Alternative splicing during fruit development among fleshy fruits

BACKGROUND

Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits.

RESULTS

We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96-17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits.

CONCLUSIONS

We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.

Thyroid dysfunction related to vascular endothelial growth factor receptor tyrosine kinase inhibitors: A real-world study based on FAERS

WHAT IS KNOWN AND OBJECTIVE

The adverse events of thyroid dysfunction caused by the use of vascular endothelial growth factor receptor tyrosine kinase inhibitors (VEGFR-TKIs) have not been confirmed in a real-world investigation. The aim of this study was to evaluate the relationship between thyroid dysfunction and treatment using Food and Drug Administration (FDA)-approved VEGFR-TKIs.

METHODS

Four data-mining algorithms were employed to detect thyroid dysfunction signals for VEGFR-TKIs, using data in the FDA Adverse Event Reporting System (FAERS) database from 68 quarters. MySQL Workbench and R were used to conduct statistical analysis.

RESULTS AND DISCUSSION

We identified 32679 reports of thyroid dysfunction, of which 1567 listed VEGFR-TKIs as the primary suspected drugs. All four algorithms showed that the strength of the signals for hypothyroidism were greater than those for hyperthyroidism, for all the VEGFR-TKIs. In most cases, the median appearance time was within 100 days of initiation of VEGFR-TKIs therapy, except in the case of ponatinib. This indicated the need to actively identify and manage thyroid dysfunction during the early stages of VEGFR-TKIs treatment.

WHAT IS NEW AND CONCLUSIONS

This study systematically identified the pharmacovigilance signals of thyroid dysfunction associated with the use of VEGFR-TKIs, using the FAERS database.

A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes

Background

With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.

Results

We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (< 50 bp) for highly similar samples, which can be validated by simulated datasets. Moreover, we demonstrated that cSupB can adapt to the complex cycle structure.

Conclusions

Although the solution is made suitable for increasingly complex genome graphs by relaxing the constraint, the directed acyclic graph, the motif cSupB and the cSupB method can be extended to any colored directed acyclic graph. We anticipate that our method will facilitate the analysis of individual haplotype variants and population genomic diversity. We have developed a C +  + program for implementing our method that is available at https://github.com/eggleader/cSupB.

Supplementary information

The online version contains supplementary material available at 10.1186/s12859-021-04149-w.

A novel long noncoding RNA, TMEM92-AS1, promotes gastric cancer progression by binding to YBX1 to mediate CCL5

Numerous studies have revealed that long noncoding RNAs (lncRNAs) with oncogene properties play vital roles in gastric cancer (GC). In this study, we aimed to elucidate the function of TMEM92-AS1 in GC progression and to investigate its underlying mechanisms. TMEM92-AS1 was filtered from the Gene Expression Omnibus database. GC tissues and adjacent normal tissues were used to detect the expression level of TMEM92-AS1. MTT, colony-formation assays, Edu, cell cycle, apoptosis and subcutaneous tumour formation assays were used to detect the role of TMEM92-AS1 in cell function. RNA transcriptome sequencing was used to seek downstream target genes. Reverse transcription (RT)-qPCR, western blot, RNA and chromatin immunoprecipitation assays were used to investigate the mechanisms involved. TMEM92-AS1 was significantly overexpressed in GC tissues and correlated with poor overall survival and disease-free survival. Furthermore, TMEM92-AS1 promoted GC cell proliferation and migration in vitro and tumorigenic ability in vivo. RNA transcriptome sequence analysis revealed a potential downstream target gene, C-C motif chemokine ligand 5 (CCL5), and a mechanistic study found that TMEM92-AS1 regulated CCL5 by binding to the transcription factor Y-box binding protein 1(YBX1), which has oncogene properties. In addition, TMEM92-AS1 was found to be associated with peripheral blood leukocyte counts, especially neutrophils. Further investigation found that TMEM92-AS1 may affect leukocytes via regulation of the expression of granulocyte colony-stimulating factor in GC tissues. Our data provide an in-depth insight into the mechanism behind the lncRNA TMEM92-AS1, how it promotes GC progression and the possible mechanism in affecting peripheral leukocyte counts. Therefore, TMEM92-AS1 is a potential target for GC individualized therapy and prognostic assessment.

