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Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species

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Abstract

Main conclusion

The work offers a comprehensive evaluation on the phylogenetics and conservation of splicing patterns of the plant SPF30 splicing factor gene family.

In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genome-wide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors.

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Acknowledgements

This work was supported by the Natural Science Foundation of Guangdong Province (2018A030313030) and Hong Kong Research Grant Council (AoE/M-05/12, AoE/M-403/16, GRF14160516, 14177617, 12100318).

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  1. Di Zhang and Jing-Fang Yang contributed equally to this work.

Authors and Affiliations

  1. School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong

    Di Zhang, Bei Gao, Tie-Yuan Liu & Mo-Xian Chen

  2. Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China

    Di Zhang, Mo-Xian Chen & Jianhua Zhang

  3. Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China

    Jing-Fang Yang, Ge-Fei Hao & Guang-Fu Yang

  4. Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants, Putian University, Putian, 351100, Fujian, People’s Republic of China

    Li-Jun Fu

  5. Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong

    Jianhua Zhang

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Figure S1 Phylogenetic tree of plant SPF30 gene family constructed by Maximum likelihood methods.

Figure S2 Weblogo plots of conserved motifs in plant SPF30 family.

Table S1SPF30 genes identified from 64 plant species.

Table S2 Predicted subcellular localization of plant SPF30 proteins.

Table S3 Characteristics of plant SPF30 gene structures.

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Zhang, D., Yang, JF., Gao, B. et al. Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species. Planta 249, 1997–2014 (2019). https://doi.org/10.1007/s00425-019-03146-x

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