Important Gene Family Research Articles

Genome-wide identification of the GRAS transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under drought stress

GRAS transcription factors are one of the most important plant-specific gene families and play diverse roles in plant development and abiotic stress. A total of 55 MsGRAS genes were obtained from the autotetraploid cultivated alfalfa genome of XinJiangDaYe. Phylogenetic analysis demonstrated that the MsGRAS genes were classified into 10 subgroups, including HAM, LAS, SCL4/7, DLT, SCR, SCL3, DELLA, PAT1, SHR, and LISCL. Gene structure analysis showed that 92.7% of MsGRAS genes lacked introns. Many hormone- and stress-related cis-regulatory elements have been identified in the promoter regions of MsGRAS genes. A total of 55 MsGRAS genes were unevenly mapped on 32 alfalfa chromosomes, except for MsGRAS53 and MsGRAS55. Gene duplication analysis demonstrated that segmental duplication was the key driving force for the expansion of this gene family during evolution. Expression analysis of 55 MsGRAS genes in various tissues and under drought stress showed that they were differentially expressed. RT-qPCR analysis revealed that the expression of eight selected MsGRAS genes was significantly induced by drought stress. Collectively, our study is the first to investigate GRAS genes in autotetraploid cultivated alfalfa, and these findings will further enrich our knowledge regarding GRAS transcription factor genes and establish a foundation for enhancing drought stress tolerance by genetic engineering in autotetraploid cultivated alfalfa.

Genome-wide analysis of the SAUR gene family and function exploration of DlSAUR32 during early longan somatic embryogenesis

The early auxin responsive small auxin up-regulated RNA (SAUR) family is an important gene family in the auxin signal transduction pathway. This study focused on the regulatory mechanism of DlSAUR genes during early somatic embryogenesis (SE) and its response to hormone treatment and abiotic stress. Mining of the available Dimocarpus longan Lour. (D. longan) genome sequence yielded 68 putative SAUR genes. Transcript profiles based on RNA-seq data showed that most of the 24 detected DlSAUR genes were highly expressed in the globular embryos (GE) (10) and most of them responded to heat stress and 2,4-D treatment. The results of qRT-PCR showed that most of DlSAUR genes were up-regulated under auxin inhibitor N-1-naphthylphthalamic acid (NPA) and auxin indole-3-acetic acid (IAA) treatments. Moreover, NPA could promote longan SE. The assay for ATAC-seq data analysis showed that chromatin accessibility of 19 of the 24 DlSAUR genes were open during early SE, and most DlSAUR genes differentially expressed during early SE were not associated with H3K4me1 signal enrichment. The DlSAUR32 was selected for subcellular localization and RNA-seq analysis, which encode a cell nuclear-localized protein. Dual-luciferase assays and transient transformation showed that the transcription factors (TFs) DlWRKY75-1 and DlWRKY75-2 might bind to the DlSAUR32 promoters to inhibition gene transcription. Transient overexpression of DlWRKY75-1 and DlWRKY75-2 decreased IAA content in N. benthamiana leaves. Thus, the regulatory network composed of DlSAUR32 and its related TFs may regulate the early longan SE and be involved in the auxin response regulatory pathway of longan.

The effects of a few important gene families on sorghum agronomic traits

Sorghum (Sorghum bicolor [L.] Moench), a main food for more than 500 million impoverished and food insecure people in arid and semi-arid regions of Sub-Saharan Africa (SSA) and South Asia, is an important crop for food and nutritional security (SA). Sorghum has the most acceptance in these drought-prone areas due to its good tolerance to harsh settings, high yield, and use as a good source of forages. In this review, the objective of this study is to document the production and use Sorghum in improvement programmed through a literature review, we used publications from journals to explore gene families, how they evolved, gene family theories, how gene families influenced agronomic features in sorghum, and in-depth studies of the key ten gene families in sorghum. The future prospects on sorghum enhancement include genomic selections and gene families, as well as comparative genomic selections. Furthermore, understanding the mechanism of these gene families is important for addressing problems that plague sorghum production, including as infections, drought, and heat stress. We can accurately improve traits using modern techniques such as marker-assisted selection, Genomic selections (GS), Marker-assisted backcrossing (MABC), Marker-assisted recurrent selection (MARS), Marker-assisted selections (MAS), and Genome-wide selections (GWAS) if we have the above gene families of interest (GWAS). Sorghum as a desirable breed: future paths and prospects.

