Allene oxide cyclase (AOC, EC 5.3.99.6) catalyzes the most important step in the jasmonic acid (JA) biosynthetic pathway and mediates plant defense response to a wide range of biotic and abiotic stresses. In this study, two AOC genes were identified from watermelon. Sequence analysis revealed that each of ClAOC1 and ClAOC2 contained an allene oxide cyclase domain and comprised eight highly conserved β-strands, which are the typical characteristics of AOC proteins. Phylogenetic analysis showed that ClAOC1 and ClAOC2 were clustered together with AOCs from dicotyledon, with the closest relationships with JcAOC from Jatropha curcas and Ljaoc1 from Lotus japonicus. Different intron numbers were observed in ClAOC1 and ClAOC2, which may result in their functional divergence. qRT-PCR analysis revealed that ClAOC1 and ClAOC2 have specific and complex expression patterns in multiple organs and under hormone treatments. Both ClAOC1 and ClAOC2 displayed the highest transcriptional levels in stem apex and fruit and exhibited relatively lower expression in stem. JA, salicylic acid (SA), and ethylene (ET) could enhance the expression of ClAOC1 and ClAOC2, particularly that of ClAOC2. Red light could induce the expression of ClAOC2 in root-knot nematode infected leaf and root of watermelon, indicating that ClAOC2 might play a primary role in red light-induced resistance against root-knot nematodes through JA signal pathway. These findings provide important information for further research on AOC genes in watermelon.Agriculture 2019, 9, 225 2 of 12 AOC genes were found to have specific and complicated tissue expression patterns in different plants. In barley, HvAOC mRNA accumulation is abundant in root tip, scutellar node, and leaf base [13]. Soybean GmAOC1 and GmAOC2 also exhibited abundant mRNA transcripts in roots, while GmAOC3 and GmAOC4 showed relatively higher expression in leaves and stems, respectively [7]. Camptotheca acuminata CaAOC is constitutively expressed in various organs, with the highest expression level in leaves [14]. In Arabidopsis, AtAOC1, AtAOC2, and AtAOC3 promoters exhibit high activities in the leaves, while only AtAOC3 and AtAOC4 show promoter activity in roots [15]. These results suggest that AOC genes are involved in the regulation of multiple plant developmental processes.The expression of jasmonate biosynthetic pathway genes, including AOCs, is regulated by JA, and overexpression or suppression of these genes can greatly affect the JA levels in plants. For example, a severe deficiency of jasmonate was found in two AOC mutants (cpm2 and hebiba) of rice [12], and partial suppression of MtAOC1 in hairy roots of Medicago truncatula also resulted in lower JA levels in mycorrhizal roots [16]. In addition, elevated JA levels were found in transgenic plants overexpressing AOC genes from different plants, such as AaAOC from Artemisia annua [5], TaAOC1 from wheat [17], and GmAOC3 from soybean [18]. JA and its related compounds are involved in plant defense reactions against biotic and abiotic stresses, and th...