Effect of Surface Property on the Release and Oral Absorption of Solid Sirolimus-Containing Self-microemulsifying Drug Delivery System

The combination of self-microemulsifying drug delivery system (SMEDDS) and mesoporous silica materials favors the oral delivery of poorly water-soluble drugs (PWSD). However, the influence of the surface property of the mesopores towards the drug release and in vivo pharmacokinetics is still unknown. In this study, SBA-15 with hydroxyl groups (SBA-15-H), methyl groups (SBA-15-M), amino groups (SBA-15-A), or carboxyl groups (SBA-15-C) was combined with SMEDDS containing sirolimus (SRL). The diffusion and self-emulsifying of SMEDDS greatly improved the drug release over the raw SRL and SRL-SBA-15-R (R referred to as the functional groups). Results of drug absorption and X-ray photoelectron spectroscopy (XPS) showed strong hydrogen binding between SRL and the amino groups of SBA-15-A, which hindered the drug release and oral bioavailability of SRL-SMEDDS-SBA-15-A. The favorable release of SRL-SMEDDS-SBA-15-C (91.31 ± 0.57%) and SRL-SMEDDS-SBA-15-M (91.76 ± 3.72%) contributed to enhancing the maximum blood concentration (C_max) and the area under the concentration-time curve (AUC_0→48). In conclusion, the release of SRL-SMEDDS-SBA-15-R was determined by the surface affinity of the SBA-15-R and the interaction between the SRL molecules and the surface of SBA-15-R. This study suggested that the SMEDDS-SBA-15 was a favorable carrier for PWSD, and the surface property of the mesopores should be considered for the optimization of the SMEDDS-SBA-15.

Drug-Induced Hospital-Acquired Acute Kidney Injury in China: A Multicenter Cross-Sectional Survey

INTRODUCTION

Drug-induced acute kidney injury (D-AKI) is one of the important types of AKI. The incidence of D-AKI in China has rarely been studied.

OBJECTIVE

This study aims to explore the disease burden, related drugs, and risk factors of D-AKI.

METHODS

A nationwide cross-sectional survey was conducted in adult patients from 23 academic hospitals in 17 provinces in China. Suspected AKI was screened based on serum creatinine changes in accordance with the 2012 Kidney Disease: Improving Global Outcomes Clinical Practice Guideline for AKI, patients who met the diagnosis of hospital-acquired AKI in January and July of 2014 were defined. Suspected AKI was firstly evaluated for the possibility of D-AKI by pharmacists using the Naranjo Scale and finally defined as D-AKI by nephrologists through reviewing AKI clinical features.

RESULTS

Altogether 280,255 hospitalized patients were screened and 1,960 cases were diagnosed as hospital-acquired AKI, among which 735 cases were defined as having D-AKI (37.50%, 735/1,960) with an in-hospital mortality rate of 13.88% and 54.34% of the survivors did not achieve full renal recovery. 1,642 drugs were related to AKI in these patients. Anti-infectives, diuretics, and proton pump inhibitors were the top 3 types of drugs relevant to D-AKI, accounting for 66.63% cumulatively. Besides age, AKI staging, severe disease, hypoalbuminemia, plasma substitute, and carbapenem related D-AKI were independent risk factors for in-hospital mortality of D-AKI patients.

CONCLUSION

In China, D-AKI has caused a substantial medical burden. Efforts should be made to pursue nephrotoxic drug stewardship to minimize attributable risk and improve the prevention, diagnosis, and treatment of D-AKI.

Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.

Anti-FXa-IIa activity test in Asian and its potential role for drug adherence evaluation in patients with direct oral anticoagulants: a nationwide multi-center synchronization study

BACKGROUND

The data of anti-FXa-IIa activity detection in Asian population is insufficient, and its potential role for drug adherence evaluation in patients with direct oral anticoagulants (DOACs) remains unclear. This study carried out multi-center anti-FXa-IIa activity detection in Asian, aiming to explore its applicability in Asian population and find its role in adherence evaluation.

METHODS

We assessed patients' self-reported adherence using the Morisky, Green, and Levine Adherence Scale (MGLS) from six hospitals. Plasma samples were collected for peak and trough concentration determination, and anti-FXa-IIa chromogenic assay was conducted using rivaroxaban/dabigatran calibrators and controls. Multivariate logistic regression models, covariate adjustment and spearman's two-tailed test were conducted in the data analysis. This study had been registered in clinical trials (NCT03666962).

