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13 pages, 2950 KiB

Open AccessArticle

Silencing of GhSINAT5 Reduces Drought Resistance and Salt Tolerance in Cotton

by Yi Wang, Jiacong Zeng, Yuehua Yu and Zhiyong Ni

Genes 2024, 15(8), 1063; https://doi.org/10.3390/genes15081063 - 12 Aug 2024

The SEVEN IN ABSENTIA (SINA) E3 ubiquitin ligase is widely involved in drought and salt stress in plants. However, the biological function of the SINA proteins in cotton is still unknown. This study aimed to reveal the function of GhSINAT5 through biochemical, genetic [...] Read more.

The SEVEN IN ABSENTIA (SINA) E3 ubiquitin ligase is widely involved in drought and salt stress in plants. However, the biological function of the SINA proteins in cotton is still unknown. This study aimed to reveal the function of GhSINAT5 through biochemical, genetic and molecular approaches. GhSINAT5 is expressed in several tissues of cotton plants, including roots, stems, leaves and cotyledons, and its expression levels are significantly affected by polyethylene glycol, abscisic acid and sodium chloride. When GhSINAT5 was silenced in cotton plants, drought and salinity stress occurred, and the length, area and volume of the roots significantly decreased. Under drought stress, the levels of proline, superoxide dismutase, peroxidase and catalase in the GhSINAT5-silenced cotton plants were significantly lower than those in the non-silenced control plants, whereas the levels of hydrogen peroxide and malondialdehyde were greater. Moreover, the expression of stress-related genes in silenced plants under drought stress suggested that GhSINAT5 may play a positive role in the plant response to drought and salt stress by regulating these stress response-related genes. These findings not only deepen our understanding of the mechanisms of drought resistance in cotton but also provide potential targets for future improvements in crop stress resistance through genetic engineering. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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Figure 1

Figure 1
The GhSINAT5 phylogenetic tree and analysis of the conserved domains. (A) Multiple sequence alignment of GhSINAT5 and Arabidopsis. (B) Phylogenetic tree analysis of the SINA ubiquitin ligases in GhSINAT5, Arabidopsis, maize, rice and tomatoes. Asterisks and arrows indicate conserved amino acids in the RING and B-box2 conserved domains. Full article ">Figure 2
Analysis of the GhSINAT5 transcript levels. (A) Analysis of the transcript levels in different tissues, with roots as the control. (B) Expression patterns at different periods after 250 mM NaCl treatment. (C) Expression patterns at different periods after 15% PEG treatment. (D) Expression patterns at different periods after 100 μM ABA treatment. Vertical bars indicate ±SDs, and significant differences from the control are indicated as * p < 0.05 and ** p < 0.01. Full article ">Figure 3
Identification of drought-resistant phenotypes of cotton with silencing of the GhSINAT5 gene. (A) GhSINAT5 gene expression assay. (B) Phenotypic analysis after 10 d of natural drought. (C) The 15% PEG-simulated drought phenotype. (D) Root length phenotype under 15% PEG drought stress. (E) Survival rate statistics under drought stress. (F) Root length under drought stress. (G) Root area under drought stress. (H) Root volume under drought stress. TRV::00-pTRV2 indicates control, TRV::00-GhSINAT5 indicates silent plants, vertical bars indicate ±SDs and significant differences from the control are indicated as ** p < 0.01. Full article ">Figure 4
Measurement of the physiological and biochemical indices under drought stress in cotton with silencing of the GhSINAT5 gene. (A) Proline content. (B) Malondialdehyde content. (C) Hydrogen peroxide content. (D) Peroxide dismutase content. (E) Superoxide dismutase content. (F) Catalase content. TRV::00-pTRV2 indicates control, TRV::00-GhSINAT5 indicates silent plants, vertical bars indicate ±SDs and significant differences from the control are indicated as * p < 0.05 and ** p < 0.01. Full article ">Figure 5
GhNCED3, GhRD22 and GhRD26 gene expression assays. (A) Expression of GhRD22. (B) Expression of GhRD26. (C) Expression of GhNCED3. TRV::00-pTRV2 indicates control, TRV::00-GhSINAT5 indicates silent plants, vertical bars indicate ±SDs and significant differences from the control are indicated as * p < 0.05 and ** p < 0.01. Full article ">Figure 6
Identification of the salt stress phenotype of cotton with silenced GhSINAT5 genes. (A) NaCl stress phenotype at 250 mM. (B) NaCl stress-induced root length at 250 mM. (C) Root length under NaCl stress at 250 mM. (D) Root area under NaCl stress at 250 mM. (E) Root volume under NaCl stress at 250 mM. TRV::00-pTRV2 indicates control, TRV::00-GhSINAT5 indicates silent plants, vertical bars indicate ±SDs and significant differences from the control are indicated as * p < 0.05. Full article ">

