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Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [RNA-seq]

ABSTRACT: Methylome changes mediated by the soybean cyst nematode resistance gene GmSHMT08

ORGANISM(S): Glycine max

PROVIDER: GSE130138 | GEO | 2020/01/26

REPOSITORIES: GEO

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Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [MethylC-Seq]

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Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [RNA-seq]

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:Purpose: Soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) and soybean cyst nematode, Heterodera glycines Ichinohe, (SCN) are the two most economically important pests of soybean, Glycine max (L.) Merr., in the Midwest. Although the soybean aphid is an aboveground pest and SCN is a belowground pest there is evidence that concomitant infestations result in improved SCN reproduction. This study is aimed to characterize the three-way interactions among soybean, soybean aphid and SCN using demographic and genetic datasets. Results: More than 1.1 billion reads (61.4 GB) of transcriptomic data were yielded from 47 samples derived from the experiment using whole roots of G. max. The phred quality scores per base for all the samples were higher than 30. The GC content ranged from 43 to 45% 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 73.8% to 94.3%. Among the mapped reads, 67.1% to 87.6% reads were uniquely mapped. Conclusions: The comprehensive understanding of these transcriptome data would help in understanding the molecular interactions among soybean, A. glycines, and H. glycines. The use of multifaceted bioinformatics approaches could facilitate finding candidate genes and their function that might play a crucial role in various pathways for host resistance against both soybean aphids and SCN. For differential gene expression analysis, EdgeR, limma, and DEseq2 could be used. Apart from standalone tools like iDEP, Galaxy (https://usegalaxy.org), CyVerse (http://www.cyverse.org), and MeV (http://mev.tm4.org) could also be used for both analysis and visualization of RNA- seq data.

2019-05-18 | GSE125103 | GEO

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