Genome-wide identification and characterization of the homeodomain-leucine zipper I family of genes in cotton (Gossypium spp.)

Homeodomain-leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom and are classified into four subfamilies, HD-Zip I to IV. This gene family has been extensively investigated in several plant species and many members have been shown to play important roles in plant development and in response to abiotic/biotic stresses. In cotton, several HD-Zip IV genes have been identified and their function investigated, but little is known about the HD-Zip I genes. Here, we performed a genome-wide survey and identified 72, 30 and 34 HD-Zip I genes in Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, respectively. Almost all G. arboreum and G. raimondii HD-Zip I genes were retained in allotetraploid G. hirsutum, and new HD-Zip I genes were evolved in G. hirsutum after polyploidization, probably through tandem and/or segmental duplication. Most HD-Zip I genes were under purifying selection although some could have undergone positive selection. Small indels and nonreciprocal homoeologous recombination (NRHR) events also played a role in shaping the HD-Zip I genes in G. hirsutum. Most HD-Zip I genes were preferentially expressed in certain tissues. Differential expression of homoeologues was observed but the differences were generally less than that between different genes. Three HD-Zip I genes were found to have a consistent response in G. hirsutum and G. barbadense cultivars resistant to Verticillium dahliae (Vd) following Vd-infection. Our results provided a comprehensive view of the cotton HD-Zip I genes and fundamental information for further research towards understanding the role of HD-Zip I genes in cotton.