Genome-Wide Analysis of Nitrate Transporter (NRT/NPF) Family in Sugarcane Saccharum spontaneum L.

  • Jiang Wang
  • Yaxin Li
  • Fan Zhu
  • Ray Ming
  • Li-Qing ChenEmail author


Nitrate is the predominant nitrogen source for plant growth and development. However, sugarcane, globally used as the primary sugar crop and biofuel feedstock, displays a low nitrate use efficiency due to a low capacity in storing nitrate in shoots. It is well studied that the nitrate transporter (NRT/NPF) family functions as the gatekeeper in governing nitrogen uptake and distribution, and optimizing nitrogen utilization in plants. This makes it a promising target for improving nitrogen use efficiency in sugarcane. Here, we carried out a comprehensive analysis of NRT/NPF genes at a genome-wide scale in Saccharum spontaneum. A BLAST search of NRT/NPF genes was initially performed against recently released sugarcane genome, followed by phylogenetic, gene structure and protein motif analysis. Additionally, NRT/NPF gene expression profile from various tissues was obtained from RNA-seq data analysis. As a result, we identified 178 NPF, 20 NRT2, and 6 NRT3 genes which spread across all 8 monoploid chromosomes. NPF and NRT3 exhibit high levels of genetic diversities as opposed to NRT2 which is more evolutionarily conserved. Interestingly, several SsNPF genes are products of gene fusions of several tandem duplications, which provide valuable structural resources for functional characterization of nitrate transporters. Moreover, several genes are tissue-specific expressed, indicating roles in tissue-specific nitrate translocations. A substantial number of NRT/NPF genes are heterogeneous in terms of their gene structures and mRNA abundance. Taken together, our work provides a genetic foundation for future investigations of molecular and physiological functions of sugarcane nitrate transporters.


Gene duplication and fusion NRT/NPF Nitrate transporter Tissue-specific expression Sugarcane 



This work was supported by a startup fund from the Department of Plant Biology, University of Illinois at Urbana-Champaign to LC, US DOE DE-SC0010686 and EBI BP2012OO2J17 to R.M. YL was supported by a scholarship from the China Scholarship Council (CSC).

This work was also funded in part by the DOE Center for Advanced Bioenergy and Bioproducts Innovation (U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018420). Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the U.S. Department of Energy.

Author’s Contributions

JW conducted the phylogenetic analysis and wrote the manuscript. YL conducted the gene structure analysis, protein motif analysis, Ka/Ks analysis and created the corresponding tables and figures. FZ conducted the RNA-seq analysis and build the expression heat-map. RM provided the RNA-seq data and lab resources. LC conceived the study and revised the manuscript.

Supplementary material

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Supplementary Fig. S1.

Gene structure and protein motif analysis of NRT2 and NRT3 genes from Saccharum. The phylogenetic relationship of each subfamily was constructed using the neighbor-joining method based on amino-acid sequences. Exon-intron structures are customized in each subfamily (with customized scale bar), the red bar represents exons, the black line represents introns, and the blue bar represents UTR (untranslated region). The different motifs are color-coded as illustrated in each subfamily, motifs are not comparable between NRT2 and NRT3 subfamilies. The scale represents amino-acid length. (PNG 63 kb)

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Authors and Affiliations

  1. 1.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  3. 3.Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of HorticultureChina Agricultural UniversityBeijingChina

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