The functional analysis of sugar transporter proteins in sugar accumulation and pollen tube growth in pummelo (Citrus grandis).

Sugar transporter proteins (STPs) play vital roles in sugar transport and allocation of carbon sources in plants. However, the evolutionary dynamics of this important gene family and their functions are still largely unknown in citrus, which is the largest fruit crop in the world. In this study, fourteen non-redundant CgSTP family members were identified in pummelo (Citrus grandis). A comprehensive analysis based on the biochemical characteristics, the chromosomal location, the exon-intron structures and the evolutionary relationships demonstrated the conservation and the divergence of CgSTPs. Moreover, CgSTP4, 11, 13, 14 were proofed to be localized in plasma membrane and have glucose transport activity in yeast. The hexose content were significantly increased with the transient overexpression of CgSTP11 and CgSTP14. In addition, antisense repression of CgSTP4 induced the shorter pollen tube length in vitro, implying the potential role of CgSTP4 in pummelo pollen tube growth. Taken together, this work explored a framework for understanding the physiological role of CgSTPs and laid a foundation for future functional studies of these members in citrus species.

Genome-Wide Characterization and In-silico Transcriptional Expression Analysis of PEBP Family in Solanum lycopersicum L.

Phosphatidylethanolamine-binding proteins (PEBPs) are an important gene family with highly conserved protein sequences represented in three taxonomic divisions. In plants, PEBP genes are an important actors in the regulation of flowering time, plant architecture and seed dormancy. Despite this, PEBP genes have not been genome-wide identified and systematically analyzed in tomato. In this study, the PEBP gene family in tomato, one of the economically important Solanum species, was comprehensively identified genome-wide and characterized by bioinformatics tools. Here, 12 PEBP genes were identified, which were classified into four clades based on their phylogenetic relationships and the presence of the structurally conserved domain/motif. In addition, the gene structure, conserved protein structure, promoter regions, and digital expression levels of these PEBP genes were determined. Digital expression profiling of SlPEBP transcripts revealed their expression in most developmental and anatomical tissues. These results will provide the further functional and evolutionary characterization of PEBP genes in tomato.

An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing.

In plant development, flowering is the most widely studied process. Floral forms show large diversity in different species due to simple variations in basic architecture. To determine the floral gene expression during the past decade, MADS-box genes have identified as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by various molecular technologies such as ChIP and next-generation DNA sequencing, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Likewise, the big data analysis revealed combined activity of transcriptional regulators and floral organ identity factors regulate the flower developmental programs. Thus, with the help of cutting-edge technologies like RNA-Sequencing, sex determination is now better understood in few non-model plants Therefore, the recent advances in next-generation sequencing (NGS) should enable researchers to identify the full range of floral gene functions, which will significantly help to understand plant development and evolution. This review summarizes the floral homeotic genes in model and non-model species to understand the flower development genes and dioecy evolution.

Evolution and functional analysis of the GRAS family genes in six Rosaceae species

BackgroundGRAS genes formed one of the important transcription factor gene families in plants, had been identified in several plant species. The family genes were involved in plant growth, development, and stress resistance. However, the comparative analysis of GRAS genes in Rosaceae species was insufficient.ResultsIn this study, a total of 333 GRAS genes were identified in six Rosaceae species, including 51 in strawberry (Fragaria vesca), 78 in apple (Malus domestica), 41 in black raspberry (Rubus occidentalis), 59 in European pear (Pyrus communis), 56 in Chinese rose (Rosa chinensis), and 48 in peach (Prunus persica). Motif analysis showed the VHIID domain, SAW motif, LR I region, and PFYRE motif were considerably conserved in the six Rosaceae species. All GRAS genes were divided into 10 subgroups according to phylogenetic analysis. A total of 15 species-specific duplicated clades and 3 lineage-specific duplicated clades were identified in six Rosaceae species. Chromosomal localization presented the uneven distribution of GRAS genes in six Rosaceae species. Duplication events contributed to the expression of the GRAS genes, and Ka/Ks analysis suggested the purification selection as a major force during the evolution process in six Rosaceae species. Cis-acting elements and GO analysis revealed that most of the GRAS genes were associated with various environmental stress in six Rosaceae species. Coexpression network analysis showed the mutual regulatory relationship between GRAS and bZIP genes, suggesting the ability of the GRAS gene to regulate abiotic stress in woodland strawberry. The expression pattern elucidated the transcriptional levels of FvGRAS genes in various tissues and the drought and salt stress in woodland strawberry, which were verified by RT-qPCR analysis.ConclusionsThe evolution and functional analysis of GRAS genes provided insights into the further understanding of GRAS genes on the abiotic stress of Rosaceae species.

