Genome-wide investigation of UDP-Glycosyltransferase family in Tartary buckwheat (Fagopyrum tataricum).

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum) belongs to Polygonaceae family and has attracted increasing attention owing to its high nutritional value. UDP-glycosyltransferases (UGTs) glycosylate a variety of plant secondary metabolites to control many metabolic processes during plant growth and development. However, there have been no systematic reports of UGT superfamily in F. tataricum. RESULTS: We identified 173 FtUGTs in F. tataricum based on their conserved UDPGT domain. Phylogenetic analysis of FtUGTs with 73 Arabidopsis UGTs clustered them into 21 families. FtUGTs from the same family usually had similar gene structure and motif compositions. Most of FtUGTs did not contain introns or had only one intron. Tandem repeats contributed more to FtUGTs amplification than segmental duplications. Expression analysis indicates that FtUGTs are widely expressed in various tissues and likely play important roles in plant growth and development. The gene expression analysis response to different abiotic stresses showed that some FtUGTs were involved in response to drought and cadmium stress. Our study provides useful information on the UGTs in F. tataricum, and will facilitate their further study to better understand their function. CONCLUSIONS: Our results provide a theoretical basis for further exploration of the functional characteristics of FtUGTs and for understanding the growth, development, and metabolic model in F. tataricum.

Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress.

MAIN CONCLUSION: This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.

Genome-wide identification, evolution, and role of SPL gene family in beet (Beta vulgaris L.) under cold stress.

BACKGROUND: SPL transcription factors play vital roles in regulating plant growth, development, and abiotic stress responses. Sugar beet (Beta vulgaris L.), one of the world's main sugar-producing crops, is a major source of edible and industrial sugars for humans. Although the SPL gene family has been extensively identified in other species, no reports on the SPL gene family in sugar beet are available. RESULTS: Eight BvSPL genes were identified at the whole-genome level and were renamed based on their positions on the chromosome. The gene structure, SBP domain sequences, and phylogenetic relationship with Arabidopsis were analyzed for the sugar beet SPL gene family. The eight BvSPL genes were divided into six groups (II, IV, V, VI, VII, and VIII). Of the BvSPL genes, no tandem duplication events were found, but one pair of segmental duplications was present. Multiple cis-regulatory elements related to growth and development were identified in the 2000-bp region upstream of the BvSPL gene start codon (ATG). Using quantitative real-time polymerase chain reaction (qRT-PCR), the expression profiles of the eight BvSPL genes were examined under eight types of abiotic stress and during the maturation stage. BvSPL transcription factors played a vital role in abiotic stress, with BvSPL3 and BvSPL6 being particularly noteworthy. CONCLUSION: Eight sugar beet SPL genes were identified at the whole-genome level. Phylogenetic trees, gene structures, gene duplication events, and expression profiles were investigated. The qRT-PCR analysis indicated that BvSPLs play a substantial role in the growth and development of sugar beet, potentially participating in the regulation of root expansion and sugar accumulation.

Genome-wide identification of the alkaloid synthesis gene family CYP450, gives new insights into alkaloid resource utilization in medicinal Dendrobium.