12 pages, 10014 KiB

Open AccessArticle

Effects of Drought Stress on Abscisic Acid Content and Its Related Transcripts in Allium fistulosum—A. cepa Monosomic Addition Lines

by Tetsuya Nakajima, Shigenori Yaguchi, Sho Hirata, Mostafa Abdelrahman, Tomomi Wada, Ryosuke Mega and Masayoshi Shigyo

Genes 2024, 15(6), 754; https://doi.org/10.3390/genes15060754 - 8 Jun 2024

Viewed by 1039

Abstract

Climate change has resulted in an increased demand for Japanese bunching onions (Allium fistulosum L., genomes FF) with drought resistance. A complete set of alien monosomic addition lines of A. fistulosum with extra chromosomes from shallot (A. cepa L. Aggregatum group, AA), [...] Read more.

Climate change has resulted in an increased demand for Japanese bunching onions (Allium fistulosum L., genomes FF) with drought resistance. A complete set of alien monosomic addition lines of A. fistulosum with extra chromosomes from shallot (A. cepa L. Aggregatum group, AA), represented as FF + 1A–FF + 8A, displays a variety of phenotypes that significantly differ from those of the recipient species. In this study, we investigated the impact of drought stress on abscisic acid (ABA) and its precursor,

β

-carotene, utilizing this complete set. In addition, we analyzed the expression levels of genes related to ABA biosynthesis, catabolism, and drought stress signal transduction in FF + 1A and FF + 6A, which show characteristic variations in ABA accumulation. A number of unigenes related to ABA were selected through a database using Allium TDB. Under drought conditions, FF + 1A exhibited significantly higher ABA and

