Genome-wide identification and expression analysis of the GRAS family under low-temperature stress in bananas

Genome-Wide Identification, Expression, and Protein Interaction of GRAS Family Genes During Arbuscular Mycorrhizal Symbiosis in Poncirus trifoliata

Arbuscular mycorrhizal (AM) fungi establish mutualistic symbiosis with most land plants, facilitating mineral nutrient uptake in exchange for photosynthates. As one of the most commercially used rootstocks in citrus, Poncirus trifoliata heavily depends on AM fungi for nutrient absorption. The GRAS gene family plays essential roles in plant growth and development, signaling transduction, and responses to biotic and abiotic stresses. However, the identification and functional characterization of GRAS family genes in P. trifoliata remains largely unexplored. In this study, a comprehensive genome-wide analysis of PtGRAS family genes was conducted, including their identification, physicochemical properties, phylogenetic relationships, gene structures, conserved domains, chromosome localization, and collinear relationships. Additionally, the expression profiles and protein interaction of these genes under AM symbiosis were systematically investigated. As a result, 41 GRAS genes were identified in the P. trifoliata genome, and classified into nine distinct clades. Collinearity analysis revealed seven segmental duplications but no tandem duplications, suggesting that segmental duplication played a more important role in the expansion of the PtGRAS gene family compared to tandem duplication. Additionally, 18 PtGRAS genes were differentially expressed in response to AM symbiosis, including orthologs of RAD1, RAM1, and DELLA3 in P. trifoliata. Yeast two-hybrid (Y2H) screening further revealed that PtGRAS6 and PtGRAS20 interacted with both PtGRAS12 and PtGRAS18, respectively. The interactions were subsequently validated through bimolecular fluorescence complementation (BiFC) assays. These findings underscored the crucial role of GRAS genes in AM symbiosis in P. trifoliata, and provided valuable candidate genes for improving nutrient uptake and stress resistance in citrus rootstocks through molecular breeding approaches.

The GRAS gene family and its roles in pineapple (Ananas comosus L.) developmental regulation and cold tolerance

BACKGROUND

Pineapple (Ananas comosus L.) is a major tropical fruit crop with considerable economic importance, and its growth and development are significantly impacted by low temperatures. The plant-specific GRAS gene family plays crucial roles in diverse processes, including flower and fruit development, as well as in stress responses. However, the role of the GRAS family in pineapple has not yet been systematically analyzed.

RESULTS

In this study, 43 AcGRAS genes were identified in the pineapple genome; these genes were distributed unevenly across 19 chromosomes and 6 scaffolds and were designated as AcGRAS01 to AcGRAS43 based on their chromosomal locations. Phylogenetic analysis classified these genes into 14 subfamilies: OS19, HAM-1, HAM-2, SCL4/7, LISCL, SHR, PAT1, DLT, LAS, SCR, SCL3, OS43, OS4, and DELLA. Gene structure analysis revealed that 60.5% of the AcGRAS genes lacked introns. Expression profiling demonstrated tissue-specific expression, with most AcGRAS genes predominantly expressed in specific floral organs, fruit tissues, or during particular developmental stages, suggesting functional diversity in pineapple development. Furthermore, the majority of AcGRAS genes were induced by cold stress, but different members seemed to play distinct roles in short-term or long-term cold adaptation in pineapple. Notably, most members of the PAT1 subfamily were preferentially expressed during late petal development and were upregulated under cold stress, suggesting their special roles in petal development and the cold response. In contrast, no consistent expression patterns were observed among genes in other subfamilies, suggesting that various regulatory factors, such as miRNAs, transcription factors, and cis-regulatory elements, may contribute to the diverse functions of AcGRAS members, even within the same subfamily.

CONCLUSIONS

This study provides the first comprehensive analysis of GRAS genes in pineapple, offers valuable insights for further functional investigations of AcGRASs and provides clues for improving pineapple cold resistance breeding.

Genome-Wide Identification and Characterization of GRAS Transcription Factor Family in Cultivated Hybrid Sugarcane ZZ1 (Saccharum officinarum) and Their Role in Development and Stress

GRAS gene family plays multifunctional roles in plant growth, development, and resistance to various biotic and abiotic stresses, belonging to the plant-specific transcription factor (TF) family. In this study, a genome-wide survey and systematic analysis of the GRAS family in cultivated hybrid sugarcane ZZ1 (Saccharum officinarum) with economic and industrial importance was carried out. We identified 747 GRAS genes with complete structural domains and classified these into 11 subfamilies by phylogenetic analyses, exhibiting a diverse range of molecular weight and isoelectric points, thereby indicating a broad structural and functional spectrum. Analysis of Protein motif and gene structure revealed a conserved yet variable arrangement of motifs within the GRAS TFs, suggesting its potential for diverse functional roles. Furthermore, the identification of numerous cis-regulatory elements by GRAS TFs promoter sequence analysis, implying their complex regulation in response to environmental and physiological signals. Tertiary structure predictions analyses using AlphaFold3 highlighted the structural flexibility and conservation within the GRAS family, with disordered regions potentially contributing to their functional versatility. Weighted Gene Co-expression Network Analysis (WGCNA) provided insights into the potential roles of ShGRAS21A in sugarcane's response to smut infection. This comprehensive investigation of the GRAS family in ZZ1 not only uncovers their structural diversity but also sheds light on their potential regulatory roles in plant growth, development, and stress response. The findings contribute to a deeper understanding of GRAS TFs functions and lay the groundwork for future studies on their role in sugarcane improvement and disease resistance.

Genome-wide identification and expression analysis of GRAS gene family in Eucalyptus grandis

BACKGROUND

The GRAS gene family is a class of plant-specific transcription factors with important roles in many biological processes, such as signal transduction, disease resistance and stress tolerance, plant growth and development. So far, no information available describes the functions of the GRAS genes in Eucalyptus grandis.

RESULTS

A total of 82 GRAS genes were identified with amino acid lengths ranging from 267 to 817 aa, and most EgrGRAS genes had one exon. Members of the GRAS gene family of Eucalyptus grandis are divided into 9 subfamilies with different protein structures, while members of the same subfamily have similar gene structures and conserved motifs. Moreover, these EgrGRAS genes expanded primarily due to segmental duplication. In addition, cis-acting element analysis showed that this family of genes was involved involved in the signal transduction of various plant hormones, growth and development, and stress response. The qRT-PCR data indicated that 18 EgrGRAS genes significantly responded to hormonal and abiotic stresses. Among them, the expression of EgrGRAS13, EgrGRAS68 and EgrGRAS55 genes was significantly up-regulated during the treatment period, and it was hypothesised that members of the EgrGRAS family play an important role in stress tolerance.

CONCLUSIONS

In this study, the phylogenetic relationship, conserved domains, cis-elements and expression patterns of GRAS gene family of Eucalyptus grandis were analyzed, which filled the gap in the identification of GRAS gene family of Eucalyptus grandis and laid the foundation for analyzing the function of EgrGRAS gene in hormone and stress response.

Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans

BACKGROUND

Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported.

RESULTS

In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells.

CONCLUSIONS

These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.