title: RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.
abstract: Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis.
authors.affiliation: Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Handa
authors.affiliation: Data Integration and Analysis Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.
authors.forename: Hiroyo
authors.initials: H
authors.lastname: Nishide
authors.affiliation: Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
authors.forename: Naoya
authors.initials: N
authors.lastname: Takeda
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Kawaguchi
authors.affiliation: Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan saitok@shinshu-u.ac.jp.
authors.forename: Katsuharu
authors.initials: K
authors.lastname: Saito
mesh_terms: D001483:Base Sequence; D005656:Fungal Proteins / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D055137:Glomeromycota / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D000070116:Lotus / Q000235:genetics* / Q000382:microbiology; D008969:Molecular Sequence Data; D038821:Mycorrhizae / Q000502:physiology*; D010940:Plant Proteins / Q000235:genetics; D018517:Plant Roots / Q000235:genetics / Q000382:microbiology; D012331:RNA, Fungal / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D053204:Root Nodules, Plant / Q000235:genetics / Q000382:microbiology; D036226:Seedlings / Q000235:genetics / Q000382:microbiology; D017423:Sequence Analysis, RNA; D013559:Symbiosis; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D005656:Fungal Proteins; D010940:Plant Proteins; D012331:RNA, Fungal; D018749:RNA, Plant; D014157:Transcription Factors
keywords: Arbuscular mycorrhiza; Lotus japonicus; Rhizophagus irregularis; Root nodule; Symbiosis; Transcriptome