RESULTS

In total, 271 patients taking rivaroxaban (n=149) or dabigatran (n=122) were enrolled. Among the 271 patients assessed by MGLS questionnaire, 188 persons (69.4%) showed high adherence, 77 persons (28.4%) was in intermediate adherence group, and only 6 patients (2.2%) had low adherence. Patients are more adherent dosed once daily of rivaroxaban compared to twice daily of dabigatran: 75.6% vs. 63.6%. Anti-FXa-IIa activity had good linear correlation with routine coagulation indexes (P<0.001), but no significant association was found between drug adherence and anti-FXa-IIa activity (P>0.05).

CONCLUSIONS

This study confirms that anti-FXa-IIa activity detection based on target drug calibrations can be used as an effective index for pharmacodynamic evaluation in Asian population, but had limited value in drug adherence evaluation for DOACs. As the limited samples, these findings could serve as a hypothesis-generating effort, and should be validated in further studies with larger sample sizes.

Correction to: Preparation and Evaluation of Cubic Nanoparticles for Improved Transdermal Delivery of Propranolol Hydrochloride

Xin Zhou is a co-corresponding author of this published article and the affiliation should read "Xin Zhou^{1, 3}".

Preparation and Evaluation of Cubic Nanoparticles for Improved Transdermal Delivery of Propranolol Hydrochloride

Transdermal drug delivery of propranolol hydrochloride (PRH) is promising for the treatment of infantile hemangioma (IH). Clinically used PRH hydrogel fails to reach the deep IH for complete recovery. In this study, the PRH-loaded cubic nanoparticles (CNPs) were prepared to promote the transdermal effect of PRH. A remote drug loading method was developed to prepare the PRH-CNPs. For the traditional passive drug loading method, the largest encapsulation efficiency (EE%) was around 50%. The remote drug loading was performed by increasing the pH of the mixture of blank CNPs and PRH solution. The optimal PRH-CNPs showed an EE% of 90.15 ± 2.44% at pH 8.5. The permeation of the PRH solution was poor while the PRH-CNPs showed greatly enhanced skin permeation. It was found that smaller-sized PRH-CNPs contributed to increased skin permeation and retention. In addition, the PRH-CNPs had higher cytotoxicity towards the EOMA cells when compared with the PRH solution. During storage for 1 month, the PRH-CNPs kept stable size distribution, pH, and EE%. In conclusion, results of this study suggested that the PRH-CNPs could be a potential candidate for the treatment of the IH by transdermal delivery.

Cationic nanoemulsions with prolonged retention time as promising carriers for ophthalmic delivery of tacrolimus

Tacrolimus, also known as FK506, is a first-line drug for the topical treatment of immune-mediated inflammatory anterior ocular diseases (IIAODs). However, due to its limited water solubility, hydrophobic nature and relatively high molecular weight, topical application of FK506 features poor bioavailability. Numbers of formulations have been attempted to enhance the erratic bioavailability of FK506 through various techniques. But until now, none of them could satisfy the clinical needs completely. Here, a novel formulation of FK506, FK506-loaded cationic nanoemulsions (FK506 CNE), was developed to prolong the precorneal residence time of FK506, thereby enhancing the bioavailability of FK506 for IIAODs therapy. FK506 CNE was prepared by high-pressure homogenization, and its composition was screened and optimized by single-factor experiments. The FK506 CNE showed spherical morphology with a mean diameter of 178.8 ± 2.7 nm and a zeta potential of +25.6 ± 0.6 mV. Results from in vivo gamma scintigraphy studies proved that the precorneal residence time of FK506 CNE was significantly increased, compared with FK506-loaded neutral nanoemulsions (FK506 NE) and saline. The data of aqueous humor pharmacokinetic study in rabbits showed that the relative bioavailability of FK506 CNE was 1.68-fold and 1.77-fold of FK506 NE and the marketed FK506 eye drops (Talymus®), respectively. Finally, hematoxylin and eosin staining images and in vitro cytotoxicity data confirmed the safety of the FK506 CNE. Taking all these into consideration, we propose that FK506 CNE is a promising topical ophthalmic nanoformulation for the management of IIAODs.

