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Background  Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited.    Results  A total of 64 putative LOX genes were identified in four cotton species ( Gossypium  ( G. hirsutum ,  G. barbadense ,  G .  arboreum , and  G .  raimondii )). In the phylogenetic tree, these genes were clustered into three categories (9-LOX, 13-LOX type I, and 13-LOX type II). Segmental duplication of putative LOX genes was observed between homologues from A2 to A t  and D5 to D t  hinting at allopolyploidy in cultivated tetraploid species ( G. hirsutum  and  G. barbadense) . The structure and motif composition of  GhLOX  genes appears to be relatively conserved among the subfamilies. Moreover, many  cis -acting elements related to growth, stresses, and phytohormone signaling were found in the promoter regions of  GhLOX  genes. Gene expression analysis revealed that all  GhLOX  genes were induced in at least two tissues and the majority of  GhLOX  genes were up-regulated in response to heat and salinity stress. Specific expressions of some genes in response to exogenous phytohormones suggest their potential roles in regulating growth and stress responses. In addition, functional characterization of two candidate genes ( GhLOX12  and  GhLOX13 ) using virus induced gene silencing (VIGS) approach revealed their increased sensitivity to salinity stress in target gene-silenced cotton. Compared with controls, target gene-silenced plants showed significantly higher chlorophyll degradation, higher H 2 O 2 , malondialdehyde (MDA) and proline accumulation but significantly reduced superoxide dismutase (SOD) activity, suggesting their reduced ability to effectively degrade accumulated reactive oxygen species (ROS).    Conclusion  This genome-wide study provides a systematic analysis of the cotton LOX gene family using bioinformatics tools. Differential expression patterns of cotton LOX genes in different tissues and under various abiotic stress conditions provide insights towards understanding the potential functions of candidate genes. Beyond the findings reported here, our study provides a basis for further uncovering the biological roles of LOX genes in cotton development and adaptation to stress conditions.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4985-2) contains supplementary material, which is available to authorized users.

Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses