Your browser doesn't support javascript.
loading
Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset.
Wu, Zhi-Hao; He, Liang-Liang; Wang, Cong-Cong; Liang, Chen; Li, Han-Ying; Zhong, Dan-Wen; Dong, Zhao-Xia; Zhang, Li-Juan; Zhang, Xiang-Qian; Ge, Liang-Fa; Chen, Shu.
Afiliación
  • Wu ZH; Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
  • He LL; Guangdong Engineering Research Center for Grassland Science, Guangzhou, China.
  • Wang CC; Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
  • Liang C; Guangdong Engineering Research Center for Grassland Science, Guangzhou, China.
  • Li HY; Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
  • Zhong DW; Guangdong Engineering Research Center for Grassland Science, Guangzhou, China.
  • Dong ZX; Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
  • Zhang LJ; Guangdong Engineering Research Center for Grassland Science, Guangzhou, China.
  • Zhang XQ; Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
  • Ge LF; Guangdong Engineering Research Center for Grassland Science, Guangzhou, China.
  • Chen S; Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
Physiol Plant ; 176(2): e14280, 2024.
Article en En | MEDLINE | ID: mdl-38644527
ABSTRACT
Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.
Asunto(s)
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Empalme Alternativo / Frío / Poaceae Idioma: En Revista: Physiol Plant Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Dinamarca
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Empalme Alternativo / Frío / Poaceae Idioma: En Revista: Physiol Plant Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Dinamarca