, Volume 249, Issue 4, pp 1133–1142 | Cite as

Genome-wide identification and comparative analysis of alternative splicing across four legume species

  • Zan WangEmail author
  • Han Zhang
  • Wenlong Gong
Original Article


Main conclusion

Alternative splicing EVENTS were genome-wide identified for four legume species, and nitrogen fixation-related gene families and evolutionary analysis was also performed.

Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. Investigation of the genome-wide conserved AS events across different species will help with the understanding of the evolution of the functional diversity in legumes, allowing for genetic improvement. Genome-wide identification and characterization of AS were performed using the publically available mRNA, EST, and RNA-Seq data for four important legume species. A total of 15,165 AS genes in Glycine max, 6077 in Cicer arietinum, 7240 in Medicago truncatula, and 7358 in Lotus japonicus were identified. Intron retention (IntronR) was the dominant AS type among the identified events, with IntronR occurring from 53.76% in M. truncatula to 43.91% in C. arietinum. We identified 1159 AS genes that were conserved among four species. Furthermore, nine nitrogen fixation-related gene families with 237 genes were identified, and 80 of them were AS, accounting for the 43.48% in G. max and 27.78% in C. arietinum. An evolutionary analysis showed that these AS genes tended to be located adjacent to each other in the evolutionary tree and are unbalanced in the distribution in the sub-family. This study provides a foundation for future studies on transcription complexity, evolution, and the role of AS on plant functional regulation.


Alternative splicing Cicer arietinum Glycine max Legume Lotus japonicas Medicago truncatula 



Alternative 3′acceptor sites


Alternative 5′donor sites


Alternative splicing


Exon skipping


Intron retention


Mutually exclusive exons



This research was funded by the National Natural Science Foundation of China (no. 31272495) and the National Key Technology R&D Program of China (2011BAD17B01).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Availability of data and materials

All the sequence data used in the study were downloaded from the nucleotide repository of National Center for Biotechnology Information (NCBI; The other data generated in the study were included in this published article and its Additional files.

Supplementary material

425_2018_3073_MOESM1_ESM.xlsx (543 kb)
Supplementary material 1 (XLSX 543 kb)
425_2018_3073_MOESM2_ESM.pdf (1.3 mb)
Molecular phylogenetic relationship of the nine nitrogen fixation related genes family in four Leguminosae plants. The bootstrap values are shown at the nodes. Red dot is represented AS genes (PDF 1360 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Animal ScienceChinese Academy of Agricultural ScienceBeijingChina

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