Genome-wide identification and comparative analysis of alternative splicing across four legume species
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.
KeywordsAlternative splicing Cicer arietinum Glycine max Legume Lotus japonicas Medicago truncatula
Alternative 3′acceptor sites
Alternative 5′donor sites
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; www.ncbi.nlm.nih.gov). The other data generated in the study were included in this published article and its Additional files.
- Awai K, Maréchal E, Block MA, Brun D, Masuda T, Shimada H, Takamiya K, Ohta H, Joyard J (2006) Two types of MGDG synthase genes, found widely in both 16:3 and 18:3 plants, differentially mediate galactolipid syntheses in photosynthetic and nonphotosynthetic tissues in Arabidopsis thaliana. Proc Natl Acad Sci USA 98:10960–10965CrossRefGoogle Scholar
- Cheng L (2014) Implementing and accelerating HMMER3 protein sequence search on CUDA-enabled GPU. Dissertation, Concordia UniversityGoogle Scholar
- Guindon S, Dufayard JF, Hordijk W, Lefort V, Gascuel O (2009) PhyML: fast and accurate phylogeny reconstruction by maximum likelihood. Infect Genet Evol 9(3):384–385Google Scholar
- Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31(19):5654–5666CrossRefPubMedCentralPubMedGoogle Scholar
- Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq: reference generation and analysis with Trinity. Nat Protoc 8(8):1494–1512CrossRefPubMedGoogle Scholar
- Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, van Dongen WMAM, Stahl M, Zipfel C, Goshe MB, Clouse S, Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis leucine-rich repeat receptor kinase BIR3 negatively regulates BAK1 receptor complex formation and stabilizes BAK1. Plant Cell 29(9):2285–2303CrossRefPubMedCentralPubMedGoogle Scholar
- Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39:225–229CrossRefGoogle Scholar
- Michaelson LV, Zäuner S, Markham JE, Haslam RP, Desikan R, Mugford S, Albrecht S, Warnecke D, Sperling P, Heinz E, Napier JA (2009) Functional characterization of a higher plant sphingolipid Delta4-desaturase. Defining the role of sphingosine and sphingosine 1-phosphate in Arabidopsis. Plant Physiol 149:487–498CrossRefPubMedCentralPubMedGoogle Scholar
- Ueda T, Anai T, Tsukaya H, Hirata A, Uchimiya H (1996) Characterization and subcellular localization of a small GTP-binding protein (Ara-4) from Arabidopsis: conditional expression under control of the promoter of the gene for heat-shock protein HSP81-1. Mol Gen Genet 250(5):533–539PubMedGoogle Scholar
- Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D’Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M, Valle G (2014) A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol 14(1):99CrossRefPubMedCentralPubMedGoogle Scholar
- Wang LY, Zhang LH, Liu ZZ, Zhao DH, Liu XM, Zhang B, Xie JB, Hong YY, Li PF, Chen SF, Dixon R, Li JL (2013) A minimal nitrogen fixation gene cluster from Paenibacillus sp WLY78 enables expression of active nitrogenase in Escherichia coli. PLoS Genet 9(10):e1003865CrossRefPubMedCentralPubMedGoogle Scholar