Genomic Identification and Characterization of the Cotton YABBY Gene Family.

BackgroundThe ALOG (Arabidopsis thaliana LSH1 and Oryza sativa G1) gene family is a class of transcription factors present in various plants. To elucidate the roles of ALOG genes in cotton, we systematically investigated the ALOG gene family across four cotton species (Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii).ResultsIn this study, a total of 43, 42, 23 and 27 ALOG genes were identified from G. hirsutum, G. barbadense, G. arboretum and G. raimondii, respectively. The results indicated that cotton ALOG gene duplications originated before the speciation of Gossypium species, whole genome duplication, segmental duplication and transposable elements all play important roles in its expansion. In addition, cotton ALOG genes had undergone purifying selection during the evolution. Cis-element analysis revealed that TATA-box and CAAT-box are the most abundant in the promoters of cotton ALOG genes. Transcriptome analysis showed that the expression of ALOG genes in specific tissue is significantly higher than that in other tissues.ConclusionThis study enhances our comprehension of cotton ALOG genes, and these findings lay the foundation for functional characterizations of ALOG gene family.

The YABBY gene family plays an important role in plant growth and development, such as response to abiotic stress and lateral organ development. YABBY TFs are well studied in numerous plant species, but no study has performed a genome-wide investigation of the YABBY gene family in Melastoma dodecandrum. Therefore, a genome-wide comparative analysis of the YABBY gene family was performed to study their sequence structures, cis-acting elements, phylogenetics, expression, chromosome locations, collinearity analysis, protein interaction, and subcellular localization analysis. A total of nine YABBY genes were found, and they were further divided into four subgroups based on the phylogenetic tree. The genes in the same clade of phylogenetic tree had the same structure. The cis-element analysis showed that MdYABBY genes were involved in various biological processes, such as cell cycle regulation, meristem expression, responses to low temperature, and hormone signaling. MdYABBYs were unevenly distributed on chromosomes. The transcriptomic data and real-time reverse transcription quantitative PCR (RT-qPCR) expression pattern analyses showed that MdYABBY genes were involved in organ development and differentiation of M. dodecandrum, and some MdYABBYs in the subfamily may have function differentiation. The RT-qPCR analysis showed high expression of flower bud and medium flower. Moreover, all MdYABBYs were localized in the nucleus. Therefore, this study provides a theoretical basis for the functional analysis of YABBY genes in M. dodecandrum.

BackgroundInositol monophosphates (IMP) are key enzymes in the ascorbic acid (AsA) synthesis pathways, which play vital roles in regulating plant growth and development and stresses tolerance. To date, no comprehensive analysis of the expression profile of IMP genes and their functions under abiotic stress in cotton has been reported.ResultsIn this study, the genetic characteristics, phylogenetic evolution, cis-acting elements and expression patterns of IMP gene family in cotton were systematically analyzed. A total of 28, 27, 13 and 13 IMP genes were identified in Gossypium hirsutum (G. hirsutum), Gossypium barbadense (G. barbadense), Gossypium arboreum (G. arboreum), and Gossypium raimondii (G. raimondii), respectively. Phylogenetic analysis showed that IMP family genes could cluster into 3 clades. Structure analysis of genes showed that GhIMP genes from the same subgroup had similar genetic structure and exon number. And most GhIMP family members contained hormone-related elements (abscisic acid response element, MeJA response element, gibberellin response element) and stress-related elements (low temperature response element, defense and stress response element, wound response element). After exogenous application of abscisic acid (ABA), some GhIMP genes containing ABA response elements positively responded to alkaline stress, indicating that ABA response elements played an important role in response to alkaline stress. qRT-PCR showed that most of GhIMP genes responded positively to alkaline stress, and GhIMP10D significantly upregulated under alkaline stress, with the highest up-regulated expression level. Virus-induced gene silencing (VIGS) experiment showed that compared with 156 plants, MDA content of pYL156:GhIMP10D plants increased significantly, while POD, SOD, chlorophyII and AsA content decreased significantly.ConclusionsThis study provides a thorough overview of the IMP gene family and presents a new perspective on the evolution of this gene family. In particular, some IMP genes may be involved in alkaline stress tolerance regulation, and GhIMP10D showed high expression levels in leaves, stems and roots under alkaline stress, and preliminary functional verification of GhIMP10D gene suggested that it may regulate tolerance to alkaline stress by regulating the activity of antioxidant enzymes and the content of AsA. This study contributes to the subsequent broader discussion of the structure and alkaline resistance of IMP genes in cotton.

