Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses

Abstract

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.

Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.

“…8 ). Specifically, these sequences were obtained from tobacco, potato, eggplant [ 16 ], cotton [ 5 ] and Arabidopsis [ 3 ] (Additional file 5: Table S5 ). The phylogenetic reconstruction delineated the evolutionary clustering of the DIR gene family into three discernible subfamilies.…”

“…DIR gene family members are widely distributed in various plant species. Advances in genome sequencing technology have facilitated the identification of DIR genes in several plant genomes, including Arabidopsis [ 3 ], Capsicum annuum [ 15 ], Solanum lycopersicum [ 1 ], Solanum melongena [ 16 ], Oryza sativa [ 11 , 17 ], Hordeum vulgare [ 18 ] and Glycine max [ 14 ]. In this study, a total of 57 NtDIRs in tobacco and 33 StDIRs in potato were identified.…”

“…Generally, the evolution of gene families is predominantly determined by the organization of gene structures, whereas within a gene family, members of the same subfamily typically exhibit high conservation in both structure and function, reflecting their evolutionary relatedness [ 32 ]. Notably, analysis of the DIR genes across three distinct subgroups revealed significant structural divergence, while members in the same subgroups displayed conserved gene structure and motifs [ 16 , 33 ]. These observations highlight the complexity of the tobacco and potato genomes and the differentiation and diversity of the function within the DIR gene family.…”

“…Similarly, in pepper ( Capsicum annuum ), 24 DIR genes have been reported [ 15 ]. A study on tomato ( Solanum lycopersicum ) identified 31 DIR genes [ 1 ], while 24 DIR genes were found in eggplant ( Solanum melongena L.) [ 16 ]. Additionally, a total of 54 rice DIR genes were found in rice ( Oryza sativa ) [ 11 , 17 ], 64 DIR genes in barley ( Hordeum vulgare ) [ 18 ], and 54 DIR genes in soybean ( Glycine max ) [ 14 ].…”

Genome-wide identification, characterization, evolution and expression analysis of the DIR gene family in potato (Solanum tuberosum)

“…The inception of dirigent ( DIR ) genes dates back to 1985, when they were initially characterized in pea ( Pisum sativum ). But the function of DIR proteins were first identified in Forsythia intermedia in 1997, and then was later reported in Arabidopsis ( Arabidopsis thaliana ) ( Ralph et al, 2006 ; Cheng et al, 2018 ; Zhang et al, 2022 ; Luo et al, 2022 ). DIR belongs to a multi-gene family.…”