Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

Genome assembly of a diversity panel of Chenopodium quinoa

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.

Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play crucial roles in plant growth, development, and responses to biotic and abiotic stresses. This study was performed to comprehensively identify and characterize the AP2/ERF gene family in quinoa (Chenopodium quinoa Willd.), a highly resilient pseudocereal crop known for its salinity tolerance. A total of 150 CqAP2/ERF genes were identified in the quinoa genome; these genes were unevenly distributed across the chromosomes. Phylogenetic analysis divided the CqAP2/ERFs into five subfamilies: 71 ERF, 49 DREB, 23 AP2, 3 RAV, and 4 Soloist. Additionally, the DREB and ERF subfamilies were subdivided into four and seven subgroups, respectively. The exon-intron structure of the putative CqAP2/ERF genes and the conserved motifs of their encoded proteins were also identified, showing general conservation within the phylogenetic subgroups. Promoter analysis revealed many cis-regulatory elements associated with light, hormones, and response mechanisms within the promoter regions of CqAP2/ERF genes. Synteny analysis revealed that segmental duplication under purifying selection pressure was the major evolutionary driver behind the expansion of the CqAP2/ERF gene family. The protein-protein interaction network predicted the pivotal CqAP2/ERF proteins and their interactions involved in the regulation of various biological processes including stress response mechanisms. The expression profiles obtained from RNA-seq and qRT-PCR data detected several salt-responsive CqAP2/ERF genes, particularly from the ERF, DREB, and RAV subfamilies, with varying up- and downregulation patterns, indicating their potential roles in salt stress responses in quinoa. Overall, this study provides insights into the structural and evolutionary features of the AP2/ERF gene family in quinoa, offering candidate genes for further analysis of their roles in salt tolerance and molecular breeding.

Genome-wide analysis of the trihelix gene family reveals that MaGT21 modulates fruit ripening by regulating the expression of MaACO1 in Musa acuminata

The trihelix transcription factor (GT) gene family members play vital roles in plant growth and development, responses to abiotic or biotic stress, and fruit ripening. However, its role in banana fruit ripening remains unclear. Here, 59 MaGT gene members were identified in banana and clustered into five subfamilies, namely GT1, GT2, GTγ, SIP1, and SH4. This classification is completely supported by their gene structures and conserved motif analysis. Transcriptome data analysis indicated that MaGT14, MaGT21, and MaGT27 demonstrated significant differential expression during fruit ripening. Quantitative real-time PCR analysis revealed that these three genes were highly induced by ethylene treatment, responded to cold and heat stress, and had a high expression abundance in ripe fruit. Subcellular localization demonstrated that MaGT21 and MaGT27 functioned as nuclear proteins, while MaGT14 functioned as a nuclear and cell membrane protein. Further investigation indicated MaGT21 could positively stimulate the transcription of the key ethylene biosynthesis gene MaACO1 by directly targeting the GT motif in the promoter. MaGT21 transient overexpression in banana fruit upregulated MaACO1 and accelerated fruit ripening. Our findings provide comprehensive and valuable information for further functional studies of MaGT genes in banana, help to understand the roles of MaGTs during banana fruit ripening.

Identification of Cold Tolerance Transcriptional Regulatory Genes in Seedlings of Medicago sativa L. and Medicago falcata L

Alfalfa species Medicago sativa L. (MS) and Medicago falcata L. (MF), globally prominent perennial leguminous forages, hold substantial economic value. However, our comprehension of the molecular mechanisms governing their resistance to cold stress remains limited. To address this knowledge gap, we scrutinized and compared MS and MF cold-stress responses at the molecular level following 24 h and 120 h low-temperature exposure (4 °C). Our study revealed that MF had superior physiological resilience to cold stress compared with MS, and its morphology was healthier under cold stress, and its malondialdehyde content and superoxide dismutase activity increased, first, and then decreased, while the soluble sugar content continued to accumulate. Transcriptome analysis showed that after 120 h of exposure, there were different gene-expression patterns between MS and MF, including 1274 and 2983 genes that were continuously up-regulated, respectively, and a total of 923 genes were included, including star cold-resistant genes such as ICE1 and SIP1. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed numerous inter-species differences in sustained cold-stress responses. Notably, MS-exclusive genes included a single transcription factor (TF) gene and several genes associated with a single DNA repair-related pathway, whereas MF-exclusive genes comprised nine TF genes and genes associated with 14 pathways. Both species exhibited high-level expression of genes encoding TFs belonging to AP2-EREBP, ARR-B, and bHLH TF families, indicating their potential roles in sustaining cold resistance in alfalfa-related species. These findings provide insights into the molecular mechanisms governing cold-stress responses in MS and MF, which could inform breeding programs aimed at enhancing cold-stress resistance in alfalfa cultivars.

Comprehensive Genomic Analysis of Trihelix Family in Tea Plant (Camellia sinensis) and Their Putative Roles in Osmotic Stress

In plants, Trihelix transcription factors are responsible for regulating growth, development, and reaction to various abiotic stresses. However, their functions in tea plants are not yet fully understood. This study identified a total of 40 complete Trihelix genes in the tea plant genome, which are classified into five clades: GT-1 (5 genes), GT-2 (8 genes), GTγ (2 genes), SH4 (7 genes), and SIP1 (18 genes). The same subfamily exhibits similar gene structures and functional domains. Chromosomal mapping analysis revealed that chromosome 2 has the most significant number of trihelix family members. Promoter analysis identified cis-acting elements in C. sinensis trihelix (CsTH), indicating their potential to respond to various phytohormones and stresses. The expression analysis of eight representative CsTH genes from four subfamilies showed that all CsTHs were expressed in more tissues, and three CsTHs were significantly induced under ABA, NaCl, and drought stress. This suggests that CsTHs plays an essential role in tea plant growth, development, and response to osmotic stress. Furthermore, yeast strains have preliminarily proven that CsTH28, CsTH36, and CsTH39 can confer salt and drought tolerance. Our study provides insights into the phylogenetic relationships and functions of the trihelix transcription factors in tea plants. It also presents new candidate genes for stress-tolerance breeding.

Molecular Characterization and Expression Analysis of YABBY Genes in Chenopodium quinoa

Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the YABBY genes in quinoa remain elusive. In this study, twelve YABBY (CqYAB) genes were identified in the quinoa genome, and they were distributed on nine chromosomes. They were classified into FIL/YAB3, YAB2, YAB5, INO, and CRC clades. All CqYAB genes consist of six or seven exons, and their proteins contain both N-terminal C2C2 zinc finger motifs and C-terminal YABBY domains. Ninety-three cis-regulatory elements were revealed in CqYAB gene promoters, and they were divided into six groups, such as cis-elements involved in light response, hormone response, development, and stress response. Six CqYAB genes were significantly upregulated by salt stress, while one was downregulated. Nine CqYAB genes were upregulated under drought stress, whereas six CqYAB genes were downregulated under cadmium treatment. Tissue expression profiles showed that nine CqYAB genes were expressed in seedlings, leaves, and flowers, seven in seeds, and two specifically in flowers, but no CqYAB expression was detected in roots. Furthermore, CqYAB4 could rescue the ino mutant phenotype in Arabidopsis but not CqYAB10, a paralog of CqYAB4, indicative of functional conservation and divergence among these YABBY genes. Taken together, these results lay a foundation for further functional analysis of CqYAB genes in quinoa growth, development, and abiotic stress responses.

Genome-wide identification and characterization of glutathione S-transferase gene family in quinoa (Chenopodium quinoa Willd.)