β

-carotene content compared with FF. Additionally, the expression levels of all ABA-related genes in FF + 1A were higher than those in FF. These results indicate that the addition of chromosome 1A from shallot caused the high expression of ABA biosynthesis genes, leading to increased levels of ABA accumulation. Therefore, it is expected that the introduction of alien genes from the shallot will upwardly modify ABA content, which is directly related to stomatal closure, leading to drought stress tolerance in FF. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Schematic diagram illustrating the key pathways involved in abscisic acid (ABA) biosynthesis, catabolism, and drought stress signal transduction. BCH1: β-carotene hydroxylase1; ABA1: zeaxanthin epoxidase; NCED3: nine-cis-epoxycarotenoid dioxygenase 3; ABA2:xanthoxin dehydrogenase; AAO: abscisic-aldehyde oxidase; ABA3: Molybdenum cofactor sulfurase; CYP707A1: ABA 8’-hydroxylase1; CYP707A3: ABA 8’-hydroxylase3; LEA4-5: late embryogenesis abundant. Full article ">Figure 2
Comparison of (A) <math display="inline"><semantics> <mi>β</mi> </semantics></math>-carotene and (B) abscisic acid (ABA) contents in different monosomic addition lines (AMALs, 1A, 2A, 3A, 4A, 5A, 6A, 7A, and 8A) and Allium fistulosum (FF) under control and drought stress conditions. Different letters (a, b for control conditions and y, z for drought conditions) indicate significant differences at p < 0.05. Asterisks *, **, and *** represent significant differences at p < 0.05, p < 0.01, and p < 0.001, respectively, as determined by Student’s t-test. NS indicates not significant at p < 0.05. Full article ">Figure 3
Correlation analysis of <math display="inline"><semantics> <mi>β</mi> </semantics></math>-carotene and abscisic acid (ABA) contents under drought stress in eight different alien monosomic addition lines and Allium fistulosum using the Pearson correlation method. Full article ">Figure 4
Comparison of (A) violaxanthin and (B) neoxanthin peak areas in FF, FF + 1A, and FF + 6A under control and drought conditions. Different letters (a, b for control conditions and z for drought conditions) indicate significant differences at p < 0.05. NS indicates not significant at p < 0.05 by Student’s t-test. Full article ">Figure 5
Heatmap of <math display="inline"><semantics> <msub> <mo form="prefix">log</mo> <mn>2</mn> </msub> </semantics></math> transformed average gene expression changes in abscisic acid (ABA) biosynthesis and catabolism-related genes under control and drought conditions in FF, FF + 1A, and FF + 6A. BCH1: β-carotene hydroxylase1; ABA1: zeaxanthin epoxidase; NCED3: nine-cis-epoxycarotenoid dioxygenase 3; ABA2: xanthoxin dehydrogenase; AAO: abscisic-aldehyde oxidase; ABA3: Molybdenum cofactor sulfurase; CYP707A1: ABA 8’-hydroxylase1; CYP707A3: ABA 8’-hydroxylase3; LEA4-5: late embryogenesis abundant. Full article ">Figure 6
Annual average ascorbic acid content in FF, FF + 1A, and FF + 6A Dunnett’s multiple comparison test was used to compare each line with FF as a control.Values are the means ± SE (n = 12). Different small letters (a and b) refer to significant differences (p < 0.05). Full article ">

13 pages, 4693 KiB

Open AccessArticle

Screening and Preliminary Identification of Asparagus officinalis Varieties under Low-Temperature Stress

by Youju Ye, Shuangshuang Wen, Jiali Ying, Yunfei Cai and Renjuan Qian

Genes 2024, 15(4), 486; https://doi.org/10.3390/genes15040486 - 12 Apr 2024

Viewed by 743

Abstract

To meet the large demand for Asparagus officinalis in the spring market and improve the economic benefits of cultivating asparagus, we explored the molecular mechanism underlying the response of A. officinalis to low temperature. First, “Fengdao No. 1” was screened out under low-temperature [...] Read more.

To meet the large demand for Asparagus officinalis in the spring market and improve the economic benefits of cultivating asparagus, we explored the molecular mechanism underlying the response of A. officinalis to low temperature. First, “Fengdao No. 1” was screened out under low-temperature treatment. Then, the transcriptome sequencing and hormone detection of “Fengdao No. 1” and “Grande” (control) were performed. Transcriptome sequencing resulted in screening out key candidate genes, while hormone analysis indicated that ABA was important for the response to low temperature. The combined analysis indicated that the AoMYB56 gene may regulate ABA in A. officinalis under low temperature. And the phylogenetic tree was constructed, and subcellular localisation was performed. From these results, we speculated that the AoMYB56 gene may regulate ABA in A. officinalis. The results of this research provide a theoretical basis for the further exploration of low-temperature response in A. officinalis. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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25 pages, 62586 KiB

Open AccessArticle

Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum

by Guoli Zhang, Yang Jiao, Zengqiang Zhao, Quanjia Chen, Zhijun Wang, Jincheng Zhu, Ning Lv and Guoqing Sun

Genes 2024, 15(3), 348; https://doi.org/10.3390/genes15030348 - 9 Mar 2024

Viewed by 1301

Abstract

Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, [...] Read more.

Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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13 pages, 2781 KiB

Open AccessArticle

Time-Series Transcriptome of Cucumis melo Reveals Extensive Transcriptomic Differences with Different Maturity

by Fengjuan Liu, Xupeng Shao, Yingying Fan, Binxin Jia, Weizhong He, Yan Wang, Fengzhong Wang and Cheng Wang

Genes 2024, 15(2), 149; https://doi.org/10.3390/genes15020149 - 24 Jan 2024

Cited by 1 | Viewed by 926

Abstract

As the most important melon cultivar grown in the north-western provinces of China, Hami melon (Cucumis melo) produces large edible fruits that serve as an important dietary component in the world. In general, as a climacteric plant, melon harvested at 60% [...] Read more.

As the most important melon cultivar grown in the north-western provinces of China, Hami melon (Cucumis melo) produces large edible fruits that serve as an important dietary component in the world. In general, as a climacteric plant, melon harvested at 60% maturity results in a product with bad quality, while the highest-quality product can be guaranteed when harvesting at 90% maturity. In order to clarify the genetic basis of their distinct profiles of metabolite accumulation, we performed systematic transcriptome analyses between 60% and 90% maturity melons. A total of 36 samples were sequenced and over 1.7 billion reads were generated. Differentially expressed genes in 60% and 90% maturity melons were detected. Hundreds of these genes were functionally enriched in the sucrose and citric acid accumulation process of C. melo. We also detected a number of distinct splicing events between 60% and 90% maturity melons. Many genes associated with sucrose and citric acid accumulation displayed as differentially expressed or differentially spliced between different degrees of maturity of Hami melons, including CmCIN2, CmSPS2, CmBGAL3, and CmSPS2. These results demonstrate that the phenotype pattern differences between 60% and 90% maturity melons may be largely resulted from the significant transcriptome regulation. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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Figure 1
Comparison of 60%(DAP33) and 90% (DAP42)maturity melon in flesh firmness (A), total soluble solids content (B), respiratory intensity (C), fructose (D), glucose (E), sucrose (F), malic acid (G), citric acid (H), and succinic acid (I) during storage. Full article ">Figure 2
An overview of the transcriptome sequencing. (A) Distribution of expression levels for all melon genes across each sample. (B) Hierarchical clustering analysis of gene expression levels in each of the 36 samples. (C) PCA analysis of clustering of the 36 samples. Full article ">Figure 3
Differentially expressed genes between 60% and 90% melon maturity. (A) Upset plot between the 6 groups of differentially expressed genes. (B) Differentially expressed in 0 day of storage between 60% and 90% melon maturity. (C) Differentially expressed in 3 day of storage between 60% and 90% melon maturity. (D) Differentially expressed in 5 day of storage between 60% and 90% melon maturity. (E) Differentially expressed in 7 day of storage between 60% and 90% melon maturity. (F) Differentially expressed in 14 day of storage between 60% and 90% melon maturity. (G) Differentially expressed in 21 day of storage between 60% and 90% melon maturity. Full article ">Figure 4
Alternative splicing events (ASEs) between 60% and 90% melon maturity. (A) Schematic representation of five types of alternative splicing events. Alternative exons are shown as pink boxes and flanking constitutive exons are shown as light blue boxes. (B) Distribution of isoform numbers for genes in melon genome. (C) Significantly differential ASEs between 60% and 90% melon maturity. D-I. Pie chart showing the percentage distribution of ASEs between 60% and 90% melon maturity in 0 (D), 3 (E), 5 (F), 7 (G), 14 (H), and 21 (I) day of storage. Full article ">

17 pages, 4218 KiB

Open AccessArticle

Genome-Wide Identification of the IQM Gene Family and Their Transcriptional Responses to Abiotic Stresses in Kiwifruit (Actinidia eriantha)

by Minyan Xu, Zhi Zhang, Chengcheng Ling, Yuhuan Jiao and Xin Zhang

Genes 2024, 15(2), 147; https://doi.org/10.3390/genes15020147 - 23 Jan 2024

Viewed by 1019

Abstract

IQM is a plant-specific calcium-binding protein that plays a pivotal role in various aspects of plant growth response to stressors. We investigated the IQM gene family and its expression patterns under diverse abiotic stresses and conducted a comprehensive analysis and characterization of the [...] Read more.

