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Yan et al. BMC Genomics (2021) 22:315 https://doi.org/10.1186/s12864-021-07623-RESEARCH ARTICLEOpen AccessGenome-wide analysis of ATP-binding cassette transporter gives insight to genes associated to bioactive metabolite transportation in Salvia miltiorrhizaLi Yan, Jianhong Zhang, Hongyu Chen and Hongmei LuoAbstractBackground: ATP-binding cassette (ABC) transporters have already been identified to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic compounds. Salvia miltiorrhiza Bunge, known as Danshen in regular Chinese medicine, can be a very valued medicinal plant made use of to treat cardiovascular and cerebrovascular illnesses. The dry roots and rhizomes of S. miltiorrhiza include biologically active secondary metabolites of tanshinone and salvianolic acid. Provided an assembled and annotated genome and also a set of transcriptome data of S. miltiorrhiza, we analysed and identified the candidate genes that probably involved in the bioactive metabolite transportation of this medicinal plant, starting with all the members of your ABC transporter family. Final results: A total of 114 genes encoding ABC transporters were identified within the genome of S. miltiorrhiza. All of these ABC genes had been divided into eight subfamilies: 3ABCA, 31ABCB, 14ABCC, 2ABCD, 1ABCE, 7ABCF, 46ABCG, and ten ABCI. Gene expression analysis revealed tissue-specific expression profiles of those ABC transporters. In certain, we located 18 very expressed transporters in the roots of S. miltiorrhiza, which could be involved in transporting the bioactive compounds of this medicinal plant. We additional investigated the co-expression profiling of these 18 genes with essential enzyme genes involved in tanshinone and salvianolic acid biosynthetic pathways utilizing quantitative reverse transcription polymerase chain reaction (RT-qPCR). From this RT-qPCR validation, we identified that 3 ABC genes (SmABCG46, SmABCG40, and SmABCG4) and a further gene (SmABCC1) co-expressed together with the key biosynthetic enzymes of those two compounds, respectively, and hence might be involved in tanshinone and salvianolic acid transport in root cells. In addition, we predicted the biological functions of S. miltiorrhiza ABC transporters working with phylogenetic relationships and evaluation from the tra.