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This study deals with specialized roots of cycads called coralloid roots accommodating a small population of heterotrophic bacteria and significantly abundant endosymbiotic cyanobacteria functioning as nitrogen fixers. This paper aimed to identify what other genes are present in the coralloid roots aside from genes for nitrogen metabolism to determine the functional repertoire of symbiotic coralloid roots. Genomic functional gene profiles were examined using DNA-based microarray GeoChip 5.0. GeoChip analysis suggests that the functional profiles between the two species are highly identical and almost all identified genes present in the coralloid roots were similar. Functional gene inventory identified elevated gene signals for metal homeostasis, carbon metabolism, stress responses, antibiotic resistance, organic contaminant degradation and nitrogen metabolism. This supports the role of symbionts residing in coralloid roots as nitrogen fixers and in increasing host tolerance to various environmental stressors as most genes covering major pathways for nitrogen cycling, metal resistance and toxin degradation were detected in our study. Moreover, indications of active photosynthesis and carbon fixing potential of symbionts in coralloid roots were also evident due to the detection of various carbon cycling genes. This could probably be associated to its apogeotropic growth via phototropism suggesting that symbionts require access to sunlight causing the negative geotropic growth of coralloid roots. [ABSTRACT FROM AUTHOR]