Genome-wide characterization and expression analysis of the YUCCA genes in castor (Ricinus Communis L.)

Auxin response factors (ARFs) are plant-specific transcription factors that bind explicitly to Auxin Response Elements and mediate downstream expression of auxin responsive genes involved at various stages of plant growth and development. This study identified 52 ARF genes located within the wheat genome. Based on phylogenetic analysis, the identified ARF proteins of wheat were classified into four classes (class I, II, III and IV). Synteny analysis revealed the orthologous relation with other monocots. The maximum numbers of predicted ARF genes were mapped on wheat chromosome 3B Ten conserved motifs of ARF was determined on all the identified sequences. Based on amino acid composition of the middle region of the ARF proteins, nine ARF proteins were transcription activators and the remaining were transcription repressors. The ARF genes of wheat contained 1–17 introns and deduced proteins of the genes having similar pattern of intron-exon distribution clustered within the same clade in the phylogenetic tree. TaARF1, TaARF4, TaARF7, TaARF34, TaARF39 were predicted to be targeted by the stress responsive miRNA Tae-miRNA160. The identified proteins were mostly localized within the nucleus and had sequence specific DNA binding activity. They were annotated in regulation of expression of early auxin responsive genes in auxin signaling pathway. Thirty-one TaARF proteins interacted and exhibited co-expressed regulation with other TaARF and Aux/IAA proteins. Increased expression of TaARF1 and TaARF23 at 120 h post inoculation (hpi) and 72 hpi in resistant and susceptible isolines respectively, specifies their roles in providing better resistance to the plant during leaf-rust infection.

(1) Background: Brassinosteroids (BRs) are important hormones involved in almost all stages of plant growth and development, and sterol dehydrogenase is a key enzyme involved in BRs biosynthesis. However, the sterol dehydrogenase gene family of Populus yunnanensis Dode (P. yunnanensis) has not been studied. (2) Methods: The PyDET2 (DEETIOLATED2) gene family was identified and analyzed. Three genes were screened based on RNA-seq of the stem tips, and the PyDET2e was further investigated via qRT-PCR (quantitative real-time polymerase chain reaction) and subcellular localization. (3) Results: The 14 DET2 family genes in P. yunnanensis were categorized into four groups, and 10 conserved protein motifs were identified. The gene structure, chromosome distribution, collinearity, and codon preference of all PyDET2 genes in the P. yunnanensis genome were analyzed. The codon preference of this family is towards the A/U ending, which is strongly influenced by natural selection. The PyDET2e gene was expressed at a higher level in September than in July, and it was significantly expressed in stems, stem tips, and leaves. The PyDET2e protein was localized in chloroplasts. (4) Conclusions: The PyDET2e plays an important role in the rapid growth period of P. yunnanensis. This systematic analysis provides a basis for the genome-wide identification of genes related to the brassinolide biosynthesis process in P. yunnanensis, and lays a foundation for the study of the rapid growth mechanism of P. yunnanensis.

BackgroundLeucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively.ResultsAll LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%.ConclusionsOur results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.

Purpose. Establishing the regularities for the monitoring of the bioenergy crop conditions using Sentinel-2 and UAV-derived imagery. Methods. A field experiment was carried out in an experimental field of the Institute of Bioenergy Crops and Sugar Beet National Academy of Agrarian Sciences of Ukraine (50.023194, 30.173895), located in a zone of unstable soil moisture in the Right Bank Forest Steppe, in 2022−2023. Results. Among the studied traditional crops, sugar sorghum, sugar beet, and fodder beet are interesting crops from the standpoint of biomass for energy, as they can produce 110 t/ha, 120 t/ha, and 135 t/ha of biomass, respectively, or 20 t/ha, 26 t/ha, and 24 t/ha of dry matter, respectively. The yield of energy crops can be predicted with an acceptable level of accuracy using many known vegetation indices. However, the relationships between vegetation indices and crop yield are not consistent at every stage of plant growth and development, leading to low accuracy in yield estimation. The combination of vegetation indices related to the structural characteristics of the canopy and chlorophyll content in the aboveground biomass can improve the accuracy of yield estimation. Moreover, combining vegetation indices related to canopy structure, chlorophyll content, and stress indices as input to yield prediction models may provide even higher correlations for yield prediction. Conclusions. Usually, plantations of miscanthus and switchgrass are fertilised annually, while willow and poplar are fertilised every 3–4 years, after each harvesting. Therefore, the nutrient provision of tree species may not be sufficient. It was found that the content of total nitrogen in the soil of bioenergy plantations highly correlates with NDVI. To use NDVI for bioenergy crop prediction, an algorithm for determining the level of plant nutrients should be developed. It was found that at the end of the growing season (September or early October), the use of vegetation indices allows for the accurate estimation of the size and condition of bioenergy plantations since most crops in this period are already harvested. Sentinel-2-derived imagery is useful for monitoring bioenergy crop plantations as it provides images with a resolution of 10 m at 3–5-day revisiting time. We investigated NDVI on a total area of Miscanthus × gigantheus plantations of 2.9 ha. The satellite-derived data accumulated and aggregated by the OneSoil application as of August 20 and September 19 resulted in NDVI values of 0.80 and 0.70, respectively, while the NDVI obtained with UAV imagery was 0.82 and 0.77, respectively. Consequently, the satellite can provide quite acceptable NDVI data for use in the monitoring of bioenergy plantation yield at the national level.

BackgroundRING-H2 finger E3 ligase (RH2FE3) genes encode cysteine-rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome-wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported.MethodsWe performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated Ka/Ks values of G. hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all-versus-all BLASTP searches. We predicted cis-regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue-specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction (qRT-PCR) analysis.ResultsWe investigated 140 G. hirsutum, 80 G. arboreum, and 89 G. raimondii putative RH2FE3 genes and their evolutionary mechanisms and compared them with orthologs in Arabidopsis and rice. A domain-based analysis of the G. hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G. hirsutum chromosomes, and 60 duplication events (4 tandem and 56 segmental duplications) and 98 orthologs were detected. cis-elements were detected in the promoter regions of G. hirsutum RH2FE3 genes. Microarray data and qRT-PCR analyses showed that G. hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the identified genes were up-regulated in response to phytohormones (brassinolide, gibberellic acid (GA), indole-3-acetic acid (IAA), and salicylic acid (SA)) and abiotic stresses (cold, heat, drought, and salt).ConclusionsThe genome-wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis-element prediction, and expression profile analysis of G. hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome-wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G. hirsutum RH2FE3 genes.

BackgroundPlant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, such as lipid transfer, signal transduction, and pathogen defense. To date, a comprehensive analysis of the potato nsLTP gene family is still lacking after the completion of potato (Solanum tuberosum L.) genome sequencing. A genome-wide characterization, classification and expression analysis of the StnsLTP gene family was performed in this study.ResultsIn this study, a total of 83 nsLTP genes were identified and categorized into eight types based on Boutrot’s method. Multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, protein domains, chromosome locations, and cis-elements in the promoter sequences, were analyzed. The chromosome distribution and the collinearity analyses suggested that the expansion of the StnsLTP gene family was greatly enhanced by the tandem duplications. Ka/Ks analysis showed that 47 pairs of duplicated genes tended to undergo purifying selection during evolution. Moreover, the expression of StnsLTP genes in various tissues was analyzed by using RNA-seq data and verified by quantitative real-time PCR, revealing that the StnsLTP genes were mainly expressed in younger tissues. These results indicated that StnsLTPs may played significant and functionally varied roles in the development of different tissues.ConclusionIn this study, we comprehensively analyzed nsLTPs in potato, providing valuable information to better understand the functions of StnsLTPs in different tissues and pathways, especially in response to abiotic stress.

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

The calmodulin-binding protein 60 (CBP60) family comprises essential Ca2+-responsive transcription factors that orchestrate salicylic acid (SA)-mediated immunity and broader stress responses. Despite being extensively characterized in model species, the CBP60 family remains poorly understood in watermelon (Citrullus lanatus), a globally significant cucurbit crop highly susceptible to aphid infestation and fusarium wilt. In this study, we performed a comprehensive genome-wide identification and characterization of the CBP60 gene family in watermelon, identifying 16 putative ClaCBP60 members, all of which harbor the conserved calmodulin-binding domain. These genes are non-randomly distributed across chromosomes, featuring a prominent cluster of 10 members on chromosome 3. Phylogenetic analysis across seven cucurbit species categorized the CBP60 proteins into four distinct subfamilies, revealing both evolutionary conservation and lineage-specific diversification. Gene structure and conserved motif analyses revealed shared core domains with subfamily-specific variations, indicative of functional divergence. Furthermore, synteny analysis showed strong collinearity with cucumber and melon, reflecting the evolutionary stability of key CBP60 loci. Transcriptional profiling under F. oxysporum infection and aphid infestation revealed dynamic expression patterns, with ClaCBP60_01 and ClaCBP60_16 exhibiting rapid and robust induction during the early stages of both stresses. These findings indicated that ClaCBP60 genes operate in a coordinated yet diversified manner to modulate defense signaling against F. oxysporum and aphid attack. This study provides a systematic insight into CBP60 family members in watermelon, establishing a foundation for validation and molecular breeding aimed at enhancing biotic tolerance.

The ubiquitin-mediated post-translational regulatory pathway regulates a broad range of cell functions in all eukaryotes. It requires the involvement of a large number of E3 ligases, of which more than one third belongs to the RING protein family as in Arabidopsis thaliana. In this study, a total of 756 RING domains in 734 predicted proteins were identified in Brassica oleracea. Their encoding genes were characterized by RING domain type, additional domain, and expression pattern, and mapped on the nine chromosomes of B. oleracea. Comparison of these results with B. rapa and A. thaliana revealed some common as well as species-specific features. Our results showed that the differential gene loss following the whole genome triplication has largely contributed to the RING protein gene number variation among these species, although other factors such as tandem duplication, RING domain loss, or modification had also contributed to this variation. Analysis of RNA-seq data showed that these RING protein genes were functionally diversified and involved in all the stages of plant growth and development, and that the triplicated members were also diverged in expression with one member often more dominantly expressed over the two others in the majority of cases. Our study lays the foundation for further functional determination of each RING protein gene among species of the genus Brassica.

Plant-specific GRAS transcription factors play important roles in regulating growth, development, and stress responses. Castor beans (Ricinus communis) are important non-edible oilseed plants, cultivated worldwide for its seed oils and its adaptability to growth conditions. In this study, we identified and characterized a total of 48 GRAS genes based on the castor bean genome. Combined with phylogenetic analysis, the castor bean GRAS members were divided into 13 distinct groups. Functional divergence analysis revealed the presence of mostly Type-I functional divergence. The gene structures and conserved motifs, both within and outside the GRAS domain, were characterized. Gene expression analysis, performed in various tissues and under a range of abiotic stress conditions, uncovered the potential functions of GRAS members in regulating plant growth development and stress responses. The results obtained from this study provide valuable information toward understanding the potential molecular mechanisms of GRAS proteins in castor beans. These findings also serve as a resource for identifying the genes that allow castor beans to grow in stressful conditions and to enable further breeding and genetic improvements in agriculture.

H1s, or linker histones, are ubiquitous proteins in eukaryotic cells, consisting of a globular GH1 domain flanked by two unstructured tails. Whilst it is known that numerous non-allelic variants exist within the same species, the degree of interspecific and intraspecific variation and divergence of linker histones remain unknown. The conserved basic binding sites in GH1 and evenly distributed strong positive charges on the C-terminal domain (CTD) are key structural characters for linker histones to bind chromatin. Based on these features, we identified five linker histones from 13 GH1-containing proteins in castor bean (Ricinus communis), which were named as RcH1.1, RcH1.2a, RcH1.2b, RcH1.3, and RcH1.4 based on their phylogenetic relationships with the H1s from five other economically important Euphorbiaceae species (Hevea brasiliensis Jatropha curcas, Manihot esculenta Mercurialis annua, and Vernicia fordii) and Arabidopsis thaliana. The expression profiles of RcH1 genes in a variety of tissues and stresses were determined from RNA-seq data. We found three RcH1 genes (RcH1.1, RcH1.2a, and RcH1.3) were broadly expressed in all tissues, suggesting a conserved role in stabilizing and organizing the nuclear DNA. RcH1.2a and RcH1.4 was preferentially expressed in floral tissues, indicating potential involvement in floral development in castor bean. Lack of non-coding region and no expression detected in any tissue tested suggest that RcH1.2b is a pseudogene. RcH1.3 was salt stress inducible, but not induced by cold, heat and drought in our investigation. Structural comparison confirmed that GH1 domain was highly evolutionarily conserved and revealed that N- and C-terminal domains of linker histones are divergent between variants, but highly conserved between species for a given variant. Although the number of H1 genes varies between species, the number of H1 variants is relatively conserved in more closely related species (such as within the same family). Through comparison of nucleotide diversity of linker histone genes and oil-related genes, we found similar mutation rate of these two groups of genes. Using Tajima’s D and ML-HKA tests, we found RcH1.1 and RcH1.3 may be under balancing selection.