Chromosome-level genome assembly reveals potential epigenetic mechanisms of the thermal tolerance in the oriental fruit fly, Bactrocera dorsalis

The oriental fruit fly, Bactrocera dorsalis (Hendel), has very strong ecological adaptability and phenotypic plasticity. Here, the genome of B. dorsalis was assembled into 549.45 Mb sequences with a contig N50 length of 12.81 Mb. Among, 95.67 % assembled genome sequences were anchored on six chromosomes with an N50 length of 94.63 Mb. According to the basic characteristics of the sex chromosomes of Tephritidae, the X chromosome of B. dorsalis was identified. Significant gene expansions were detected in several important gene families related to adaptability. In particular, we annotated 50 histone modification enzymes (HMEs) in this genome. A comparative transcriptome analysis indicated that 12 HME genes were differentially expressed in two thermo-tolerant strains (heat and cold). Interestingly, four and seven of the 12 HME genes responded to heat shock or cold hardening, respectively. These evidences suggested that the histone modification as an epigenetic modification may be involved in the thermal tolerance of B. dorsalis, but with different regulation mechanisms in thermal acclimation and hardening. The high quality genome of B. dorsalis provides an invaluable resource for further functional genomic study. Moreover, comparative genomic analysis will shed insights on revealing the mechanisms of adaptive evolution in this fly.

A chromosome-level genome of Semiothisa cinerearia provides insights into its genome evolution and control

BackgroundSemiothisa cinerearia belongs to Geometridae, which is one of the most species-rich families of lepidopteran insects. It is also one of the most economically significant pests of the Chinese scholar tree (Sophora japonica L.), which is an important urban greenbelt trees in China due to its high ornamental value. A genome assembly of S. cinerearia would facilitate study of the control and evolution of this species.ResultsWe present a reference genome for S. cinerearia; the size of the genome was ~ 580.89 Mb, and it contained 31 chromosomes. Approximately 43.52% of the sequences in the genome were repeat sequences, and 21,377 protein-coding genes were predicted. Some important gene families involved in the detoxification of pesticides (P450) have expanded in S. cinerearia. Cytochrome P450 gene family members play key roles in mediating relationships between plants and insects, and they are important in plant secondary metabolite detoxification and host-plant selection. Using comparative analysis methods, we find positively selected gene, Sox15 and TipE, which may play important roles during the larval-pupal metamorphosis development of S. cinerearia.ConclusionThis assembly provides a new genomic resource that will aid future comparative genomic studies of Geometridae species and facilitate future evolutionary studies on the S. cinerearia.

Comparative Transcriptome Analysis to Reveal Differentially Expressed Cytochrome P450 in Response to Imidacloprid in the Aphid Lion, Chrysoperla zastrowi sillemi (Esben-Petersen).

Simple SummaryChrysoperla zastrowi sillemi (CZS) is a generalist predator of arthropod pests in different crops and is distributed in wide geographical regions. Being a natural predator, CZS shares an ecological niche with the pests and is exposed to several groups of pesticides including imidacloprid. Due to continuous exposure, it has developed resistance to several insecticides. Transcriptomes of imidacloprid-resistant and susceptible strains have been generated and compared for expression differences. From the transcriptome, sequences belonging to the CYP gene family have been mined for their nomenclature and classification into the four CYP clans. Putative functions of the CYP families in CZS have been identified by phylogenetic analysis including CYP sequences from Drosophila and Tribolium. Further, differential expressions of CYP genes have been validated using qRT-PCR. We found nine CYP genes to be downregulated and one to be upregulated after imidacloprid treatment. The information from current study can be exploited for the effective implementation of IPM as it aims at sustainable and eco-friendly crop yield improvement.The aphid lion, Chrysoperla zastrowi sillemi (Neuroptera: Chrysopidae) is a highly effective beneficial predator of many agricultural pests and has developed resistance to several insecticides. Understanding the molecular mechanism of insecticide resistance in the predators is crucial for its effective application in IPM programs. Therefore, transcriptomes of imidacloprid-resistant and susceptible strains have been assessed using RNA-seq. Cytochrome P450 is one of the important gene families involved in xenobiotic metabolism. Hence, our study focused on the CYP gene family where mining, nomenclature, and phylogenetic analysis revealed a total of 95 unique CYP genes with considerable expansion in CYP3 and CYP4 clans. Further, differential gene expression (DGE) analysis revealed ten CYP genes from CYP3 and CYP4 clans to be differentially expressed, out of which nine genes (CYP4419A1, CYP4XK1, CYP4416A10, CYP4416A-fragment8, CYP6YL1, CYP6YH6, CYP9GK-fragment16, CYP9GN2, CYP9GK6) were downregulated and one (CYP9GK3) was upregulated in the resistant strain as compared to the susceptible strain. Expression validation by quantitative real-time PCR (qRT-PCR) is consistent with the DGE results. The expansion and differential expression of CYP genes may be an indicator of the capacity of the predator to detoxify a particular group of insecticides.

Origin and evolution of fatty acid desaturase genes in oil crop Brassica napus

Fatty acid (FA) desaturases, as the key enzymes in lipid metabolism, are responsible for biosynthesis of the unsaturated fatty FAs, which play important roles in maintaining cell membrane integrity and multiple stress responses. Although attention has been drawn to some plant FA desaturase genes, their global landscape in oil crops is still lacking. Here, we performed systematic characterization and phylogenomic synteny network analyses of the FA desaturase gene family in polyploid oil crop B. napus and other 54 species covering major streptophyte lineages. A total of 1653 FA desaturase genes were identified from these plant genomes. Based on the broad-scale family phylogeny and functional domains, we proposed a unified eight-group classification system for angiosperm FA desaturases, and found that the origin of genes responsible for FA desaturation evolved early and some genes were absent in different species. Phylogenomic analyses revealed deeply conserved syntenic relationships within each of the eight FA desaturase groups. B. napus contains up to 93 FA desaturase genes from the eight groups. Recurrent duplication events in Brassicaceae contributed to the expansion of FA desaturase genes in B. napus, leading to further functional diversification. These FA desaturase genes exhibited spatio-temporal specific expression patterns in different tissues of B. napus, and a set of FA desaturase genes seem to be orchestrated by key transcriptional factors during seed development, such as zf-HD, B3, GATA3, PEI1, NFYA7, YAB1 and YAB2. Altogether, our data have inferred the evolutionary trajectory of this important gene family across distinct plant lineages, providing theoretical basis for future manipulation of FA desaturase genes to improve the seed oil quality of B. napus.

The Evolution of Glycoside Hydrolase Family 1 in Insects Related to Their Adaptation to Plant Utilization.

Simple Summaryβ-glucosidase is a crucial enzyme in the adaptation of insects to plant cell wall digestion and plant metabolite detoxication. However, the evolution of this enzyme remains unclear. Here, we fill this gap by investigating the evolution of insect glycoside hydrolase family GH1, accounting for the majority of members of β-glucosidase. We found the GH1 gene family to be present in all insect species with large gene numbers in insects directly feeding on plant cell wall components. Furthermore, the large gene numbers were associated with a complex evolutionary history, including tandem duplication and neofunctionalization. These results highlight the evolutionary traits of an important insect enzyme and provide further insights into our understanding of the evolution of insect–plant interactions.Insects closely interact with plants with multiple genes involved in their interactions. β-glucosidase, constituted mainly by glycoside hydrolase family 1 (GH1), is a crucial enzyme in insects to digest plant cell walls and defend against natural enemies with sequestered plant metabolites. To gain more insights into the role of this enzyme in plant–insect interactions, we analyzed the evolutionary history of the GH1 gene family with publicly available insect genomes. We found that GH1 is widely present in insects, while the gene numbers are significantly higher in insect herbivores directly feeding on plant cell walls than in other insects. After reconciling the insect GH1 gene tree with a species tree, we found that the patterns of duplication and loss of GH1 genes differ among insect orders, which may be associated with the evolution of their ecology. Furthermore, the majority of insects’ GH1 genes were tandem-duplicated and subsequently went through neofunctionalization. This study shows the evolutionary history of an important gene family GH1 in insects and facilitates our understanding of the evolution of insect–plant interactions.

