Abstract
Ripening affects the nutritional contents and quality of fleshy fruits, and it plays an important role during the process of fruit development. Studies have demonstrated that ubiquitin-conjugating (UBC or E2) genes can regulate fruit ripening, but the characterization of UBCs in pear is not well documented. The recently published genome-wide sequences of Pyrus bretschneideri and Pyrus communis have allowed a comprehensive analysis of this important gene family in pear. Using bioinformatics approaches, we identified 83 (PbrUBCs) and 84 (PcpUBCs) genes from P. bretschneideri and P. communis, respectively, which were divided into 13 subfamilies. In total, 198 PbrUBC paralogous, 215 PcpUBC paralogous, and 129 orthologous gene pairs were detected. Some paralogous gene pairs were found to be distributed on the same chromosome, suggesting that these paralogs may be caused by tandem duplications. The expression patterns of most UBC genes were divergent between Pyrus bretschneideri and Pyrus communis during pear fruit development. Remarkably, the transcriptome data showed that UBC genes might play a more important role in fruit ripening for further study. This is the first report on the systematic analysis of two Pyrus UBC gene families, and these data will help further study the role of UBC genes in fruit development and ripening, as well as contribute to the functional verification of UBC genes in pear.
Highlights
Ubiquitination is an essential cellular process for eukaryotes [1]
We identified 83 and 84 putative UBC proteins in the P. bretschneideri and P. communis genome, named PbrUBC01-83 and PcpUBC01-84 according to their order on the chromosomes, respectively
As a part of the ubiquitin proteasome system, ubiquitin-conjugating enzymes have been proved to play an important role in plant growth and development [1,11,21]
Summary
Ubiquitination is an essential cellular process for eukaryotes [1]. The ubiquitin proteasome pathway involves many aspects of eukaryotic cell regulation because of its ability to degrade intracellular proteins [2,3]. E2s act in the middle step of the protein ubiquitination pathway [4]. Previous reports suggested that the E2 family members have a certain degree of expansion during evolution, for example, more ancestral eukaryotes such as algae have fewer E2 enzymes (< or =20) than certain plants and animals (>40) [5]. The Saccharomyces cerevisiae genome encodes 13 UBC proteins [6]; 19, 18, and 12 UBC proteins are identified in the algae Chlamydomonas reinhardtii, Micromonas sp. RCC299, and Ostreococcus, respectively; 20 in Caenorhabditis elegans [7]; and 75, 74, 52, 48, 34, and 37 UBC proteins in Zea mays, Musa nana, Solanum lycopersicum, Oryza sativa, Carica papaya, and A. thaliana, respectively [1,8,9,10,11,12]
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