Total RNA of wild-type R108 and Mtphr2 was extracted from the mycorrhizal roots using TRIzol® Reagent. Three technical replicates were used for each sample. RNA samples were sequenced at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) using Illumina Novaseq 6000 platform. RNA-seq data were aligned and assembled to Medicago truncatula genome v4.0 using HISAT2 and StringTie software (Kim et al., 2015; Pertea et al., 2015).