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants

In contrast to most land plant species, sorbitol, instead of sucrose, is the major photosynthetic product in many Rosaceae species. It has been well illustrated that three key functional genes encoding sorbitol-6-phosphate dehydrogenase (S6PDH), sorbitol dehydrogenase (SDH), and sorbitol transporter (SOT), are mainly responsible for the synthesis, degradation and transportation of sorbitol. In this study, the genome-wide identification of S6PDH, SDH and SOT genes was conducted in four Rosaceae species, peach, mei, apple and pear, and showed the sorbitol bio-pathway to be dominant (named sorbitol present group, SPG); another three related species, including tomato, poplar and Arabidopsis, showed a non-sorbitol bio-pathway (named sorbitol absent group, SAG). To understand the evolutionary differences of the three important gene families between SAG and SPG, their corresponding gene duplication, evolutionary rate, codon bias and positive selection patterns have been analyzed and compared. The sorbitol pathway genes in SPG were found to be expanded through dispersed and tandem gene duplications. Branch-specific model analyses revealed SDH and S6PDH clade A were under stronger purifying selection in SPG. A higher frequency of optimal codons was found in S6PDH and SDH than that of SOT in SPG, confirming the purifying selection effect on them. In addition, branch-site model analyses revealed SOT genes were under positive selection in SPG. Expression analyses showed diverse expression patterns of sorbitol-related genes. Overall, these findings provide new insights in the evolutionary characteristics for the three key sorbitol metabolism-related gene families in Rosaceae and other non-sorbitol dominant pathway species.

Molecular Cloning, Characterization, and Expression Analysis of SIMILAR TO RCD-ONE (SRO) Family Genes Responding to Abiotic and Biotic Stress in Cucumber

SIMILAR TO RCD-ONE (SRO) is a plant-specific small protein family that controls many biological processes including physiological development and stress responses. The SRO gene family has been studied in several plant species, but no detailed characterization and expression profiles of this important gene family were performed in cucumber. In this study, we characterize the SRO genes in cucumber, and determined their transcript levels in various tissues and under exposure to diverse biotic and abiotic stressors. Four SRO genes (named as CsSRO1–CsSRO4) were identified and isolated, which were distributed on three different chromosomes. Gene duplication analysis showed that only one pair of segmental duplication event was identified, but no tandem duplication events were detected. All CsSROs consist of the PARP domain and a C-terminal RST domain, while the N-terminal WWE domain was only present in CsSRO2 and CsSRO4. SROs from 15 plant species are divided into two groups (I and II), and group I can be further divided into four subgroups (Ia to Id) according to the phylogenetic tree. The conserved motif and gene structure analyses showed that SROs within the same branch of the phylogenetic tree have analogous conserved motifs configuration and gene structures. However, SRO genes possessed variable numbers of introns in different subgroups, which may affect the evolution of new family members. RNA-Seq data and qRT-PCR results showed that the four CsSRO genes have distinct expression pattern in various tissues and under diverse stresses, suggesting their multiple functions in plant growth and stress responses. The findings provide a basis for further research aiming at functional characterization of the regulatory mechanism to reveal the roles of CsSRO genes in developmental and stress-related processes of cucumber.

Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis).

BackgroundWRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses.ResultsA total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways.ConclusionsWe conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.

Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions.

Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.

FOXA1, FOXA2, SOX10 and GAS2 Gene Expression in Oral Squamous Cell Carcinoma and Their Relationship with Clinicopathological Indices

