Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing
| Autor: | Li Song, Zhenzhi Pan, Lin Chen, Binhui Guo, Yi Dai |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
AcademicSubjects/SCI01140 Spliceosome root development AcademicSubjects/SCI00010 Biology AcademicSubjects/SCI01180 01 natural sciences Plant Roots Transcriptome 03 medical and health sciences chemistry.chemical_compound alternative splicing Nutrient Nitrate Gene Expression Regulation Plant nitrate Genetics soybean Molecular Biology Gene Genetics (clinical) 030304 developmental biology Investigation 0303 health sciences Nitrates Gene Expression Profiling Alternative splicing mRNA surveillance Cell biology chemistry RNA splicing AcademicSubjects/SCI00960 Soybeans 010606 plant biology & botany |
| Zdroj: | G3: Genes|Genomes|Genetics |
| ISSN: | 2160-1836 |
| Popis: | In plants, nitrate acts not only as a signaling molecule that affects plant development but also as a nutrient. The development of plant roots, which directly absorb nutrients, is greatly affected by nitrate supply. Alternative gene splicing plays a crucial role in the plant stress response by increasing transcriptome diversity. The effects of nitrate supply on alternative splicing (AS), however, have not been investigated in soybean roots. We used high-quality high-throughput RNA-sequencing data to investigate genome-wide AS events in soybean roots in response to various levels of nitrate supply. In total, we identified 355 nitrate-responsive AS events between optimal and high nitrate levels (NH), 335 nitrate-responsive AS events between optimal and low nitrate levels (NL), and 588 nitrate-responsive AS events between low and high nitrate levels (NLH). RI and A3SS were the most common AS types; in particular, they accounted for 67% of all AS events under all conditions. This increased complex and diversity of AS events regulation might be associated with the soybean response to nitrate. Functional ontology enrichment analysis suggested that the differentially splicing genes were associated with several pathways, including spliceosome, base excision repair, mRNA surveillance pathway and so on. Finally, we validated several AS events using reverse transcription–polymerase chain reaction to confirm our RNA-seq results. In summary, we characterized the features and patterns of genome-wide AS in the soybean root exposed to different nitrate levels, and our results revealed that AS is an important mechanism of nitrate-response regulation in the soybean root. |
| Databáze: | OpenAIRE |
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