Simple SummaryWe identified and analyzed the Cerasus humilis YABBY (ChYABBY) gene family and further explored the expression changes in ChYABBYs in different growth stages. At the same time, the changes in physiological indexes in different periods of fruit were measured, the correlation between them and YABBY gene expression was analyzed, and the possible regulatory mechanism was speculated. This research provides an important basis for further understanding the structure and function of the ChYABBY gene, and lays a foundation for the identification of YABBY genes in Rosaceae plants.YABBY belongs to the family of plant-specific transcription factors, known for their role in plant morphology, growth, and development. Its name is derived from the first discovered member—the YABBY1 gene of Arabidopsis thaliana (named due to its mutated phenotype showing a “Y-shaped” bifurcation). Despite extensive research across various plant species, no studies have conducted a genome-wide investigation of the YABBY gene family in Cerasus humilis. This study identified six ChYABBY (Cerasus humilis YABBY) genes distributed across five chromosomes through a comprehensive bioinformatic analysis of the C. humilis genome. The gene expression during the four growth phases was confirmed using real-time-quantitative fluorescent PCR (qPCR). ChYABBY is segmented into five distinct subfamilies. Genetic lineage analysis determined the close genetic relationship between the YABBY genes of C. humilis and Malus pumila. An examination of the gene architecture and preserved motifs revealed that ChYABBY typically comprises 5–6 introns, with motif1, motif2, and motif3 being preserved domains across all ChYABBY protein sequences. Promoter analysis suggests that ChYABBY genes play various roles in the growth and maturation of C. humilis. An examination of the homology revealed the absence of tandem replication in the ChYABBY gene family, with a single pair of fragment-replicating genes. The heat map and q-PCR results indicate that the expression of the ChYABBY gene is tissue-specific and correlates with some aspects of the fruit growth and development. This suggests a potential role for this gene family in fruit maturation. The determination of total sugar and total flavonoid content indicated that the content of the two substances was high when the fruit was green. The antioxidant capacity of the fruit at each stage was different. This research provides an important basis for further understanding the structure and function of the ChYABBY gene, and lays a foundation for the identification of YABBY genes in Rosaceae plants.

Glycoside hydrolase family 1 (GH1) proteins are widely distributed in plants and function as β-glucosidases involved in cell wall metabolism, signal transduction, and stress responses. They enhance plant tolerance to abiotic stresses by optimizing osmotic regulation, mediating the activation of secondary metabolites, and mitigating ion toxicity. In this study, we identified a total of 153 GH1 gene family members across four cotton species: Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii. Phylogenetic analysis classified the GH1 genes into five distinct subgroups. Further analysis of gene structure and conserved motifs revealed that genes within the same subgroup share highly similar exon-intron organizations and consistent motif distributions, suggesting functional conservation among subgroup members. Chromosomal localization combined with MCScanX-based collinearity analysis indicates that segmental duplication is the primary mechanism driving the expansion of the GH1 gene family. Furthermore, promoter fanalysis revealed multiple stress-related cis-regulatory elements, including ABRE and MBSI, indicating potential regulation by abscisic acid (ABA) and stress-responsive transcription factors. RT-qPCR analysis of ten representative GH1 genes under 200 mM NaCl treatment revealed distinct expression patterns, with four genes significantly upregulated and five significantly downregulated relative to the control group. Additionally, functional verification through virus-induced gene silencing (VIGS) demonstrated that silencing Gohir.A02G106100 resulted in reduced plant height and shoot fresh weight compared to the controls. The findings indicated that plants with silenced Gohir.A02G106100 exhibited significantly greater sensitivity to salt stress than the negative control plants, suggesting that this gene may play a role in cotton's response to salt stress.