The medicinal Dendrobium species of Orchidaceae possess significant pharmaceutical value, and modern pharmacological research has shown that Dendrobium contains many important active ingredients. Alkaloids, the crucial components of medicinal Dendrobium, demonstrate beneficial healing properties in cardiovascular, cataract, gastrointestinal, and respiratory diseases. Members of the cytochrome P450 monooxygenase (CYP) gene family play essential roles in alkaloid synthesis, participating in alkaloid terpene skeleton construction and subsequent modifications. Although studies of the CYP family have been conducted in some species, genome-wide characterization and systematic analysis of the CYP family in medicinal Dendrobium remain underexplored. In this study, we identified CYP gene family members in the genomes of four medicinal Dendrobium species recorded in the Pharmacopoeia: D. nobile, D. chrysotoxum, D. catenatum, and D. huoshanense. Further, we analyzed the motif composition, gene replication events, and selection pressure of this family. Syntenic analysis revealed that members of the clan 710 were present on chromosome 18 in three medicinal Dendrobium species, except for D. nobile, indicating a loss of clan 710 occurring in D. nobile. We also conducted an initial screening of the CYP genes involved in alkaloid synthesis through transcriptome sequencing. Quantitative real-time reverse transcription PCR showed that the expression of DnoNew43 and DnoNew50, homologs of secologanin synthase involved in the alkaloid synthesis pathway, was significantly higher in the stems than in the leaves. This result coincided with the distribution of dendrobine content in Dendrobium stems and leaves, indicating that these two genes might be involved in the dendrobine synthesis pathway. Our results give insights into the CYP gene family evolution analysis in four medicinal Dendrobium species for the first time and identify two related genes that may be involved in alkaloid synthesis, providing a valuable resource for further investigations into alkaloid synthesis pathway in Dendrobium and other medicinal plants.

Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe.

BACKGROUND: Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS: In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS: Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.

Genome-wide identification and expression analysis of NIN-like protein (NLP) genes: Exploring their potential roles in nitrate response in tea plant (Camellia sinensis).

NIN-like proteins (NLPs) are evolutionarily conserved transcription factors that are unique to plants and play a pivotal role in responses to nitrate uptake and assimilation. However, a comprehensive analysis of NLP members in tea plants is lacking. The present study performed a genome-wide analysis and identified 33 NLP gene family members of Camellia sinensis that were distributed unequally across 5 chromosomes. Subcellular localisation predictions revealed that all CsNLP proteins were localised in the nucleus. Conservative domain analysis revealed that all of these proteins contained conserved RWP-RK and PB1 domains. Phylogenetic analysis grouped the CsNLP gene family into four clusters. The promoter regions of CsNLPs harboured cis-acting elements associated with plant hormones and abiotic stress responses. Expression profile analysis demonstrated that CsNLP8 was significantly upregulated in roots under nitrate stress conditions. Subcellular localisation analysis found CsNLP8 localised to the nucleus. Dual-luciferase reporter assay demonstrated that CsNLP8 positively regulated the expression of a nitrate transporter gene (CsNRT2.2). These findings provide a comprehensive characterisation of NLP genes in Camellia sinensis and offer insights into the biological function of CsNLP8 in regulating the response to nitrate-induced stress.

Genome-Wide Identification, Characterization and Expression Profiling of the CONSTANS-like Genes in Potato (Solanum tuberosum L.).

CONSTANS-like (COL) genes play important regulatory roles in flowering, tuber formation and the development of the potato (Solanum tuberosum L.). However, the COL gene family in S. tuberosum has not been systematically identified, restricting our knowledge of the function of these genes in S. tuberosum. In our study, we identified 14 COL genes, which were unequally distributed among eight chromosomes. These genes were classified into three groups based on differences in gene structure characteristics. The COL proteins of S. tuberosum and Solanum lycopersicum were closely related and showed high levels of similarity in a phylogenetic tree. Gene and protein structure analysis revealed similarities in the exon-intron structure and length, as well as the motif structure of COL proteins in the same subgroup. We identified 17 orthologous COL gene pairs between S. tuberosum and S. lycopersicum. Selection pressure analysis showed that the evolution rate of COL homologs is controlled by purification selection in Arabidopsis, S. tuberosum and S. lycopersicum. StCOL genes showed different tissue-specific expression patterns. StCOL5 and StCOL8 were highly expressed specifically in the leaves of plantlets. StCOL6, StCOL10 and StCOL14 were highly expressed in flowers. Tissue-specific expression characteristics suggest a functional differentiation of StCOL genes during evolution. Cis-element analysis revealed that the StCOL promoters contain several regulatory elements for hormone, light and stress signals. Our results provide a theoretical basis for the understanding of the in-depth mechanism of COL genes in regulating the flowering time and tuber development in S. tuberosum.

