOD-35427 | biostudies-arrayexpress