BackgroundRoot systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) are responsible for the formation of Casparian strips.ResultsTo investigate the function of CASPs in cotton, we identified and characterized 48, 54, 91 and 94 CASPs from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively, at the genome-wide level. However, only 29 common homologous CASP genes were detected in the four Gossypium species. A collinearity analysis revealed that whole genome duplication (WGD) was the primary reason for the expansion of the genes of the CASP family in the four cotton species. However, dispersed duplication could also contribute to the expansion of the GaCASPs gene family in the ancestors of G. arboreum. Phylogenetic analysis was used to cluster a total of 85 CASP genes from G. arboreum and Arabidopsis into six distinct groups, while the genetic structure and motifs of CASPs were conserved in the same group. Most GaCASPs were expressed in diverse tissues, with the exception of that five GaCASPs (Ga08G0113, Ga08G0114, Ga08G0116, Ga08G0117 and Ga08G0118) that were highly expressed in root tissues. Analyses of the tissue and subcellular localization suggested that GaCASP27 genes (Ga08G0117) are membrane protein genes located in the root. In the GaCASP27 silenced plants and the Arabidopsis mutants, the lateral root number significantly increased. Furthermore, GaMYB36, which is related to root development was found to regulate lateral root growth by targeting GaCASP27.ConclusionsThis study provides a fundamental understanding of the CASP gene family in cotton and demonstrates the regulatory role of GaCASP27 on lateral root growth and development.

There have been conflicting results reported about the effect on cotton (Gossypium spp.) lint yield of altering planting and irrigation termination (IT) timing. The objectives of this study were to identify a planting window (PW), on a heat unit (HU) basis, and IT timing, as a function of crop growth stage, for optimum yield potential of Upland (G. hirsutum L.) and American Pima (G. babadense L.) cotton. Two PWs of Upland 'Deltapine 90' (DPL 90), Pima 'S-6', and IT treatments were included in field experiments for 11 site-years. Planting windows were defined as PW1 and PW2 for plantings prior to and following 600 HU accumulated after 1 January, respectively. Two IT treatments were imposed for each planting. Irrigation termination in the desert Southwest generally results in cessation of growth (crop termination). The first IT treatment (IT1), was imposed to ensure full development of bolls set up to cutout, and the second (IT2) was after two additional irrigations. From covariate analysis, there was no evidence of interaction between PW and IT, indicating that these treatments responded the same across the different environments for both cotton species. There were, however, differences in lint yields among treatments. For DPL 90, PW1 IT2 yielded 83 and 97 Ib/acre more than PW1 IT1 and PW2 IT2; and for Pima S-6, PW1 IT2 was 118 and 204 Ib/acre more than PW1 IT1 and PW2 IT2, respectively. Early planting is necessary for optimum yield potential of full-season cotton varieties; with the greatest yield coming from early planting and termination after the development of a second fruiting cycle (PW1 IT2). However, if a reduction in input costs and the avoidance of late-season insect pests are important considerations then cotton should be planted early (300 to 600 HU after 1 Jan) and terminated at the end of the first fruiting cycle (approximately 600 HU past cutout) to maintain the lint yield potential of full-season maturity types of Upland and Pima cotton.

The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5–25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.

