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Background  During fresh fruit consumption, sensory texture is one factor that affects the organoleptic qualities. Chemical components of plant cell walls, including pectin, cellulose, hemicellulose and lignin, play central roles in determining the textural qualities. To explore the genes and regulatory pathways involved in fresh citrus’ perceived sensory texture, we performed mRNA-seq analyses of the segment membranes of two citrus cultivars, Shiranui and Kiyomi, with different organoleptic textures.    Results  Segment membranes were sampled at two developmental stages of citrus fruit, the beginning and end of the expansion period. More than 3000 differentially expressed genes were identified. The gene ontology analysis revealed that more categories were significantly enriched in ‘Shiranui’ than in ‘Kiyomi’ at both developmental stages. In total, 108 significantly enriched pathways were obtained, with most belonging to metabolism. A detailed transcriptomic analysis revealed potential critical genes involved in the metabolism of cell wall structures, for example,  GAUT4  in pectin synthesis,  CESA1 ,  3  and  6 , and  SUS4  in cellulose synthesis,  CSLC5 ,  XXT1  and  XXT2  in hemicellulose synthesis, and  CSE  in lignin synthesis. Low levels, or no expression, of genes involved in cellulose and hemicellulose, such as  CESA4, CESA7 ,  CESA8 ,  IRX9  and  IRX14 , confirmed that secondary cell walls were negligible or absent in citrus segment membranes. A chemical component analysis of the segment membranes from mature fruit revealed that the pectin, cellulose and lignin contents, and the segment membrane’s weight (% of segment) were greater in ‘Kiyomi’.    Conclusion  Organoleptic quality of citrus is easily overlooked. It is mainly determined by sensory texture perceived in citrus segment membrane properties. We performed mRNA-seq analyses of citrus segment membranes to explore the genes and regulatory pathways involved in fresh citrus’ perceived sensory texture. Transcriptomic data showed high repeatability between two independent biological replicates. The expression levels of genes involved in cell wall structure metabolism, including pectin, cellulose, hemicellulose and lignin, were investigated. Meanwhile, chemical component contents of the segment membranes from mature fruit were analyzed. This study provided detailed transcriptional regulatory profiles of different organoleptic citrus qualities and integrated insights into the mechanisms affecting citrus’ sensory texture.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4669-y) contains supplementary material, which is available to authorized users.

Transcriptomic insights into citrus segment membrane’s cell wall components relating to fruit sensory texture