Comparative transcriptome analysis between Solanum lycopersicum L. and Lotus japonicus L. during arbuscular mycorrhizal development

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with diverse plant species. The AM fungi enhance mineral uptake from the soil, which benefits the growth of the host plants. Previous microarray and RNA-seq analyses have identified a large number of AM-responsive plant genes. However, little is known whether the gene expression profile of mycorrhiza is different among genetically distant plant species. The aim of this study was to assess the conservation and divergence of AM-responsive genes between two different hosts, Solanum lycopersicum L. and Lotus japonicus L., during AM development using RNA-seq data. In each host plant, gene expression was compared between AM roots and non-mycorrhizal (NM) roots. Potential orthologs of AM-responsible genes between S. lycopersicum and L. japonicus were identified with reciprocal BLAST searches. Only one quarter to one third of the AM-inducible genes in each plant species were co-upregulated in both species. The co-upregulated genes included those known to be essential for AM development and function. The co-upregulated genes exhibited a wide range of fold changes in the AM symbiosis, and the fold change value for individual co-upregulated genes was positively correlated between the two hosts. Most of the species-dependent upregulated genes exhibited low levels of induction. We also analyzed gene expression in AM fungi colonizing roots of S. lycopersicum and L. japonicus. Overall, the gene expression profiles of Rhizophagus irregularis were similar among the roots of the two different hosts, although hundreds of fungal genes were differentially expressed between the two hosts. In particular, genes related to the mitochondrial electron transport chain were highly expressed in AM fungi colonizing L. japonicus roots, indicating that adenosine triphosphate (ATP) production was enhanced in the L. japonicus-R. irregularis symbiosis. Overall, these results show that a certain proportion of AM-responsive genes is conserved across plant species. The species-dependent AM-responsive genes may be related to the physiological differences between AM and NM roots in each plant species.