title: Characterization and expression analysis of genes encoding ubiquitin conjugating domain-containing enzymes in Carica papaya.
abstract: BACKGROUND
  Ripening affects the quality and nutritional contents of fleshy fruits and is a crucial process of fruit development. Although several studies have suggested that ubiquitin-conjugating enzyme (E2s or UBC enzymes) are involved in the regulation of fruit ripening, little is known about the function of E2s in papaya (Carica papaya).
  
  
  RESULTS
  In the present study, we searched the papaya genome and identified 34 putative UBC genes, which were clustered into 17 phylogenetic subgroups. We also analyzed the nucleotide sequences of the papaya UBC (CpUBC) genes and found that both exon-intron junctions and sequence motifs were highly conserved among the phylogenetic subgroups. Using real-time PCR analysis, we also found that all the CpUBC genes were expressed in roots, stems, leaves, male and female flowers, and mature fruit, although the expression of some of the genes was increased or decreased in one or several specific organs. We also found that the expression of 13 and two CpUBC genes were incresesd or decreased during one and two ripening stages, respectively. Expression analyses indicates possible E2s playing a more significant role in fruit ripening for further studies.
  
  
  CONCLUSIONS
  To the best of our knowledge, this is the first reported genome-wide analysis of the papaya UBC gene family, and the results will facilitate further investigation of the roles of UBC genes in fruit ripening and will aide in the functional validation of UBC genes in papaya.
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Dengwei
authors.initials: D
authors.lastname: Jue
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Xuelian
authors.initials: X
authors.lastname: Sang
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Shu
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Liqin
authors.initials: L
authors.lastname: Liu
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Yicheng
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Jia
authors.affiliation: Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zou
authors.affiliation: Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
authors.forename: Shengyou
authors.initials: S
authors.lastname: Shi
mesh_terms: D000595:Amino Acid Sequence; D029441:Carica / Q000737:chemistry / Q000235:genetics* / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000032:analysis / Q000235:genetics*; D016415:Sequence Alignment; D044763:Ubiquitin-Conjugating Enzymes / Q000032:analysis / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D044763:Ubiquitin-Conjugating Enzymes