Possible Involvement of Tissue Plasminogen Activator/Brain-Derived Neurotrophic Factor Pathway in Anti-Depressant Effects of Electroacupuncture in Chronic Unpredictable Mild Stress-Induced Depression in Rats

OBJECTIVE

Using a rat model of chronic unpredictable mild stress (CUMS), to investigate the effects of electroacupuncture (EA) on the tissue plasminogen activator (tPA)/brain-derived neurotrophic factor (BDNF) pathway.

METHODS

Sixty male Sprague-Dawley rats were randomly divided into four groups: normal, model, fluoxetine (fluox), or EA. Experimental groups were subjected to 28 d of CUMS modeling. One hour after CUMS, the fluox and EA groups were treated with fluox and a 20 min EA intervention, respectively. Depressive-like behaviors were assessed by open field and sucrose preference tests. After the rats were sacrificed, brains were dissected and processed using hematoxylin and eosin (HE) staining to observe changes in the morphology and quantity of neurons in the hippocampal cornu ammonis 3 area. Western blot and real-time polymerase chain reaction (PCR) demonstrated the effects of EA on the tPA/BDNF pathway-related molecules in the hippocampi and raphe nuclei.

RESULTS

Compared to the model group, the number of horizontal and vertical movements and the percentage of sucrose consumption in the EA groups were significantly increased (P < 0.01). Compared to the model group, HE staining showed that the hippocampal neurons in the EA and fluox groups were arranged neatly, with rich layers and complete cell structures. The Western blot and real-time PCR showed that the levels of tPA, BDNF, tropomyosin receptor kinase B, and BDNF micro RNA (mRNA) in the hippocampi of the EA group were higher than in the model group (P < 0.01, P < 0.01, P < 0.05, P < 0.01, respectively). The content of p75NTR, proBDNF, and tPA mRNA in the hippocampi of the EA group displayed no significant differences compared to the model group. The tPA mRNA content in the raphe nuclei of the EA group was higher than in the model group (P < 0.01), and the BDNF content in the raphe nuclei was lower than in the model group (P < 0.05). There were no significant differences in tPA and BDNF mRNA between the EA and model groups.

CONCLUSION

EA may reverse depressive-like behaviors in CUMS, which may be related to the tPA/BDNF pathway in the hippocampus.

SOX2 gene expression and its role in triple negative breast cancer tissues

The aim of this work was to study the expression of SOX2 gene in triple negative breast cancer and its role. One hundred and twenty specimens of paraffin-embedded triple negative breast cancer (TNBC) tissues were collected from Harbin Medical University Cancer Hospital, Heilongjiang, China between January 2014 and March 2018. The expression of SOX2 was detected using immunohistochemistry, and the relationship between the expression of SOX2 and clinical features was analyzed. Breast cancer cell lines (normal group, SOX2 interference group, SOX2 overexpression group) were cultured in vitro to detect the proliferation and cloning ability of the cell lines. The expression of SOX2 was related to lymph node metastasis and stage of breast cancer (P less than 0.05), but was not related to age, menopause or tumor size (P > 0.05); the expression of SOX2 in the overexpression group was significantly greater than that in the normal group after 72 hours, and no significant difference between the overexpression group and the interference group was observed. The number of clone cells with a diameter of 0.5 mm in the interference group was lower compared to the normal group, and that of the overexpression group was higher, but not significant. SOX2 is associated with the high invasiveness of breast cancer and can be used as a therapeutic target to inhibit the metastasis of cancer cells. SOX2 can promote the proliferation of breast cancer cells and affect the size of clone cells in its involvement in clone.

Pharmacokinetics and tissue distribution of monotropein and deacetyl asperulosidic acid after oral administration of extracts from Morinda officinalis root in rats

BACKGROUND

Iridoid glycosides (IGs), including monotropein (MON) and deacetyl asperulosidic acid (DA) as the main ingredients, are the major chemical components in Morinda officinalis How. (MO) root, possessing various pharmacological properties including anti-osteoporosis, anti-inflammation and anti-rheumatism activities.The aim of the present study was to further elucidate the pharmacological actions of MO by investigating the pharmacokinetics and tissue distribution of IGs in MO.