Genome-wide analysis of transcription factors in hippocampal tissue of cerebral palsy rats after acupuncture treatment.

BACKGROUND: Acupuncture has been shown to be effective in treating cerebral palsy (CP), reducing muscle tension, and improving motor function. However, macro-screening of key gene sets and gene-causal interaction networks for their therapeutic mechanisms have not been studied. METHODS: Applying high-throughput sequencing technology, this research discussed differentially expressed mRNAs and differential alternative splicing pre-mRNAs at the transcriptome level in rats with CP treated with acupuncture and moxibustion, and analyzed the regulatory mechanisms of these differentially expressed genes (DEGs) in CP. Changes in the levels of transcripts and alternative splicing in the hippocampi of CP rats after acupuncture treatment were analyzed. Global genes that were differentially expressed and alternative splicing events (ASEs) and regulated ASEs (RASEs) in acupuncture treatment of CP rats were analyzed. RESULTS: The RNA-seq data of acupuncture-treated rat hippocampi revealed 198 DEGs, 125 of which were related to CP, and the transcriptional regulation of RNA polymerase II was up-regulated; moreover, there were 1168 significantly different ASEs associated with CP and transcriptional regulation. There were 14 overlapping gene expression changes in transcription factors (TFs) and DEGs. CONCLUSIONS: This study found that 14 TFs were differentially expressed and a large number of TFs underwent differential alternative splicing. It is speculated that these TFs and the translated proteins of the two different transcripts produced by the differential alternative splicing of these TFs may play corresponding functions in acupuncture treatment of young rats with CP by modulating the differential expression of their target mRNAs.

Genome-wide analysis of fatty acid desaturase genes in chia (Salvia hispanica) reveals their crucial roles in cold response and seed oil formation.

Chia (Salvia hispanica) is a functional food crop with high α-linolenic acid (ALA), the omega-3 essential fatty acid, but its worldwide plantation is limited by cold-intolerance and strict short-photoperiod flowering feature. Fatty acid desaturases (FADs) are responsible for seed oil accumulation, and play important roles in cold stress tolerance of plants. To date, there is no report on systemically genome-wide analysis of FAD genes in chia (ShiFADs). In this study, 31 ShiFAD genes were identified, 3 of which contained 2 alternative splicing transcripts, and they were located in 6 chromosomes of chia. Phylogenetic analysis classified the ShiFAD proteins into 7 groups, with conserved gene structure and MEME motifs within each group. Tandem and segmental duplications coursed the expansion of ShiFAD genes. Numerous cis-regulatory elements, including hormone response elements, growth and development elements, biotic/abiotic stress response elements, and transcription factor binding sites, were predicted in ShiFAD promoters. 24 miRNAs targeting ShiFAD genes were identified at whole-genome level. In total, 15 SSR loci were predicted in ShiFAD genes/promoters. RNA-seq data showed that ShiFAD genes were expressed in various organs with different levels. qRT-PCR detection revealed the inducibility of ShiSAD2 and ShiSAD7 in response to cold stress, and validated the seed-specific expression of ShiSAD11a. Yeast expression of ShiSAD11a confirmed the catalytic activity of its encoded protein, and its heterologous expression in Arabidopsis thaliana significantly increased seed oleic acid content. This work lays a foundation for molecular dissection of chia high-ALA trait and functional study of ShiFAD genes in cold tolerance.

Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum).

YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.

Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa.

Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.

Genome-wide investigation and expression analysis of the AP2/ERF family for selection of agarwood-related genes in Aquilaria sinensis (Lour.) Gilg.

