Agronomy and Horticulture Department


Date of this Version



Published in The Plant Genome 6:2 (2013), pp. 1–13. doi: 10.3835/plantgenome2012.06.0007


Copyright (c) D. Ruzicka, et al.


Associations between arbuscular mycorrhizal (AM) fungi and plants are an ancient and widespread plant microbe symbioses. Most land plants can associate with this specialized group of soil fungi (in the Glomeromycota), which enhance plant nutrient uptake in return for C derived from plant photosynthesis. Elucidating the mechanisms involved in the symbiosis between obligate symbionts such as AM fungi and plant roots is challenging because AM fungal transcripts in roots are in low abundance and reference genomes for the fungi have not been available. A deep sequencing metatranscriptomics approach was applied to a wild-type tomato and a tomato mutant (Solanum lycopersicum L. cultivar RioGrande 76R) incapable of supporting a functional AM symbiosis, revealing novel AM fungal and microbial transcripts expressed in colonized roots. We confirm transcripts known to be mycorrhiza associated and report the discovery of more than 500 AM fungal and novel plant transcripts associated with mycorrhizal tomato roots including putative Zn, Fe, aquaporin, and carbohydrate transporters as well as mycorrhizal-associated alternative gene splicing. This analysis provides a fundamental step toward identifying the molecular mechanisms of mineral and carbohydrate exchange during the symbiosis. The utility of this metatranscriptomic approach to explore an obligate biotrophic interaction is illustrated, especially as it relates to agriculturally relevant biological processes.

Schachtman PG 2013 Inside Arbuscular Mycorrhizal Roots SUPPL 1.xls (36 kB)
SupplementTable1.xls Table of primer sequences used for qRT‐PCR.

Schachtman PG 2013 Inside Arbuscular Mycorrhizal Roots SUPPL 2.xlsx (11 kB)
SupplementTable2.xls Table summarizing PCR results for sequence assemblies tested with qPCR.

Schachtman PG 2013 Inside Arbuscular Mycorrhizal Roots SUPPL 3.xlsx (4797 kB)
SupplementTable3.xls Summary table of all 30,063 sequence assemblies. Columns include contig name, total number of sequence reads, contig length, number of sequence reads in each tissue sample, NCBI BLAST results, putative sequence annotation, and GMAP alignment results.