Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Verification of an introgression line, ‘IL10–1’, with M. incognita-resistance provides the opportunity to unravel the resistance mechanism of cucumber against M. incognita. In the present study, analyses of physiological responses and transcriptional events between IL10–1 (resistant line) and CC3 (susceptible line) were conducted after M. incognita infection. Physiological observations showed abnormal development of giant cells and M. incognita in IL10–1, which were the primary differences compared with CC3. Furthermore, Gene ontology (GO) analysis revealed that genes encoding cell wall proteins were up-regulated in IL10–1 and that the highly expressed lipid transfer protein gene (Csa6G410090) might be the principal regulator of this up-regulation. Simultaneously, analyses of gene expression profiles revealed more auxin-related genes were suppressed in IL10–1 than in those of CC3, which corresponded with the lower level of indole acetic acid (IAA) in the roots of IL10–1 than in those of CC3. Additionally, poor nucleus development as a clear indication of abnormal giant cells in IL10–1 was related to inhibition of the cell cycle. Of those genes related to the cell cycle, the F-box domain Skp2-like genes were down-regulated in IL10–1, whereas more of these genes were up-regulated in CC3. All of these findings indicate that suppressed expression of genes related to auxin and the cell cycle and highly expressed cell wall proteins play important roles in the abnormal development of giant cells, which hinders the development of M. incognita, thereby causing resistance to M. incognita in IL10–1. Knowledge from this research will provide a useful foundation for developing effective strategies in M. incognita-resistance breeding.

GATA transcription factors are a class of transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain, which play important roles in plant growth and development. The GATA gene family has been characterized in various plant species. However, GATA family genes have not been identified in cucumber. In this study, 26 GATA family genes were identified in cucumber genome, whose physicochemical characteristics, chromosomal distributions, phylogenetic tree, gene structures conserved motifs, cis-regulatory elements in promoters, homologous gene pairs, downstream target genes were analyzed. Tissue expression profiles of cucumber GATA family genes exhibited that 17 GATA genes showed constitutive expression, and some GATA genes showed tissue-specific expression patterns. RNA-seq analysis of green and virescent leaves revealed that seven GATA genes might be involved in the chloroplast development and chlorophyll biosynthesis. Importantly, expression patterns analysis of GATA genes in response to abiotic and biotic stresses indicated that some GATA genes respond to either abiotic stress or biotic stress, some GATA genes such as Csa2G162660, Csa3G017200, Csa3G165640, Csa4G646060, Csa5G622830 and Csa6G312540 were simultaneously functional in resistance to abiotic and biotic stresses. Overall, this study will provide useful information for further analysis of the biological functions of GATA factors in cucumber.

GATA transcription factor is crucial for plant growth and development, physiological metabolism, and environmental response, which has been reported in many plants. Although the identification of maize GATA genes has been reported previously, the number of maize GATA genes was incomplete, and the expression patterns of maize GATA genes were not analyzed. Therefore, in this study, the GATA gene family of maize (Zea mays L.) was systematically analyzed. Forty-one GATA family genes were identified in the maize and were divided into four groups. The gene structure of each subgroup was basically consistent with that of the motif. The maize GATA genes were distributed on 10 chromosomes, including 3 and 17 pairs of tandem and segmental duplication genes, respectively. Fourteen types of cis-acting elements were identified in the promoter sequences of maize GATA family genes, involving four categories: light response, stress, hormone, and growth and development. The tissue-specific expression analysis of maize GATA family genes revealed that 4 GATA genes were highly expressed in almost all the maize tissues, and 11 GATA genes were not expressed in almost all tissues. The other maize GATA family genes showed a tissue-specific expression pattern. The results of RNA-seq reanalysis of publicly available transcriptome sequencing big data revealed that the gene ZmGATA37 was significantly down-regulated in response to abiotic stresses including high temperature, low temperature, drought, waterlogging, and salt, and significantly up-regulated in response to biotic stresses including smut disease, Maize Iranian mosaic virus infection, beet armyworm and aphid infestations. This indicated that the ZmGATA37 gene plays an important role in maize growth and development. Our findings offer new insight into the potential role of GATA transcription factors in abiotic and biotic stresses and provide a theoretical groundwork for the molecular mechanisms underlying maize adaptation to such stress.

