Genome-wide identification and characterization of the TIFY gene family in kiwifruit

Abstract

Background The TIFY gene family is a group of plant-specific transcription factors involved in regulation of plant growth and development and a variety of stress responses. However, the TIFY family has not yet been well characterized in kiwifruit, a popular fruit with important nutritional and economic value. Results A total of 27 and 21 TIFY genes were identified in the genomes of Actinidia eriantha and A. chinensis, respectively. Phylogenetic analyses showed that kiwifruit TIFY genes could be classified into four major groups, JAZ, ZML, TIFY and PPD, and the JAZ group could be further clustered into six subgroups (JAZ I to JAZ VI). Members within the same group or subgroup have similar exon-intron structures and conserved motif compositions. The kiwifruit TIFY genes are unevenly distributed on the chromosomes, and the segmental duplication events played a vital role in the expansion of the TIFY genes in kiwifruit. Syntenic analyses of TIFY genes between kiwifruit and other five plant species (including Arabidopsis thaliana, Camellia sinensis, Oryza sativa, Solanum lycopersicum and Vitis vinifera) and between the two kiwifruit species provided valuable clues for understanding the potential evolution of the kiwifruit TIFY family. Molecular evolutionary analysis showed that the evolution of kiwifruit TIFY genes was primarily constrained by intense purifying selection. Promoter cis-element analysis showed that most kiwifruit TIFY genes possess multiple cis-elements related to stress-response, phytohormone signal transduction and plant growth and development. The expression pattern analyses indicated that TIFY genes might play a role in different kiwifruit tissues, including fruit at specific development stages. In addition, several TIFY genes with high expression levels during Psa (Pseudomonas syringae pv. actinidiae) infection were identified, suggesting a role in the process of Pas infection. Conclusions In this study, the kiwifruit TIFY genes were identified from two assembled kiwifruit genomes. In addition, their basic physiochemical properties, chromosomal localization, phylogeny, gene structures and conserved motifs, synteny analyses, promoter cis-elements and expression patters were systematically examined. The results laid a foundation for further understanding the function of TIFY genes in kiwifruit, and provided a new potential approach for the prevention and treatment of Psa infection.

Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz)

“…Based on subcellular localization data, the majority of cassava TIFY proteins (23 of 28) were anticipated to be found in the nucleus. Tao et al. (2022) reported that, except for one ZML protein predicted to be located in the mitochondrion, all other kiwifruit ( Actinidia eriantha and A. chinensis ) TIFYs were predicted to be located in the nucleus, which is similar with the present study.…”

“…Based on subcellular localization data, the majority of cassava TIFY proteins (23 of 28) were anticipated to be found in the nucleus. Tao et al (2022) reported that, except for one ZML protein predicted to be located in the mitochondrion, all other kiwifruit (Actinidia eriantha and A. chinensis) TIFYs were predicted to be located in the nucleus, which is similar with the present study. The secondary structure analysis discovered that random coil was the most common secondary structure in cassava TIFY amino acid sequences, accounting for up to 73.77% (MeJAZ12), followed by alpha helix, extended strand, and beta turns.…”

“…This classification, together with the findings of a study of conserved domains, suggests that their functions have evolved through time. Furthermore, the JAZ subfamily of cassava proteins was classified into six distinct subgroups (Figure 1; Figure 2A), which is consistent with the findings of a previous study in which JAZ proteins from some species, including apple (Malus × domestica) (Li et al, 2015), Populus trichocarpa (Wang et al, 2017), and kiwifruit (Tao et al, 2022). Previous research has shown that the exon-intron structure may be used to provide further support for phylogenetic groupings, as this type of divergence typically plays a substantial part in the establishment of gene families (Shiu and Bleecker, 2003).…”

Genome-Wide Identification of the LHC Gene Family in Kiwifruit and Regulatory Role of AcLhcb3.1/3.2 for Chlorophyll a Content

“…Kiwifruit is one of the most successfully domesticated fruit trees of the 20th century and has become a popular fruit with high nutritional value [ 27 ]. Interestingly, kiwifruit variations in fresh colors were caused by the contents and proportions of chlorophylls, carotenoids, and anthocyanins, which regulate green, yellow, and red flesh [ 28 ].…”

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

“…SbACP5 and SbACP7 shared a large fragment replication, so they were in the same branch of the evolutionary tree, and their gene structure and conserved motif were basically same. The segmented copies of genes tend to have the same function and expression patterns [ 48 ]. In this study, different from previous studies, SbACP5 and SbACP7 had different response patterns to drought and salt treatment, which might be caused by redundancy of function.…”