Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Abstract

SUMMARY Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past 5 years generated an enormous amount of RNA‐seq data, encompassing various tissues, developmental conditions and genotypes. In this study, we have collected data from 1298 publicly available soybean transcriptome samples, processed the raw sequencing reads and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground and seed/seed‐related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1349 genes showed heavily biased expression patterns towards particular tissues. A transcript‐level analysis revealed that 95% (70 963 of 74 490) of the assembled transcripts have intron chains exactly matching those from known transcripts, whereas 3256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user‐friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.

High-resolution transcriptome atlas and improved genome assembly of common buckwheat,Fagopyrum esculentum

“…The genes in the fraction with the broadest expression patterns were enriched in the GO categories "photoperiodism, flowering" and "protein transporter activity", while those in the fraction with the narrowest expression patterns were enriched in "serine-type endopeptidase inhibitor activity", "negative regulation of endopeptidase activity", and "endomembrane system" (Table S8). RNA-seq data, especially high-resolution transcriptome maps, are an important resource for the identification of stably expressed genes, which are useful as reference genes for qRT-PCR (Zhou et al, 2017;Machado et al, 2020). We used the standard deviation of gene expression divided by mean expression (standard deviation; SD)/mean) as a measure of expression stability, and we identified 20 transcripts with SD/mean ratios < 0.2, 205 with ratios < 0.25, and 720 with ratios < 0.3.…”

High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum

“…RNA-seq data, especially high-resolution transcriptome maps, are an important resource for the identification of stably expressed genes, which are useful as reference genes for qRT-PCR (Zhou et al, 2017;Machado et al, 2020). We used the standard deviation of gene expression divided by mean expression (standard deviation; SD)/mean) as a measure of expression stability, and we identified 20 transcripts with SD/mean ratios < 0.2, 205 with ratios < 0.25, and 720 with ratios < 0.3.…”

Advances in Transcriptome Analyses Using RNA Sequencing Technology in Soybean Plants [Glycine max]

“…'Williams 82', and characterized their expression under dehydration and salt stress. Recently, Machado et al (2020) analyzed 1 298 RNA-Seq samples and constructed a comprehensive soybean (Glycine max) expression atlas. They found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample.…”