Dirigent proteins (DIR) play important roles in the biosynthesis of lignins and lignans, defensive responses, secondary metabolism, and disease resistance in plants. The DIR gene family has been identified and studied in many plants. However, the identification of DIR gene family in eggplant has not been conducted yet. Therefore, in this study, based on the available genome information of eggplant, the DIR family genes in eggplant were identified with bioinformatics methods. The expression pattern analyses of eggplant DIR family genes in different organs and stresses were also conducted to understand their biological functions. The results showed that a total of 24 DIR genes were identified in the eggplant, which were divided into three subfamilies (DIR-a, DIR-b/d, and DIR-e). Synteny analysis of DIR genes among eggplant, Arabidopsis, and rice showed that 15 eggplant DIR genes were colinear with 18 Arabidopsis DIR genes, and 16 eggplant DIR genes were colinear with 15 rice DIR genes. Phylogenetic tree analysis showed that 19 pairs of orthologous genes were identified between eggplant and pepper. The cis-acting elements analysis implied that the eggplant DIR genes contained a lot of cis-elements associated with stress and hormone response. The organ-specific expression analysis of eggplant DIR family genes revealed that only the SmDIR3 gene was highly expressed in all the 19 organs of eggplant. Some SmDIR genes, including SmDIR7, SmDIR8, SmDIR11, SmDIR14, SmDIR18, SmDIR19, SmDIR20, and SmDIR23, were not or were lowly expressed in the eggplant organs, while the other eggplant DIR family genes showed an organ-specific expression pattern. Furthermore, 19 of 24 SmDIR genes were differentially expressed in response to abiotic and biotic stresses. 5 SmDIR genes, including SmDIR3, SmDIR5, SmDIR6, SmDIR12, and SmDIR22, were differentially expressed under multiple types of abiotic and biotic stresses. Especially notable, the SmDIR22 gene was differentially expressed under three types of abiotic stresses and two types of biotic stresses, which indicated that the SmDIR22 gene plays an important role in the response to abiotic and biotic stresses. These results provide valuable evidence for a better understanding of the biological role of DIR genes in eggplant.

The FKBP (FK506-binding protein) gene family is an important member of the PPlase protease family and plays a vital role during the processes of plant growth and development. However, no studies of the FKBP gene family have been reported in cucumber. In this study, 19 FKBP genes were identified in cucumber, which were located on chromosomes 1, 3, 4, 6, and 7. Phylogenetic analysis divided the cucumber FKBP genes into three subgroups. The FKBP genes in the same subgroup exhibited similar structures and conserved motifs. The cis-acting elements analysis revealed that the promoters of cucumber FKBP genes contained hormone-, stress-, and development-related cis-acting elements. Synteny analysis of the FKBP genes among cucumber, Arabidopsis, and rice showed that 12 kinds of syntenic relationships were detected between cucumber and Arabidopsis FKBP genes, and 3 kinds of syntenic relationships were observed between cucumber and rice FKBP genes. The tissue-specific expression analysis showed that some FKBP genes were expressed in all tissues, while others were only highly expressed in part of the 10 types of tissues. The expression profile analysis of cucumber FKBP genes under 13 types of stresses showed that the CsaV3_1G007080 gene was differentially expressed under abiotic stresses (high temperature, NaCl, silicon, and photoperiod) and biotic stresses (downy mildew, green mottle mosaic virus, Fusarium wilt, phytophthora capsica, angular leaf spot, and root-knot nematode), which indicated that the CsaV3_1G007080 gene plays an important role in the growth and development of cucumber. The interaction protein analysis showed that most of the proteins in the FKBP gene family interacted with each other. The results of this study will lay the foundation for further research on the molecular biological functions of the cucumber FKBP gene family.