Background: The use of molecular methods in cancer diagnosis has led to a better prognosis. One of the important gene families in the carcinogenic pathways of various cancers is the forkhead box (FOX) family genes. Moreover, developmental transcription factors and proapoptotic proteins play critical roles in cell function and carcinogenesis. Objectives: The current study aimed to evaluate the expression of A1 FOXA1, FOXA2, SOX10, and growth arrest specific 2 (GAS2) genes in oral squamous cell carcinoma (OSCC) tumors due to biomarker discovery and early diagnosis of cancer. Methods: To evaluate the expression of FOXA1, FOXA2, SOX10, and GAS2 genes, 30 OSCC samples and 30 normal specimens were obtained from Imam Khomeini Hospital Cancer Institute. RNA extraction and cDNA synthesis were done by relevant kits. After a specific primer design for FOXA1, FOXA2, SOX10, and GAS2 genes, real-time PCR was done to evaluate the genes’ expression for molecular biomarker discovery and validation. ANOVA and independent t-test were used to analyze the data. Results: Significant differences were observed in the expression of the studied genes in tumor and control tissues (P < 0.001). The results showed that FOXA1, GAS2, and SOX10 expressions in tumor and normal cells have significant differences (P < 0.001). Regardless of FOXA1, FOXA2 and SOX10, there was a significant difference in the expression of GAS2 genes in term patients’ age (P < 0.05) and overexpressed in patients over 55 years. SOX10 gene is upregulated in grade II OSCC tumors but there is no significant difference in expression of FOXA1, FOXA2, and GAS2 in different stages and grades. The ROC curve analysis, FOXA1, and FOXA2 showed AUC = 0.66 and AUC = 0.57 respectively. Meanwhile, SOX10 and GAS2 showed AUC = 0.9 and AUC = 1 respectively. Conclusions: In general, the expression of FOXA1, GAS2, and SOX10 genes in cancer and control tissues were different, and therefore the role of these genes in OSCC is confirmed. Also, in the present study, the biomarker potential of SOX10 and GAS2 genes for OSCC diagnosis was demonstrated. In the current study, the important role of the studied genes in OSCC diagnosis was shown. However, further studies are needed to confirm this.

Deciphering the Molecular Mechanisms of Insecticide Resistance From the Transcriptome Data of Field Evolved Spinosad Resistant and Susceptible Populations of Plutella xylostella (Lepidoptera: Plutellidae).

Diamondback moth, Plutella xylostella is a serious pest of cruciferous vegetables and causes substantial economic loss all over the world. This study was undertaken to decipher the molecular mechanisms involved in the field evolved insecticide resistance in P. xylostella upon exposure to spinosad. To do so, spinosad-resistant and susceptible larval populations were subjected to transcriptome analysis using Illumina paired-end sequencing. De novo assembly was generated from raw reads of both the samples which resulted in the identification of 41,205 unigenes. Functional annotation and digital gene expression analysis were carried out to determine the differentially expressed genes. 1,348 unigenes were found to have a significant differential expression in the resistant population. Several genes involved in insecticide resistance like CYP P450, GSTs, small heat shock protein, and UDP glycosyltransferase were found to be up-regulated while genes related to mitochondrial energy metabolism and cuticular processes were down-regulated. Further, gene mining and phylogenetic analysis of two important gene families namely, CYP and GSTs were performed and the results revealed that these genes could play a major role in the development of field evolved spinosad resistance in P. xylostella by gene duplication and differential gene expression.

Genome-wide identification of sugar transporter gene family in Brassicaceae crops and an expression analysis in the radish

BackgroundSugar not only is an important biomacromolecule that plays important roles in plant growth, development, and biotic and abiotic stress tolerance but also provides a skeleton for other macromolecules, such as proteins and nucleic acids. Sugar transporter proteins (STPs) play essential roles in plant sugar transport and ultimately affect the abovementioned life processes. However, the evolutionary dynamics of this important gene family in Brassicaceae crops are still largely unknown, and the functional differentiation of radish STP genes remains unclear.ResultsIn the present study, a comparative genomic study of STP genes in five representative Brassicaceae crops was conducted, and a total of 25, 25, 28, 36 and 49 STP genes were individually identified in Raphanus sativus (Rs), Brassica oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj), which were divided into four clades by phylogenetic analysis. The number of STP genes was no direct correlation with genome size and the total number of coding genes in Brassicaceae crops, and their physical and chemical properties showed no significant difference. Expression analysis showed that radish STP genes play vital roles not only in flower and seedpod development but also under heavy metal (cadmium, chromium and lead), NaCl and PEG-6000 stresses, Agrobacterium tumefaciens infection, and exogenous sugar treatment. RsSTP13.2 was significantly upregulated in the resistant radish cultivar by A. tumefaciens infection and induced by heavy metal, NaCl and PEG-6000 stress, indicating that it is involved in resistance to both biotic and abiotic stress in radish.ConclusionsThe present study provides insights into the evolutionary patterns of the STP gene family in Brassicaceae genomes and provides a theoretical basis for future functional analysis of STP genes in Brassicaceae crops.