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.

中文翻译：

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甘蔗蔗糖硝酸盐转运蛋白（NRT / NPF）家族的全基因组分析。

硝酸盐是植物生长和发育的主要氮源。然而，由于甘蔗中储存硝酸盐的能力低，全球用作主要糖料作物和生物燃料原料的甘蔗显示出较低的硝酸盐利用效率。众所周知，硝酸盐转运蛋白（NRT / NPF）家族在控制氮的吸收和分配以及优化植物中的氮利用方面起着看门人的作用。这使其成为提高甘蔗氮利用效率的有希望的目标。在这里，我们进行了自发糖酵母全基因组范围内的NRT / NPF基因的全面分析。首先针对最近发布的甘蔗基因组对NRT / NPF基因进行BLAST搜索，然后进行系统发育，基因结构和蛋白质基序分析。另外，从RNA-seq数据分析获得了来自各种组织的NRT / NPF基因表达谱。结果，我们鉴定了178个NPF，20个NRT2和6个NRT3基因，它们分布在所有8个单倍体染色体上。NPF和NRT3表现出高水平的遗传多样性，而NRT2在进化上更保守。有趣的是，几个SsNPF基因是几次串联重复的基因融合的产物，为硝酸盐转运蛋白的功能表征提供了宝贵的结构资源。此外，一些基因是组织特异性表达的，表明在组织特异性硝酸盐易位中的作用。就其基因结构和mRNA丰度而言，大量的NRT / NPF基因是异质的。两者合计，我们的工作为甘蔗硝酸盐转运蛋白的分子和生理功能的未来研究提供了遗传基础。