The present investigation was envisaged for large scale in-silico genome wide identification and characterization of glutathione S-transferases (GSTs) in Chenopodium quinoa. In this study, a total of 120 GST genes (CqGSTs) were identified and divided into 11 classes of which tau and phi were highest in numbers. The average protein length of protein was found to be 279.06 with their corresponding average molecular weight of 31,819.4 kDa. The subcellular localization analysis results showed that proteins were centrally localized in the cytoplasm followed by chloroplast, mitochondria and plastids. Structural analysis revealed the presence of 2 -14 exons in CqGST genes. Most of the proteins possessed two exon one intron organization. MEME analysis identified 15 significantly conserved motifs with a width of 6-50 amino acids. Motifs 1, 3, 2, 5, 6, 8, 9 and 13 were found specifically in tau class family; motifs 3, 4, 5, 6, 7 and 9 were found in phi class gene family, while motifs 3, 4, 13 and 14 were found in metaxin class. Multiple sequence alignment revealed highly conserved N-terminus with active site serine (Ser; S) or cysteine (Cys; C) residue for the activation of GSH binding and GST catalytic activity. The gene loci were found to be unevenly distributed across 18 different chromosomes with a maximum of 17 genes located on chromosome number 7. Dominance of alpha helix was followed by coil, extended strand and beta turns. Gene duplication analysis revealed that segmental duplication and purifying type selection were highest in number and found to be main source of expansion of GST gene family. Cis acting regulatory elements analysis showed the presence of 21 different elements involved in stress, hormone and light response and cellular development. The evolutionary relationship of CqGST proteins carried out using maximum likelihood method revealed that all the tau and phi class GSTs were closely associated with those of G. max, O. sativa and A. thaliana. Molecular docking of GST molecules with the fungicide metalaxyl showed that the CqGSTF1 had the lowest binding energy. The comprehensive study of CqGST gene family in quinoa provides groundwork for further functional analysis of CqGST genes in the species at molecular level and has potential applications in plant breeding.

Genome-Wide Identification and Expression Profiling Analysis of the Trihelix Gene Family and response of PgGT1 under Abiotic Stresses in Platycodon grandiflorus

The trihelix gene family plays an important role in plant growth and abiotic stress responses. Through the analysis of genomic and transcriptome data, 35 trihelix family members were identified for the first time in Platycodon grandiflorus; they were classified into five subfamilies: GT-1, GT-2, SH4, GTγ, and SIP1. The gene structure, conserved motifs and evolutionary relationships were analyzed. Prediction of physicochemical properties of the 35 trihelix proteins founded, the number of amino acid molecules is between 93 and 960, theoretical isoelectric point is between 4.24 and 9.94, molecular weight is between 9829.77 and 107435.38, 4 proteins among them were stable, and all GRAVY is negative. The full-length cDNA sequence of the PgGT1 gene of the GT-1 subfamily was cloned by PCR. It is a 1165 bp ORF encoding a 387 amino acid protein, with a molecular weight of 43.54 kDa. The predicted subcellular localization of the protein in the nucleus was experimentally verified. After being treated with NaCl, PEG6000, MeJA, ABA, IAA, SA, and ethephon, the expression of PgGT1 gene showed an up-regulated trend except for the roots treated with NaCl and ABA. This study laid a bioinformatics foundation for the research of trihelix gene family and the cultivation of excellent germplasm of P. grandiflorus.

GT Transcription Factors of Rosa rugosa Thunb. Involved in Salt Stress Response

Rosa rugosa was a famous aromatic plant while poor salt tolerance of commercial cultivars has hindered its culture in saline-alkali soil. In many plants, the roles of GT (or trihelix) genes in salt stresses responses have been emerging. In the wild R. rugosa, a total of 37 GTs (RrGTs) were grouped into GT-1, GT-2, GTγ, SH4, and SIP1 lineages. SIP1 lineage expanded by transposition. The motifs involved in the binding of GT cis-elements were conserved. Four RrGTs (RrGT11/14/16/18) significantly differentially expressed in roots or leaves under salt stress. The responsive patterns within 8 h NaCl treatment indicated that RrGTγ-4 (RrGT18) and RrGT-1 (RrGT16) were significantly induced by salt in roots of R. rugosa. Subcellular localizations of RrSIP1 (RrGT11) and RrGTγ-4 were on chloroplasts while RrGT-1 and RrSIP2 (RrGT14) located on cell nucleus. Regulation of ion transport could be the most important role of RrSIPs and RrGTγ-4. And RrGT-1 could be a halophytic gene with higher transcription abundance than glycophytic GT-1. These results provide key clue for further investigations of roles of RrGTs in salt stress response and would be helpful in the understanding the salt tolerance regulation mechanism of R. rugosa.