Genome-wide identification of the GRF family in sweet orange (Citrus sinensis) and functional analysis of the CsGRF04 in response to multiple abiotic stresses
Ontology highlight
ABSTRACT:
SUBMITTER: Fu M
PROVIDER: S-EPMC10770916 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The family of aquaporins (AQPs), or major intrinsic proteins (MIPs), includes integral membrane proteins that function as transmembrane channels for water and other small molecules of physiological significance. MIPs are classified into five subfamilies in higher plants, including plasma membrane (PIPs), tonoplast (TIPs), NOD26-like (NIPs), small basic (SIPs) and unclassified X (XIPs) intrinsic proteins. This study reports a genome-wide survey of MIP encoding genes in sweet orange (Citrus sinensis L. Osb.), the most widely cultivated Citrus spp. A total of 34 different genes encoding C. sinensis MIPs (CsMIPs) were identified and assigned into five subfamilies (CsPIPs, CsTIPs, CsNIPs, CsSIPs and CsXIPs) based on sequence analysis and also on their phylogenetic relationships with clearly classified MIPs of Arabidopsis thaliana. Analysis of key amino acid residues allowed the assessment of the substrate specificity of each CsMIP. Gene structure analysis revealed that the CsMIPs possess an exon-intron organization that is highly conserved within each subfamily. CsMIP loci were precisely mapped on every sweet orange chromosome, indicating a wide distribution of the gene family in the sweet orange genome. Investigation of their expression patterns in different tissues and upon drought and salt stress treatments, as well as with 'Candidatus Liberibacter asiaticus' infection, revealed a tissue-specific and coordinated regulation of the different CsMIP isoforms, consistent with the organization of the stress-responsive cis-acting regulatory elements observed in their promoter regions. A special role in regulating the flow of water and nutrients is proposed for CsTIPs and CsXIPs during drought stress, and for most CsMIPs during salt stress and the development of HLB disease. These results provide a valuable reference for further exploration of the CsMIPs functions and applications to the genetic improvement of both abiotic and biotic stress tolerance in citrus.
| S-EPMC4580632 | biostudies-literature
Project description:Autophagy is a highly conserved intracellular degradation pathway that breaks down damaged macromolecules and/or organelles. It is involved in plant development and senescence, as well as in biotic and abiotic stresses. However, the autophagy process and related genes are largely unknown in citrus. In this study, we identified 35 autophagy-related genes (CsATGs-autophagy-related genes (ATGs) of Citrus sinensis, Cs) in a genome-wide manner from sweet orange (Citrus sinensis). Bioinformatic analysis showed that these CsATGs were highly similar to Arabidopsis ATGs in both sequence and phylogeny. All the CsATGs were randomly distributed on nine known (28 genes) and one unknown (7 genes) chromosomes. Ten CsATGs were predicted to be segmental duplications. Expression patterns suggested that most of the CsATG were significantly up- or down-regulated in response to drought; cold; heat; salt; mannitol; and excess manganese, copper, and cadmium stresses. In addition, two ATG18 members, CsATG18a and CsATG18b, were cloned from sweet orange and ectopically expressed in Arabidopsis. The CsATG18a and CsATG18b transgenic plants showed enhanced tolerance to osmotic stress, salt, as well as drought (CsATG18a) or cold (CsATG18b), compared to wild-type plants. These results highlight the essential roles of CsATG genes in abiotic stresses.
| S-EPMC7215763 | biostudies-literature
Project description:BackgroundTrehalose-6-phosphate synthase (TPS) is an essential enzyme for synthesizing trehalose and is a significant regulator of plant development and stress response. Sweet orange (Citrus sinensis) is an economically important fruit tree crop and a common transgenic material. At present, little information is available about the TPS gene family in sweet orange.MethodsThe TPS gene family were identified from sweet orange genome by bioinformatics analysis. Additionally, the expression of CisTPS genes was analyzed under phytohormones and abiotic stresses by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).ResultsHere, eight TPS genes were identified and were found to be randomly distributed in five sweet orange chromosomes. TPS and trehalose-6-phosphate phosphatase (TPP) domains were observed in all CisTPS proteins. The phylogenetic tree showed that CisTPS genes were divided into two subfamilies, and genes in each subfamily had conserved intron structures and motif compositions. The cis-acting elements of CisTPS genes suggested their roles in phytohormone and stress responses. All CisTPS genes were ubiquitously expressed in roots, leaves, and stems, and six members were highly expressed in roots. Expression profiles showed that CisTPS genes exhibited tissue specificity and were differentially expressed in response to phytohormones and abiotic stresses. This study lays a foundation for revealing the functions of the TPS gene family in trehalose regulation in sweet orange, and provides a valuable reference for this gene family in other plants.
| S-EPMC9466596 | biostudies-literature
Project description:Three-amino-acid-loop-extension (TALE) transcription factors comprise one of the largest gene families in plants, in which they contribute to regulation of a wide variety of biological processes, including plant growth and development, as well as governing stress responses. Although sweet orange (Citrus sinensis) is among the most commercially important fruit crops cultivated worldwide, there have been relatively few functional studies on TALE genes in this species. In this study, we investigated 18 CsTALE gene family members with respect to their phylogeny, physicochemical properties, conserved motif/domain sequences, gene structures, chromosomal location, cis-acting regulatory elements, and protein-protein interactions (PPIs). These CsTALE genes were classified into two subfamilies based on sequence homology and phylogenetic analyses, and the classification was equally strongly supported by the highly conserved gene structures and motif/domain compositions. CsTALEs were found to be unevenly distributed on the chromosomes, and duplication analysis revealed that segmental duplication and purifying selection have been major driving force in the evolution of these genes. Expression profile analysis indicated that CsTALE genes exhibit a discernible spatial expression pattern in different tissues and differing expression patterns in response to different biotic/abiotic stresses. Of the 18 CsTALE genes examined, 10 were found to be responsive to high temperature, four to low temperature, eight to salt, and four to wounding. Moreover, the expression of CsTALE3/8/12/16 was induced in response to infection with the fungal pathogen Diaporthe citri and bacterial pathogen Candidatus Liberibacter asiaticus, whereas the expression of CsTALE15/17 was strongly suppressed. The transcriptional activity of CsTALE proteins was also verified in yeast, with yeast two-hybrid assays indicating that CsTALE3/CsTALE8, CsTALE3/CsTALE11, CsTALE10/CsTALE12, CsTALE14/CsTALE8, CsTALE14/CsTALE11 can form respective heterodimers. The findings of this study could lay the foundations for elucidating the biological functions of the TALE family genes in sweet orange and contribute to the breeding of stress-tolerant plants.
| S-EPMC8811264 | biostudies-literature
Project description:SBP-box is an important plant-specific transcription factor family and is involved in diverse biological processes. Here, we identified a total of 15 SBP-BOX genes in the important fruit crop sweet orange (Citrus sinensis) and characterized their gene structures, conserved domain and motif, chromosomal location, and cis-acting regulatory elements. SBP genes were classified into four subfamilies based on the amino acid sequence homology, and the classification is equally strongly supported by the gene and protein structures. Our analysis revealed that segmental duplication events were the main driving force in the evolution of CsSBP genes, and gene pairs might undergo extensive purifying selection. Further synteny analysis of the SBP members among sweet orange and other plant species provides valuable information for clarifying the CsSBP family evolutionary relationship. According to publicly available RNA-seq data and qRT-PCR analysis from various sweet orange tissues, CsSBP genes may be expressed in different tissues and developmental stages. Gene expression analysis showed variable expression profiles of CsSBP genes under various abiotic stresses, such as high and low-temperature, salt, and wound treatments, demonstrating the potential role of SBP members in sweet orange response to abiotic stress. Noticeably, all CsSBP genes were also downregulated in sweet orange upon the infection of an important fungal pathogen Diaporthe citri. Our results provide valuable information for exploring the role of SBP-Box in sweet orange.
