title: Digital inventory of Arabidopsis transcripts revealed by 61 RNA sequencing samples.
abstract: Alternative splicing is an essential biological process to generate proteome diversity and phenotypic complexity. Recent improvements in RNA sequencing accuracy and computational algorithms have provided unprecedented opportunities to examine the expression levels of Arabidopsis (Arabidopsis thaliana) transcripts. In this article, we analyzed 61 RNA sequencing samples from 10 totally independent studies of Arabidopsis and calculated the transcript expression levels in different tissues, treatments, developmental stages, and varieties. These data provide a comprehensive profile of Arabidopsis transcripts with single-base resolution. We quantified the expression levels of 40,745 transcripts annotated in The Arabidopsis Information Resource 10, comprising 73% common transcripts, 15% rare transcripts, and 12% nondetectable transcripts. In addition, we investigated diverse common transcripts in detail, including ubiquitous transcripts, dominant/subordinate transcripts, and switch transcripts, in terms of their expression and transcript ratio. Interestingly, alternative splicing was the highly enriched function for the genes related to dominant/subordinate transcripts and switch transcripts. In addition, motif analysis revealed that TC motifs were enriched in dominant transcripts but not in subordinate transcripts. These motifs were found to have a strong relationship with transcription factor activity. Our results shed light on the complexity of alternative splicing and the diversity of the contributing factors.
authors.affiliation: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.) johnsunx1@gmail.com.
authors.forename: Xiaoyong
authors.identifier: http://orcid.org/0000-0002-2425-3526
authors.initials: X
authors.lastname: Sun
authors.affiliation: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.).
authors.forename: Qiuying
authors.initials: Q
authors.lastname: Yang
authors.affiliation: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.).
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Deng
authors.affiliation: Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.).
authors.forename: Xinfu
authors.initials: X
authors.lastname: Ye
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics*; D017343:Genes, Plant; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant