Deep learning‐enabled discovery and characterization of HKT genes in Spartina alterniflora

作者：Maogeng Yang, Shoukun Chen, Shoukun Chen, Zhangping Huang, Shang Gao, Tingxi Yu, Tingting Du, Hao Zhang, Xiang Li, Chunming Liu, Shihua Chen, Shihua Chen, Huihui Li · 发表于：The Plant Journal · 年份：2023 · DOI：10.1111/tpj.16397 · 被引用次数：27 · 研究领域：Plant Stress Responses and Tolerance、Plant nutrient uptake and metabolism、Plant Molecular Biology Research

SUMMARY Spartina alterniflora is a halophyte that can survive in high‐salinity environments, and it is phylogenetically close to important cereal crops, such as maize and rice. It is of scientific interest to understand why S. alterniflora can live under such extremely stressful conditions. The molecular mechanism underlying its high‐saline tolerance is still largely unknown. Here we investigated the possibility that high‐affinity K + transporters (HKTs), which function in salt tolerance and maintenance of ion homeostasis in plants, are responsible for salt tolerance in S. alterniflora. To overcome the imprecision and unstable of the gene screening method caused by the conventional sequence alignment, we used a deep learning method, DeepGOPlus, to automatically extract sequence and protein characteristics from our newly assemble S. alterniflora genome to identify SaHKTs. Results showed that a total of 16 HKT genes were identified. The number of S. alterniflora HKTs (SaHKTs) is larger than that in all other investigated plant species except wheat. Phylogenetically related SaHKT members had similar gene structures, conserved protein domains and cis ‐elements. Expression profiling showed that most SaHKT genes are expressed in specific tissues and are differentially expressed under salt stress. Yeast complementation expression analysis showed that type I members SaHKT1;2, SaHKT1;3 and SaHKT1;8 and type II members SaHKT2;1, SaHKT2;3 and SaHKT2;4 had low‐affinity K + uptake ability...