Aquilaria sinensis is an important non-timber tree species for producing high-value agarwood, which is widely used as a traditional medicine and incense. Agarwood is the product of Aquilaria trees in response to injury and fungal infection. The APETALA2/ethylene responsive factor (AP2/ERF) transcription factors (TFs) play important roles in plant stress responses and metabolite biosynthesis. In this study, 119 AsAP2/ERF genes were identified from the A. sinensis genome and divided into ERF, AP2, RAV, and Soloist subfamilies. Their conserved motif, gene structure, chromosomal localization, and subcellular localization were characterized. A stress/defense-related ERF-associated amphiphilic repression (EAR) motif and an EDLL motif were identified. Moreover, 11 genes that were highly expressed in the agarwood layer in response to whole-tree agarwood induction technique (Agar-Wit) treatment were chosen, and their expression levels in response to methyl jasmonate (MeJA), salicylic acid (SA), or salt treatment were further analyzed using the quantitative real time PCR (qRT-PCR). Among the 11 genes, eight belonged to subgroup B-3. All 11 genes were significantly upregulated under salt treatment, while eight genes were significantly induced by both MeJA and SA. In addition, the gene clusters containing these upregulated genes on chromosomes were observed. The results obtained from this research not only provide useful information for understanding the functions of AP2/ERF genes in A. sinensis but also identify candidate genes and gene clusters to dissect their regulatory roles in agarwood formation for future research.

A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress.

The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.

Role of Wheat Phosphorus Starvation Tolerance 1 Genes in Phosphorus Acquisition and Root Architecture.

The wheat plant requires elevated phosphorus levels for its normal growth and yield, but continuously depleting non-renewable phosphorus reserves in the soil is one of the biggest challenges in agricultural production worldwide. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been reported to play a key role in efficient P uptake, deeper rooting, and high yield in rice. However, the function of the PSTOL1 gene in wheat is still unclear. In this study, a total of 22 PSTOL1 orthologs were identified in the wheat genome, and found that wheat PSTOL1 orthologs are unevenly distributed on chromosomes, and these genes were under strong purifying selection. Under different phosphorus regimes, wheat PSTOL1 genes showed differential expression patterns in different tissues. These results strengthen the classification of Pakistan-13 as a P-efficient cultivar and Shafaq-06 as a P-inefficient cultivar. Phenotypic characterization demonstrated that Pakistan-13 wheat cultivar has significantly increased P uptake, root length, root volume, and root surface area compared to Shafaq-06. Some wheat PSTOL1 orthologs are co-localized with phosphorus starvation's related quantitative trait loci (QTLs), suggesting their potential role in phosphorus use efficiency. Altogether, these results highlight the role of the wheat PSTOL1 genes in wheat P uptake, root architecture, and efficient plant growth. This comprehensive study will be helpful for devising sustainable strategies for wheat crop production and adaptation to phosphorus insufficiency.

Genome-Wide Analysis of U-box E3 Ubiquitin Ligase Family in Response to ABA Treatment in Salvia miltiorrhiza.

Plant U-box (PUB) proteins are ubiquitin ligases (E3) involved in multiple biological processes and in response to plant stress. However, the various aspects of the genome and the differences in functions between the U-box E3 (UBE3) ubiquitin ligases remain quite obscure in Salvia miltiorrhiza. The 60 UBE3 genes in the S. miltiorrhiza genome were recognized in the present study. The phylogenetic analysis, gene structure, motifs, promoters, and physical and chemical properties of the genes were also examined. Based on the phylogenetic relationship, the 60 UBE3 genes were categorized under six different groups. The U-box domain was highly conserved across the family of UBE3 genes. Analysis of the cis-acting element revealed that the UBE3 genes might play an important role in a variety of biological processes, including a reaction to the abscisic acid (ABA) treatment. To investigate this hypothesis, an ABA treatment was developed for the hairy roots of S. miltiorrhiza. Thirteen out of the UBE3 genes significantly increased after the ABA treatment. The co-expression network revealed that nine UBE3 genes might be associated with phenolic acids or tanshinone biosynthesis. The findings of the present study brought fresh and new understanding to the participation of the UBE3 gene family in plants, specifically in their biological responses mediated by the ABA. In S. miltiorrhiza, this gene family may be crucial during the ABA treatment. Significantly, the results of this study contribute novel information to the understanding of the ubiquitin ligase gene and its role in plant growth.