YABBY gene family is a plant-specific transcription factor with DNA binding domain involved in various functions i.e. regulation of style, length of flowers, and polarity development of lateral organs in flowering plants. Computational methods were utilized to identify members of the YABBY gene family, with Carrot (Daucus carota) ‘s genome as a foundational reference. The structure of genes, location of the chromosomes, protein motifs and phylogenetic investigation, syntony and transcriptomic analysis, and miRNA targets were analyzed to unmask the hidden structural and functional characteristics YABBY gene family in Carrots. In the following research, it has been concluded that 11 specific YABBY genes irregularly dispersed on all 9 chromosomes and proteins assembled into five subgroups i.e. AtINO, AtCRC, AtYAB5, AtAFO, and AtYAB2, which were created on the well-known classification of Arabidopsis. The wide ranges of YABBY genes in carrots were dispersed due to segmental duplication, which was detected as prevalent when equated to tandem duplication. Transcriptomic analysis showed that one of the DcYABBY genes was highly expressed during anthocyanin pigmentation in carrot taproots. The cis-regulatory elements (CREs) analysis unveiled elements that particularly respond to light, cell cycle regulation, drought induce ability, ABA hormone, seed, and meristem expression. Furthermore, a relative study among Carrot and Arabidopsis genes of the YABBY family indicated 5 sub-families sharing common characteristics. The comprehensive evaluation of YABBY genes in the genome provides a direction for the cloning and understanding of their functional properties in carrots. Our investigations revealed genome-wide distribution and role of YABBY genes in the carrots with best-fit comparison to Arabidopsis thaliana.

The YABBY gene family, specific to seed plants, encodes a class of transcription factors in the lamina maintenance and development of lateral organs. Magnoliids are sisters to the clade-containing eudicots and monocots, which have rapidly diversified among the common ancestors of these three lineages. However, prior to this study, information on the function of the YABBY genes in magnoliids was extremely limited to the third major clades and the early diverging lineage of Mesangiospermae. In this study, the sum of 55 YABBY genes including five genes in INO, six in CRC, eight in YAB2, 22 in YAB5, and 14 in FIL clade were identified from seven magnoliid plants. Sequence analysis showed that all encoded YABBY protein sequences possess the highly conserved YABBY domain and C2C2 zinc-finger domain. Gene and protein structure analysis indicates that a certain number of exons were highly conserved and similar in the same class, and YABBY genes encode proteins of 71–392 amino acids and an open reading frame of 216–1179 bp in magnoliids. Additionally, the predicted molecular weight and isoelectric point of YABBY proteins in three species ranged from 7689.93 to 43578.13 and from 5.33 to 9.87, respectively. Meanwhile, the YABBY gene homolog expression of Litsea was detected at a temporal and spatial level during various developmental stages of leaf and reproductive tissues. This research could provide a brief overview of YABBY gene family evolution and its differential expression in magnoliids. Therefore, this comprehensive diversification analysis would provide a new insight into further understanding of the function of genes in seven magnoliids.

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal upstream regulators of MAPK cascades, integrating signals that coordinate plant development and stress responses. However, the specific functions of MAPKKKs, particularly within the MEKK subfamily, in mediating cotton resistance to Verticillium wilt and Fusarium wilt remain poorly characterized. To address this, we conducted a systematic, cross-species analysis of the MAPKKK family in four key cotton species: Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii. Genome-wide identification and phylogenetic analysis revealed 660 MAPKKK genes, classifying them into the MEKK, Raf, and ZIK subfamilies. Evolutionary analysis indicated that Whole-Genome Duplication (WGD) events were the primary driver of family expansion. Promoter cis-element and Gene Ontology (GO) enrichment analyses implicated these genes in hormone signaling and stress adaptation. Expression profiling demonstrated functional modularity, with distinct members responding specifically to cold stress or cooperatively to drought and salt stresses. Upon pathogen infection, members diverged into regulatory modules associated with immune homeostasis, tissue-specific defense, and core signaling potentially governing systemic acquired resistance (SAR). The temporal expression patterns of core candidate genes were validated by qRT-PCR. This study provides, for the first time, a comprehensive evolutionary and functional framework for the MEKK subfamily within the cotton MAPKKK family. It reveals the conserved and divergent roles of this subfamily in stress adaptation and identifies key candidate genes for breeding disease-resistant cotton varieties.

