Abstract: In order to analyze the molecular mechanism of efficient manganese removal by acid-resis⁃ tant Rhodotorula MF4 in acid mine drainage，aiming at the problems of low efficiency and high cost of tra⁃ ditional manganese pollution control methods，the genes related to manganese metabolism are screened by whole genome sequencing and bioinformatics analysis system，and their functions are analyzed.The genom⁃ ic library is constructed based on the Illumina sequencing platform，and the genome assembly is completed by combining FastQC、SPAdes and other tools. A 20.07 Mb genome（GC content 60.29%）is obtained， and the BUSCO integrity is 97.3%. Through blastp alignment and hmmer domain screening，16 key genes （87 scaffolds）are identified，including SMF1、PHO84、MTM1，etc.，involving manganese transport，de⁃ toxification and tolerance functions.Subcellular localization shows that the related genes are distributed in the plasma membrane，mitochondria，nucleus and other regions，and the multi-copy genes shows func⁃ tional diversity. GO and KEGG annotations shows that the candidate genes are mainly involved in energy metabolism，ion transport and stress response.PHO84 mediates transmembrane transport through ATPase， and MTM1 is involved in mitochondrial solute carrier metabolism. Studies have shown that Rhodotorula MF4 achieves efficient manganese removal by synergistically regulating the dynamic balance and energy metabolism of manganese ions through multiple genes，which can provide a molecular theoretical basis for the optimization of AMD bioremediation technology and the construction of manganese-resistant engineer⁃ ing strains.

Key words: Rhodotorula MF4, acid mine drainage, manganese metabolism genes, whole genome se? quencing, bioinformatics analysis, bioremediation