Identification and expression analysis of the sucrose synthase gene family in pomegranate (Punica granatum L.).

BACKGROUND: Sucrose synthase (SUS, EC 2.4.1.13) is one of the major enzymes of sucrose metabolism in higher plants. It has been associated with C allocation, biomass accumulation, and sink strength. The SUS gene families have been broadly explored and characterized in a number of plants. The pomegranate (Punica granatum) genome is known, however, it lacks a comprehensive study on its SUS genes family. METHODS: PgSUS genes were identified from the pomegranate genome using a genome-wide search method. The PgSUS gene family was comprehensively analyzed by physicochemical properties, evolutionary relationship, gene structure, conserved motifs and domains, protein structure, syntenic relationships, and cis-acting elements using bioinformatics methods. The expression pattern of the PgSUS gene in different organs and fruit development stages were assayed with RNA-seq obtained from the NCBI SRA database as well as real-time quantitative polymerase chain reaction (qPCR). RESULTS: Five pomegranate SUS genes, located on four different chromosomes, were divided into three subgroupsaccording to the classification of other seven species. The PgSUS family was found to be highly conserved during evolution after studying the gene structure, motifs, and domain analysis. Furthermore, the predicted PgSUS proteins showed similar secondary and tertiary structures. Syntenic analysis demonstrated that four PgSUS genes showed syntenic relationships with four species, with the exception of PgSUS2. Predictive promoter analysis indicated that PgSUS genes may be responsive to light, hormone signaling, and stress stimulation. RNA-seq analysis revealed that PgSUS1/3/4 were highly expressed in sink organs, including the root, flower, and fruit, and particularly in the outer seed coats. qPCR analysis showed also that PgSUS1, PgSUS3, and PgSUS4 were remarkably expressed during fruit seed coat development. Our results provide a systematic overview of the PgSUS gene family in pomegranate, developing the framework for further research and use of functional PgSUS genes.

Comprehensive analysis of the BES1 gene family and its expression under abiotic stress and hormone treatment in Populus trichocarpa.

The BRI1 EMS SUPPRESSOR 1/BRASSINAZOLE RESISTANT 1 (BES1/BZR1) plays a vital role in plant growth and development and stress responses, but there are few studies on poplar BES1 genes. In this study, we identified 14 BES1 genes in the Populus trichocarpa genome and analyzed the expression under hormone treatment and abiotic stress. The PtrBES1 genes were classified into seven subgroups (I-VII) through phylogenetic analysis. All the paralogous gene pairs were shown to be subjected to expansion by segment duplication and purification selection during the PtrBES1 family evolution. Promoter cis-element analysis showed that the PtrBES1 promoter contains stress related cis-elements including ABRE-motif, MBS and TC-rich elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the PtrBES1 genes were upregulated upon NaCl, Polyethylene glycol 6000 (PEG6000) stress as well as the major stress hormone abscisic acid (ABA) treatment. Under the three treatments, PtrBES1-7 showed high expression levels in leaves and roots. Physiological experiments showed that the overexpression PtrBES1-7 line could enhance tolerance to drought stress in P. trichocarpa by improving the ability to scavenge ROS (reactive oxygen species). This is specifically reflected in the fact that the overexpression line contains less ROS (O2- and H2O2) and more antioxidant enzymes (1.42 times SOD and 1.5 times POD) than the control line. The preliminary results of this study provided a solid basis for the future functional studies of the BES1 gene family in P. trichocarpa.

Genome-wide identification of U-box genes and protein ubiquitination under PEG-induced drought stress in potato.

