A global survey of bicarbonate stress-induced pre-mRNA alternative splicing in soybean via integrative analysis of Iso-seq and RNA-seq.

Autor: Liu X; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China., Li M; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China., Chen T; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China., Zhang R; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China., Wang Y; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China., Xiao J; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China., Ding X; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China. Electronic address: xiaodong.ding@neau.edu.cn., Zhang S; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: zhangshuzhen@neau.edu.cn., Li Q; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China. Electronic address: lstrong@neau.edu.cn.
Jazyk: angličtina
Zdroj: International journal of biological macromolecules [Int J Biol Macromol] 2024 Oct; Vol. 278 (Pt 4), pp. 135067. Date of Electronic Publication: 2024 Aug 26.
DOI: 10.1016/j.ijbiomac.2024.135067
Abstrakt: Alternative splicing (AS) plays important roles in modulating environmental stress responses in plants. However, little is known about the functions of bicarbonate-induced AS in cultivated soybean (Glycine max L. Merr.). In this study, we combined PacBio isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) to elucidate the bicarbonate-induced AS events in soybean root and leaf tissues. Compared to RNA-seq, Iso-seq identified more novel genes and transcripts, as well as more AS events, indicating that Iso-seq is more efficient in AS detection. Combining these two technologies, we found that intron retention (IR) is the most frequent AS event type. We identified a total of 913 and 1974 bicarbonate stress-responsive differentially alternative spliced genes (DAGs) in soybean leaves and roots respectively, from our RNA-seq results. Additionally, we determined a transcription factor (GmNTL9) and a splicing factor (GmRSZ22), and validated their roles in bicarbonate stress response by AS. Overall, our study opens an avenue for evaluating plant AS regulatory networks, and the obtained global landscape of alternative splicing provides valuable insights into the AS-mediated bicarbonate-responsive mechanisms in plant species.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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