The amino acid/auxin permease (AAAP) gene family plays an important role in the long-distance amino acid transport pathway and takes part in various stages of plant growth and development. However, little is known about the AAAP gene family in Medicago truncatula. Here, we identified 86 putative MtAAAP family members using genome sequence information. Based on phylogenetic analysis, these MtAAAP genes were categorized into eight distinct subfamilies. The MtAAAP genes were mapped on 8 chromosomes and duplication events appeared widely, with 19 and 21 pairs of MtAAAP genes showing segment and tandem duplication events, respectively. Ratio of Ka/Ks indicated that duplicated genes underwent purifying selection. Analysis of RNA-seq data showed that MtAAAP genes exhibited specific expression patterns among different tissues and abiotic stress, indicating that MtAAAP members were involved in plant developmental regulation and stress responses. Expression patterns of 16 MtAAAP genes under abiotic stress were verified by qRT-PCR. The present study provides a foundation for the functional analysis of MtAAAPs in developmental regulation and stress responses.

Crown gall is one of the most dangerous bacterial diseases affecting the production of fruit tree nurseries in Egypt and many countries of the world. In the present study, ten isolates of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing rhizobacteria were isolated from the rhizosphere of apricot (Prunus armeniaca L.) and plum (Prunus domestica L.) trees to evaluate their ability to decrease tumor formation by Agrobacterium tumefaciens (synonym Rhizobium radiobacter). The ten isolates were identified as Pseudomonas strains based on 16S rRNA gene sequence analysis and deduced protein sequences obtained from a partial ACC deaminase structural gene (acdS) sequence. Co-inoculating castor bean (Ricinus communis L.) and kalanchoe (Kalanchoe sp.) plants with A. tumefaciens and four ACC deaminase-producing Pseudomonas isolates decreased tumor formation. However, six ACC deaminase-producing Pseudomonas isolates produced varying results in these two plant species. The results showed that isolates of Pseudomonas vancouverensis reduced tumor formation when co-inoculated with A. tumefaciens in castor bean and kalanchoe plants. However, the isolate P. putida inhibited tumor formation in castor bean plants but did not achieve the same effect in kalanchoe plants. Additionally, isolates of P. frederiksbergensis and P. kilonensis decreased tumor formation in kalanchoe plants while increasing tumor formation in castor bean plants. The results showed that ACC deaminase-producing P. vancouverensis is a promising biocontrol agent against A. tumefaciens.

Bioenergy crops are potential renewable sources of bio-diesel which have low emission profiles, environmentally beneficial, and capable of substituting petro-diesel. However, since most of them are introduced or are not native, it is essential to reduce the ecological and economic consequences of invasive pest introductions and the potential invasiveness of species not yet introduced. The Australian Weed Risk Assessment (WRA) is a plant screening method and has the highest accuracy. The objective of this study was to conduct an agronomic and invasive weed risk assessment of three potential bioenergy fuel species namely: moringa (Moringa oliefera), physic nut (Jatropha curcas), and castor bean (Rincinus communis) for the Caribbean Islands. The WRA gave overall scores for moringa (0), jatropha (13) and castor oil (13). Based on their climatic adaptation and distribution, jatropha (5) and castor oil (5), the dispersal mechanism score was high (5) for both of them. The study revealed that jatropha and castor bean should not be considered as bioenergy crops within the ecological limits of the study, and that moringa should be further evaluated as bioenergy crop against invasiveness, given its agronomic potential as a high yielding oil crop. Key words: Weed risk assessment, Moringa oliefera, Jatropha curcas, Rincinus communis, bioenergy plants.

The basic leucine zipper (bZIP) transcription factors comprise a family of transcriptional regulators present extensively in plants, involved in regulating diverse biological processes such as flower and vascular development, seed maturation, stress signaling and pathogen defense. Castor bean (Ricinus communis L. Euphorbiaceae) is one of the most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. We performed a comprehensive genome-wide identification and analysis of the bZIP transcription factors that exist in the castor bean genome in this study. In total, 49 RcbZIP transcription factors were identified, characterized and categorized into 11 groups (I-XI) based on their gene structure, DNA-binding sites, conserved motifs, and phylogenetic relationships. The dimerization properties of 49 RcbZIP proteins were predicted on the basis of the characteristic features in the leucine zipper. Global expression profiles of 49 RcbZIP genes among different tissues were examined using high-throughput sequencing of digital gene expression profiles, and resulted in diverse expression patterns that may provide basic information to further reveal the function of the 49 RcbZIP genes in castor bean. The results obtained from this study would provide valuable information in understanding the molecular basis of the RcbZIP transcription factor family and their potential function in regulating the growth and development, particularly in seed filling of castor bean.