Abiotic stress is an important limiting factor in crop growth and yield around the world. Owing to the continued genetic erosion of the upland cotton germplasm due to intense selection and inbreeding, attention has shifted towards wild cotton progenitors which offer unique traits that can be introgressed into the cultivated cotton to improve their genetic performance. The purpose of this study was to characterize the Pkinase gene family in a previously developed genetic map of the F2 population derived from a cross between two cotton species: Gossypium hirsutum (CCRI 12-4) and Gossypium darwinii (5-7). Based on phylogenetic analysis, Pkinase (PF00069) was found to be the dominant domain with 151 genes in three cotton species, categorized into 13 subfamilies. Structure analysis of G. hirsutum genes showed that a greater percentage of genes and their exons were highly conserved within the group. Syntenic analysis of gene blocks revealed 99 duplicated genes among G. hirsutum, Gossypium arboreum and Gossypium raimondii. Most of the genes were duplicated in segmental pattern. Expression pattern analysis showed that the Pkinase gene family possessed species-level variation in induction to salinity and G. darwinii had higher expression levels as compared to G. hirsutum. Based on RNA sequence analysis and preliminary RT-qPCR verification, we hypothesized that the Pkinase gene family, regulated by transcription factors (TFs) and miRNAs, might play key roles in salt stress tolerance. These findings inferred comprehensive information on possible structure and function of Pkinase gene family in cotton under salt stress.

Members of the YABBY gene family have a general role that promotes abaxial cell fate in a model eudicot, Arabidopsis thaliana. To understand the function of YABBY genes in monocots, we have isolated all YABBY genes in Oryza sativa (rice), and revealed the spatial and temporal expression pattern of one of these genes, OsYABBY1. In rice, eight YABBY genes constitute a small gene family and are classified into four groups according to sequence similarity, exon-intron structure, and organ-specific expression patterns. OsYABBY1 shows unique spatial expression patterns that have not previously been reported for other YABBY genes, so far. OsYABBY1 is expressed in putative precursor cells of both the mestome sheath in the large vascular bundle and the abaxial sclerenchyma in the leaves. In the flower, OsYABBY1 is specifically expressed in the palea and lemma from their inception, and is confined to several cell layers of these organs in the later developmental stages. The OsYABBY1-expressing domains are closely associated with cells that subsequently differentiate into sclerenchymatous cells. These findings suggest that the function of OsYABBY1 is involved in regulating the differentiation of a few specific cell types and is unrelated to polar regulation of lateral organ development.

Systematic analysis and comparison of ABC proteins superfamily confer structural, functional and evolutionary insights into four cotton species

Plant-specific transcription factor (PSTFs) YABBY is one of the vital transcription factors that play a crucial role in abaxial organ development, carpel formation and abiotic stress. Although the Cucumber genome (Cucumis sativus) has been published, functional studies are still needed to understand cucumber. The cucumber genome was used in this study to identify YABBY gene family member by using a set of various bioinformatic tools. Eight YABBY gene family members were identified that were unevenly distributed on different chromosomes. Eight members of the YABBY gene family in cucumber were divided into five subgroups (FIL/YAB3), CRC, INO, YAB2, and YAB5 based on the published Arabidopsis YABBY gene classification. The structure of PSTF YABBY was seen to be conserved throughout the process of evolution through Motif analysis, Conserved Domain Analysis and Gene structure Intron Exon Display. PSTF YABBY has roles in wound healing, abiotic stress like cold, heat and drought stress, phytohormone responses and transcription initiation. CsYABBY4 was seen to be over-expressed under long day and heat stress conditions, implying its significant role in heat stress.