IQM is a plant-specific calcium-binding protein that plays a pivotal role in various aspects of plant growth response to stressors. We investigated the IQM gene family and its expression patterns under diverse abiotic stresses and conducted a comprehensive analysis and characterization of the AeIQMs, including protein structure, genomic location, phylogenetic relationships, gene expression profiles, salt tolerance, and expression patterns of this gene family under different abiotic stresses. Based on phylogenetic analysis, these 10 AeIQMs were classified into three distinct subfamilies (I–III). Analysis of the protein motifs revealed a considerable level of conservation among these AeIQM proteins within their respective subfamilies in kiwifruit. The genomic distribution of the 10 AeIQM genes spanned across eight chromosomes, where four pairs of IQM gene duplicates were associated with segmental duplication events. qRT-PCR analysis revealed diverse expression patterns of these AeIQM genes under different hormone treatments, and most AeIQMs showed inducibility by salt stress. Further investigations indicated that overexpression of AeIQMs in yeast significantly enhanced salt tolerance. These findings suggest that AeIQM genes might be involved in hormonal signal transduction and response to abiotic stress in Actinidia eriantha. In summary, this study provides valuable insights into the physiological functions of IQMs in kiwifruit. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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14 pages, 4090 KiB

Open AccessArticle

CFHTF2 Is Needed for Vegetative Growth, Conidial Morphogenesis and the Osmotic Stress Response in the Tea Plant Anthracnose (Colletotrichum fructicola)

by Chengkang Zhang, Ziwen Zhou, Tianlong Guo, Xin Huang, Chengbin Peng, Zhideng Lin, Meixia Chen and Wei Liu

Genes 2023, 14(12), 2235; https://doi.org/10.3390/genes14122235 - 18 Dec 2023

Viewed by 1235

Abstract

Tea is an important cash crop worldwide, and its nutritional value has led to its high economic benefits. Tea anthracnose is a common disease of tea plants that seriously affects food safety and yield and has a far-reaching impact on the sustainable development [...] Read more.

Tea is an important cash crop worldwide, and its nutritional value has led to its high economic benefits. Tea anthracnose is a common disease of tea plants that seriously affects food safety and yield and has a far-reaching impact on the sustainable development of the tea industry. In this study, phenotypic analysis and pathogenicity analysis were performed on knockout and complement strains of HTF2—the transcriptional regulator of tea anthracnose homeobox—and the pathogenic mechanism of these strains was explored via RNA-seq. The MoHox1 gene sequence of the rice blast fungus was indexed, and the anthracnose genome was searched for CfHTF2. Evolutionary analysis recently reported the affinity of HTF2 for C. fructicola and C. higginsianum. The loss of CfHTF2 slowed the vegetative growth and spore-producing capacity of C. fructicola and weakened its resistance and pathogenesis to adverse conditions. The transcriptome sequencing of wild-type N425 and CfHTF2 deletion mutants was performed, and a total of 3144 differentially expressed genes (DEGs) were obtained, 1594 of which were upregulated and 1550 of which were downregulated. GO and KEGG enrichment analyses of DEGs mainly focused on signaling pathways such as the biosynthesis of secondary metabolites. In conclusion, this study lays a foundation for further study of the pathogenic mechanism of tea anthracnose and provides a molecular basis for the analysis of the pathogenic molecular mechanism of CfHTF2. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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Figure 1
Phylogenetic trees and conserved domains of HTF2 in different species. Full article ">Figure 2
(A) Schematic diagram of the CfHTF2 gene knockout, (B) knockout mutant PCR detection, (C) Southern blot analysis of candidate knockout transformants of genes involved in DNA methylation, (D) fluorescent observation of the CfHtf2-C7 strains. Full article ">Figure 3
Morphological characteristics of N425, ΔCfhtf2-178 and CfHtf2-C7 colonies on different media. The culture phenotype was cultured for 5 days. Full article ">Figure 4
Spore production and conidia of N425, ΔCfhtf2-178 and CfHtf2-C7. (A) Conidia produced on the surface of the medium; (B) conidial structure; (C) attached spore structure. The culture phenotype was cultured for 10 days. Full article ">Figure 5
Statistical analysis of cell-sensitive colonies of wild-type N425, ΔCfhtf2-178 and CfHtf2-C7 tea anthracnose plants under stress (sorbitol, sodium chloride and potassium chloride). Full article ">Figure 6
Pathogenicity of N425 and ΔCfhtf2-178. Full article ">Figure 7
The number of differentially expressed genes in N425 and ΔCfhtf2-178. Full article ">Figure 8
GO and KEGG enrichment analyses of the DEGs. Full article ">

