Biochemical Genetics

, Volume 56, Issue 4, pp 397–422 | Cite as

Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris)

  • Surendra Neupane
  • Qin Ma
  • Febina M. Mathew
  • Adam J. Varenhorst
  • Ethan J. Andersen
  • Madhav P. NepalEmail author
Original Article


Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.


Legume disease-resistant genes Comparative genomics Synteny Gene duplication Purifying selection R gene targeting MicroRNAs 



This project was supported by South Dakota Agricultural Experiment Station (SDAES) USDA-NIFA hatch Project to M. Nepal (SD00H469-13) and South Dakota Soybean Research and Promotion Council (SDSRPC-SA1800238).

Author Contributions

SN conducted gene identification and analysis. MPN conceived and supervised the project as well as helped SN draft the manuscript. QM, FM, EJA and AV contributed to data analysis, interpretation and revision of the manuscript.

Compliance with Ethical Standards

Conflict of interest

The authors declare no competing interests.

Supplementary material

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Supplementary material 1 (PDF 8864 kb)
10528_2018_9851_MOESM2_ESM.xlsx (133 kb)
Supplementary material 2 (XLSX 133 kb)
10528_2018_9851_MOESM3_ESM.pdf (998 kb)
Supplementary material 3 (PDF 997 kb)


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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsUSA
  2. 2.Department of Agronomy, Horticulture and Plant ScienceSouth Dakota State UniversityBrookingsUSA

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