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

• Published in: The Plant journal : for cell and molecular biology 2020-08, Vol.103 (5), p.1894-1909
• Main Authors: Machado, Fabricio B., Moharana, Kanhu C., Almeida‐Silva, Fabricio, Gazara, Rajesh K., Pedrosa‐Silva, Francisnei, Coelho, Fernanda S., Grativol, Clícia, Venancio, Thiago M.
• Format: Article
• Language: English
• Subjects: Alternative splicing; Animal feed; Atlases as Topic; Clustering; Data collection; Feeds; Gene expression; Gene Expression Profiling; Gene Library; Genes; Genes, Essential - genetics; Genes, Plant - genetics; Genetics; Genomics; Genotypes; Glycine max; Glycine max - genetics; housekeeping genes; Human nutrition; Isoforms; legumes; Nutrition; Ribonucleic acid; RNA; RNA, Plant - genetics; Soybeans; Splicing; tissue‐specific genes; Transcription; transcription factor; transcriptome; Transcriptome - genetics; webserver
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.14850

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. Significance Statement Here we report an integrative and systematic analysis of 1298 RNA‐Seq samples to build a soybean gene expression atlas. This resource is accessible via a user‐friendly web interface as well as available for download.