| S-EPMC8396319 | biostudies-literature
Project description:Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.
| S-EPMC4141690 | biostudies-literature
Project description:GRAS genes are suggested to be grouped into plant-specific transcriptional regulatory families that have been reported to participate in multiple processes, including plant development, phytohormone signaling, the formation of symbiotic relationships, and response to environmental signals. GRAS genes have been characterized in a number of plant species, but little is known about this gene family in Citrus sinensis. In this study, we identified a total of 50 GRAS genes and characterized the gene structures, conserved motifs, genome localizations and cis-elements within their promoter regions. According to their structural and phylogenetic features, the identified sweet orange GRAS members were divided into 11 subgroups, of which subfamily CsGRAS34 was sweet orange-specific. Based on publicly available RNA-seq data generated from callus, flower, leaf and fruit in sweet orange, we found that some sweet orange GRAS genes exhibited tissue-specific expression patterning. Three of the six members of subfamily AtSHR, particularly CsGRAS9, and two of the six members of subfamily AtPAT1 were preferentially expressed in leaf. Moreover, protein-protein interactions with CsGRAS were predicted. Gene expression analysis was performed under conditions of phosphate deficiency, and GA3 and NaCl treatment to identify the potential functions of GRAS members in regulating stress and hormone responses. This study provides the first comprehensive understanding of the GRAS gene family in the sweet orange genome. As such, the study generates valuable information for further gene function analysis and identifying candidate genes to improve abiotic stress tolerance in citrus plants.
| S-EPMC6377710 | biostudies-literature
Project description:Sweet orange (Citrus sinensis) is a sub-tropical fruit crop with important economic value that is popular worldwide; however, various pathogens significantly affect citrus cultivation and distribution. AlkB homolog (ALKBH) proteins play crucial roles in RNA metabolism and translation in plants; however, no systematic investigations have been performed on ALKBH in sweet oranges. In this study, ten ALKBH gene family members were identified in Citrus sinensis genome. Standardized analyses, including physical properties, phylogenetic analysis, gene structure, motif composition, cis-acting element prediction, chromosome distribution, and synteny analysis, were conducted. The phylogenetic analysis suggested that the ten proteins were clustered into three groups, each of which had similar motifs and gene structures. Gene expression profiling revealed that almost all CsALKBH proteins were highly expressed in callus, and ALKBH9/10-like group members responded positively to biotic stress. Overall, this study is the first to report a genome-wide assessment of the ALKBH family in sweet oranges and provides valuable insights for candidate gene selection and elucidating the molecular mechanism of sweet orange response to pathogenic infections.
| S-EPMC9857262 | biostudies-literature
Project description:Auxin response factors (ARFs) are an important family of proteins in auxin-mediated response, with key roles in various physiological and biochemical processes. To date, a genome-wide overview of the ARF gene family in citrus was not available. A systematic analysis of this gene family in citrus was begun by carrying out a genome-wide search for the homologs of ARFs. A total of 19 nonredundant ARF genes (CiARF) were found and validated from the sweet orange. A comprehensive overview of the CiARFs was undertaken, including the gene structures, phylogenetic analysis, chromosome locations, conserved motifs of proteins, and cis-elements in promoters of CiARF. Furthermore, expression profiling using real-time PCR revealed many CiARF genes, albeit with different patterns depending on types of tissues and/or developmental stages. Comprehensive expression analysis of these genes was also performed under two hormone treatments using real-time PCR. Indole-3-acetic acid (IAA) and N-1-napthylphthalamic acid (NPA) treatment experiments revealed differential up-regulation and down-regulation, respectively, of the 19 citrus ARF genes in the callus of sweet orange. Our comprehensive analysis of ARF genes further elucidates the roles of CiARF family members during citrus growth and development process.
| S-EPMC4378189 | biostudies-literature
Project description: Not available
| S-EPMC10909352 | biostudies-literature