Review

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13 pages, 2493 KiB

Open AccessReview

Involvement of Alfin-Like Transcription Factors in Plant Development and Stress Response

by Ruixin Jin, Haitao Yang, Tayeb Muhammad, Xin Li, Diliaremu Tuerdiyusufu, Baike Wang and Juan Wang

Genes 2024, 15(2), 184; https://doi.org/10.3390/genes15020184 - 29 Jan 2024

Cited by 2 | Viewed by 1389

Abstract

Alfin-like (AL) proteins are an important class of transcription factor (TF) widely distributed in eukaryotes and play vital roles in many aspects of plant growth and development. AL proteins contain an Alfin-like domain and a specific PHD-finger structure domain at the N-terminus and [...] Read more.

Alfin-like (AL) proteins are an important class of transcription factor (TF) widely distributed in eukaryotes and play vital roles in many aspects of plant growth and development. AL proteins contain an Alfin-like domain and a specific PHD-finger structure domain at the N-terminus and C-terminus, respectively. The PHD domain can bind to a specific (C/A) CAC element in the promoter region and affect plant growth and development by regulating the expression of functional genes. This review describes a variety of AL transcription factors that have been isolated and characterized in Arabidopsis thaliana, Brassica rapa, Zea mays, Brassica oleracea, Solanum lycopersicum, Populus trichocarpa, Pyrus bretschenedri, Malus domestica, and other species. These studies have focused mainly on plant growth and development, different abiotic stress responses, different hormonal stress responses, and stress responses after exposure to pathogenic bacteria. However, studies on the molecular functional mechanisms of Alfin-like transcription factors and the interactions between different signaling pathways are rare. In this review, we performed phylogenetic analysis, cluster analysis, and motif analysis based on A. thaliana sequences. We summarize the structural characteristics of AL transcription factors in different plant species and the diverse functions of AL transcription factors in plant development and stress regulation responses. The aim of this study was to provide a reference for further application of the functions and mechanisms of action of the AL protein family in plants. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Genetics and Genomics)

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Phylogenetic analysis of Arabidopsis thaliana, Brassica rapa, Zea mays, Brassica oleracea, Solanum lycopersicum, Populus trichocarpa and Oryza sativa AL transcription factors. The graph was constructed in MEGA11 using the LG + F approach. Full article ">Figure 2
Cluster analysis of A. thaliana, Z. mays, B. oleracea, B. rapa, S. lycopersicum, O. sativa, and P. trichocarpa AL transcription factors. (A): Phylogenetic tree of 82 AL transcription factor proteins; (B): Conserved structural domains. Purple for Alfin structure, blue for PHD structure; (C): Gene structure. CDS and UTR are shown in different coolers, and introns are represented by a black line. Full article ">Figure 3
Motif analysis of A. thaliana, Z. mays, B. oleracea, B. rapa, S. lycopersicum, O. sativa, and P. trichocarpa AL transcription factors (A): Structure of 82 AL transcription factor protein conserved motifs. Different color boxes represent different motifs; (B): 20 motifs. Protein conserved motifs were analyzed using MEME (Introduction-MEME Suite) (<a href="https://meme-suite.org/meme/tools/meme" target="_blank">https://meme-suite.org/meme/tools/meme</a>, accessed on 13 January 2024) for AL transcription factors in seven species. Full article ">Figure 4
Research progresses on AL transcription factors. Full article ">

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