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

Abstract

BackgroundThe 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.ResultsMore 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-747) contains supplementary material, which is available to authorized users.

Symbiont modulates expression of specific gene categories in Angomonas deanei

“…2A-B). The influence of symbionts in host gene expression has been shown in other symbiotic associations (Lehnert et al 2012, 2014, Kodama et al 2014, Zhao et al 2014). Comparative transcriptional analysis performed in orchid Cymbidium hybridum in the presence or absence of the mycorrhizal fungus showed that the symbiont positively influences plant gene expression.…”

“…The influence of symbionts on host gene expression has been studied in several other organisms: in flowering plants, the association with glomeromycotan fungi; in coral, the association of cnidarians with algae; and in lichens, the association with algae and fungi (Oldroyd et al 2009, Devers et al 2011, Junttila & Rudd 2012, Lehnert et al 2014, Zhao et al 2014). However, these studies are limited to taxonomically distinct groups of symbionts and carried out using either less robust large-scale RNA sequencing or only quantitative polymerase chain reaction (qPCR) techniques.…”

A mixotrophy is in question: new data on fungal community associated with photosynthetic terrestrial orchid Goodyera repens

“…Suppression of both bacteria and micromycetes was shown for root endophyte fungal species of Orchidaceae. They can also contribute to host plant fitness and successful establish ment of symbiotic relationships (Chen et al 2012, Zhao et al 2014. Another RAF species from G. repens roots, Verti cil lium leptobactrum, turned out to be active against plant pa tho genic nematodes and possesses a high biocontrol poten tial for agriculture (Hajji et al 2017).…”

“…Besides the mycobionts forming intracellular symbiotic interface within root cells, hyphal coils known as pelotons, orchids harbour a plethora of fungal root endophytes, sometimes referred as RAF (root-associated fungi), showing no specific intraradical structures (Bayman & Otero 2006, Kohout et al 2013. The interactions of such fungi with host plants are mostly unrevealed, but there are some reports on their plant-beneficial role due to ac ti vity against phytopathogenic microfungi and bacteria (Chen et al 2012, Zhao et al 2014. Another unique feature of orchid mycorrhiza is that despite of the complicated symbiotic contact zone and fine-tuned interactions between partners, there are no particular "orchid mycorrhizal fun gi" at all.…”

Transcriptome responses of grafted Citrus sinensis plants to inoculation with the arbuscular mycorrhizal fungus Glomus versiforme

“…AM inoculation leads to increased disease resistance and higher activities/ increased abundance of antioxidant enzymes, stress-responsive proteins, defensive enzymes, chitinase, specific lectins and increased concentrations of some plant hormones (Foo et al 2014;Zhao et al 2014;Xiao et al 2015).…”