Protein ubiquitination is one of the most important posttranslational modifications in eukaryotic cells, and it is involved in a variety of biological processes, including abiotic stress response. The ubiquitination modification is highly specific, which depends on the accurate recognition of substrate proteins by ubiquitin ligase. Plant U-box (PUB) proteins are a class of ubiquitin ligases, multiple members of which have shown to participate in water-deficit stress in Arabidopsis and rice. U-box gene family and large-scale profiling of the ubiquitome in potato has not been reported to date, although it is one of the most important food crops. The identified 66 U-box genes from the potato genome database were unevenly distributed on 10 chromosomes. These StPUBs have a large number of tandem repeat sequences. Analysis of gene expression characteristics revealed that many StPUBs responded to abiotic stress. Three hundred and fourteen lys modification sites were identified under PEG-induced drought stress, which were distributed on 200 proteins, with 25 differential ubiquitination modification sites, most of which were up-regulated. The ubiquitination modification in potato protein was enhanced under PEG-induced drought stress, and U-box ubiquitin ligase was involved. This study provides an overall strategy and rich data set to clarify the effects of ubiquitination on potatoes under PEG-induced drought stress and the ubiquitination modification involved in potato U-box genes in response to PEG-induced drought stress.

Comprehensive analysis of LIM gene family in wheat reveals the involvement of TaLIM2 in pollen development.

LIM domain proteins were involved in organizing the cytoskeleton, adjusting the metabolism and gene expression, some of them were specific express in pollen. LIM gene family in plants were studied in sunflower, tobacco, foxtail millet, rape, rice and Arabidopsis thaliana, however, it has not been investigated in wheat to date. In the present study, we totally characterized 29 TaLIM genes through genome-wide analysis, which were divided into two categories and five subclasses according to phylogenetic analysis. RNA-Seq analysis indicated the expression patterns of TaLIM genes have specific temporal and spatial characteristics, especially TaLIM2 was highly expressed in fertility anthers. Phenotypic and cytological of BSMV: TaLIM2 showed that it had defects in the later stage of pollen development and germination, which further testified that TaLIM2 was closely related to fertility conversion. These findings will be useful for functional analysis of LIM genes in wheat fertility and contribute to hybrid wheat breeding.

Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species.

Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the selective oxidative cleavage steps from carotenoids to apocarotenoids, which are essential for the synthesis of biologically important molecules such as retinoids, and the phytohormones abscisic acid (ABA) and strigolactones. In addition, CCDs play important roles in plant biotic and abiotic stress responses. Till now, a comprehensive characterization of the CCD gene family in the economically important crop cotton (Gossypium spp.) is still missing. Here, we performed a genome-wide analysis and identified 33, 31, 16 and 15 CCD genes from two allotetraploid Gossypium species, G. hirsutum and G. barbadense, and two diploid Gossypium species, G. arboreum and G. raimondii, respectively. According to the phylogenetic tree analysis, cotton CCDs are classified as six subgroups including CCD1, CCD4, CCD7, CCD8, nine-cis-epoxycarotenoid dioxygenase (NCED) and zaxinone synthase (ZAS) sub-families. Evolutionary analysis shows that purifying selection dominated the evolution of these genes in G. hirsutum and G. barbadense. Predicted cis-acting elements in 2 kb promoters of CCDs in G. hirsutum are mainly involved in light, stress and hormone responses. The transcriptomic analysis of GhCCDs showed that different GhCCDs displayed diverse expression patterns and were ubiquitously expressed in most tissues; moreover, GhCCDs displayed specific inductions by different abiotic stresses. Quantitative reverse-transcriptional PCR (qRT-PCR) confirmed the induction of GhCCDs by heat stress, salinity, polyethylene glycol (PEG) and ABA application. In summary, the bioinformatics and expression analysis of CCD gene family provide evidence for the involvement in regulating abiotic stresses and useful information for in-depth studies of their biological functions in G. hirsutum. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02805-9.