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This study investigated the function of three ubiquitin specific protease subfamilies (UBP15-19, UBP12/13 and UBP3/4) in Arabidopsis thaliana via reverse genetic analysis. In the investigation of the UBP15-19 subfamily, T-DNA insertion lines were utilized to determine phenotypic characteristics compared to wild-type individuals, such as reduced inflorescence, leaf, flower and silique size. Phenotypic alterations were also detected that affected development and reproduction. A phylogenetic analysis of this subfamily uncovered three subgroups in the monocotyledonous and dicotyledonous plants, but a single group in the mosses suggested that subgroup evolution began prior to the separation of dicots and monocots but following the divergence of the monocot/dicot lineage from the mosses. Interestingly, these studies indicated that some members of the UBP15-19 subfamily perform specific functions whereas others share a level of redundancy with family members. The UBP12/13 subfamily was found to be important throughout plant development in that mutant individuals displayed abnormalities in embryo development, seed germination, plant growth and reproduction. Embryonic development during seed maturation was affected, double homozygous mutant seeds displayed a shortened half life, and the resulting plants developed into dwarfs that rarely produced seeds. The myristoylation of UBP3 was determined to be essential for its gene-specific functions; however the addition of various C-terminal extensions to UBP3 were tolerated. This suggested that a precise cellular localization is essential for UBP3-specific functions. Thus UBPs are important in Arabidopsis at many stages of growth and development.