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Open Access Highly Accessed Research article

Deep sequencing–based comparative transcriptional profiles of Cymbidium hybridum roots in response to mycorrhizal and non-mycorrhizal beneficial fungi

Xiaolan Zhao1, Jianxia Zhang2, Chunli Chen1, Jingze Yang1, Haiyan Zhu1, Min Liu1 and Fubing Lv3*

Author Affiliations

1 Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou 510642, People’s Republic of China

2 Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou 510650, People’s Republic of China

3 Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, East 1st Street 1, Jinying Road, Tianhe District, Guangzhou 510640, People’s Republic of China

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BMC Genomics 2014, 15:747  doi:10.1186/1471-2164-15-747

Published: 31 August 2014



The Orchidaceae is one of the largest families in the plant kingdom and orchid mycorrhizae (OM) are indispensable in the life cycle of all orchids under natural conditions. In spite of this, little is known concerning the mechanisms underlying orchid- mycorrhizal fungi interactions. Our previous work demonstrated that the non-mycorrhizal fungus Umbelopsis nana ZH3A-3 could improve the symbiotic effects of orchid mycorrhizal fungus Epulorhiza repens ML01 by co-cultivation with Cymbidium hybridum plantlets. Thus, we investigated the C. hybridum transcript profile associated with different beneficial fungi.


More than 54,993,972 clean reads were obtained from un-normalized cDNA library prepared from fungal- and mock- treated Cymbidium roots at four time points using RNA-seq technology. These reads were assembled into 16,798 unique transcripts, with a mean length of 1127 bp. A total of 10,971 (65.31%) sequences were annotated based on BLASTX results and over ninety percent of which were assigned to plant origin. The digital gene expression profiles in Cymbidium root at 15 days post inoculation revealed that 1674, 845 and 1743 genes were sigificantly regulated in response to ML01, ZH3A-3 and ML01+ ZH3A-3 treatments, respectively. Twenty-six genes in different regulation patterns were validated using quantitative RT-PCR. Our analysis showed that general defense responses were co- induced by three treatments, including cell wall modification, reactive oxygen species detoxification, secondary biosynthesis and hormone balance. Genes involved in phosphate transport and root morphogenesis were also detected to be up-regulated collectively. Among the OM specifically induced transcripts, genes related to signaling, protein metabolism and processing, defense, transport and auxin response were identifed. Aside from these orchid transcripts, some putative fungal genes were also identified in symbiotic roots related to plant cell wall degradation, remodeling the fungal cell wall and nutrient transport.


The orchid root transcriptome will facilitate our understanding of orchid - associated biological mechanism. The comparative expression profiling revealed that the transcriptional reprogramming by OM symbiosis generally overlapped that of arbuscular mycorrhizas and ectomycorrhizas. The molecular basis of OM formation and function will improve our knowledge of plant- mycorrhzial fungi interactions, and their effects on plant and fungal growth, development and differentiation.

Root transcriptome; Digital gene expression; Plant mycorrhizal symbiosis; Cymbidium hybridum; Epulorhiza repens ML01; Umbelopsis nana ZH3A-3