In eukaryotic systems, messenger RNA regulations, including splicing, 3′-end formation, editing, localization, and translation, are achieved by different RNA-binding proteins and noncoding RNAs. The YTH domain is a newly identified RNA-binding domain that was identified by comparing its sequence with that of splicing factor YT521-B. Previous study showed that the YTH gene plays an important role in plant resistance to abiotic and biotic stress. In this study, 211 YTH genes were identified in 26 species that represent four major plant lineages. Phylogenetic analysis revealed that these genes could be divided into eight subgroups. All of the YTH genes contain a YT521 domain and have different structures. Ten YTH genes were identified in navel orange (Citrus sinensis). The expression profiles of these CitYTH genes were analyzed in different tissues and at different fruit developmental stages, and CitYTH genes displayed distinct expression patterns under heat, cold, salt, and drought stress. Furthermore, expression of the CitYTH genes in response to exogenous hormones was measured. Nuclear localization was also confirmed for five of the proteins encoded by these genes after transient expression in Nicotiana benthamiana cells. This study provides valuable information on the role of CitYTHs in the signaling pathways involved in environmental stress responses in Citrus.

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A complex molecular regulatory network plays an important role in the development and ripening of fruits and leads to significant differences in apparent characteristics. Comparative transcriptome and sRNAome analyses were performed to reveal the regulatory mechanisms of fruit ripening in a spontaneous early-ripening navel orange mutant (‘Ganqi 4’, Citrus sinensis L. Osbeck) and its wild type (‘Newhall’ navel orange) in this study. At the transcript level, a total of 10792 genes were found to be differentially expressed between MT and WT at the four fruit development stages by RNA-Seq. Additionally, a total of 441 differentially expressed miRNAs were found in the four periods, and some of them belong to 15 families. An integrative analysis of the transcriptome and sRNAome data revealed some factors that regulate the mechanisms of formation of early-ripening traits. First, secondary metabolic materials, especially endogenous hormones, carotenoids, cellulose and pectin, obviously changed during fruit ripening in MT and WT. Second, we found a large number of differentially expressed genes (PP2C, SnRK, JAZ, ARF, PG, and PE) involved in plant hormone signal transduction and starch and sucrose metabolism, which suggests the importance of these metabolic pathways during fruit ripening. Third, the expression patterns of several key miRNAs and their target genes during citrus fruit development and ripening stages were examined. csi-miR156, csi-miR160, csi-miR397, csi-miR3954, and miRN106 suppressed specific transcription factors (SPLs, ARFs, NACs, LACs, and TCPs) that are thought to be important regulators involved in citrus fruit development and ripening. In the present study, we analyzed ripening-related regulatory factors from multiple perspectives and provide new insights into the molecular mechanisms that operate in the early-ripening navel orange mutant ‘Ganqi 4’.