METHODS

An ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS) method was developed and validated for simultaneous determination of MON and DA levels in plasma and various tissues of Wistar rats. MON, DA and acetaminophen (ACE) as the internal standard (IS) were extracted from rat plasma and tissue samples by direct deproteinization with methanol. The rats were administered orally at 1650 mg/kg MO and 25, 50 and 100 mg/kg MO iridoid glycosides (MOIGs) or intravenously at MOIG 25 mg/kg for pharmacokinetic study of MON and DA. In addition, 100 mg/kg MOIG was administered orally for tissue distribution study of MON and DA. Non-compartmental pharmacokinetic profiles were constructed. Tissue distributions were calculated according to the validated methods.

RESULTS

Significant differences in the pharmacokinetic parameters were observed in male and female rats. The AUC0-t, Cmax and bioavailability of MON and DA in female rats were higher than those in male rats. MON and DA mainly distributed in the intestine and stomach after oral administration, and noteworthily high concentrations of MON and DA were detected in the rat hypothalamus.

CONCLUSION

The results of the present study may shed new lights on the biological behavior of MOIGs in vivo, help explain their pharmacological actions, and provide experimental clues for rational clinical use of these IGs extracted from the MO root.

[Management strategies of granulation in tracheal post-tracheostomy caused by prolonged mechanical ventilation]

Objective:To analyze the effect and safety of treatment in patients with airway stenosis caused by tracheotomy for mechanical ventilation. Method: We treated the patients with airway stenosis caused by granulation tissue. The patients with grade Ⅰ,Ⅱ airway stenosis were treated with adjustable flange tracheostomy tube, and the holmium laser under a fibro-laryngoscope were applied for the patients with grade Ⅲ airway stenosis.Two hundred and sixteen patients were enrolled in this study. Forty-four patients had been found tracheal stenosis caused by granulomatous hyperplasia, accounting for 20.4% of all patients, including 12 cases of gradeⅠ, 18 cases of grade Ⅱ, and 14 cases of grade Ⅲ.Result:Thirty patients with grade Ⅰ and Ⅱ were replaced with adjustable flange tracheostomy cannula. Fourteen cases of grade Ⅲ airway stenosis were treated with Ho:YAG laser under a fibro laryngoscope. All cases were completed operation successfully. None of cases bleeding, perforated and asphyxia during operation. The clinical symptoms disappeared after operation, and endoscopy showed that airways of patients were smooth. No recurrence were found after operation.Conclusion: Replacement of adjustable flange tracheostomy tube and Ho:YAG laser can safely and effectively treat airway obstruction caused by tracheal granulation tissue hyperplasia after tracheotomy.

[Photochemical induced vestibular ischemiawith icy water test in guinea pigs]

Objective:To ascertain the effects of a new method of photochemical reaction in vestibular function in guinea pigs.Method:Local photochemical reaction was initiated by systemic injection of rose bengal(20mg), photoillumination of the vestibule through medial wall of epitympanum for 30 minutes was started immediately after the injection of rose bengal, with a optic fiber connected to a xenon light (wavelength, 540nm; photointense, 500-600 mW/cm ²). There were 20 guinea pigs divided random equally into 2 groups. Group 1 was injected with rose bengal. Group 2 was control, injected with physiological saline solution. The ice caloric tests were performed on the second day.Result:The test group (7 ears) and the control group (6 ears) with test nystagmus showed mean frequencies were（2.0±0.33）times/s and（3.7±0.33）times/s,the mean amplitude were (3.1±0.39)mm and (3.5±0.54)mm,and the mean duration were (44.7±17.22)s and (62.0±7.22)s respectively.The nystagmus frequency difference was statistically significant, but the amplitude and the duration of the nystagmus were not significantly different. There was no obvious spontaneous nystagmus in the two groups, and there were negative results of ice water test (3 ears in the test group and 4 ears in the control group).Conclusion:Photochemical reaction can induce the ischemic state of the vestibule system in guinea pig, and produce an acute vestibular dysfunction, and ice water test shows that the frequency of nystagmus is reduced.

An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome

Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement. In general, accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. As one of the most reliable strategies, the determination of collinearity information may facilitate reliable orthology inferences among genes from multiple related genomes. Currently, the identification of collinear segments has mainly been based on conservation of gene order and orientation. Over the course of plant genome evolution, various evolutionary events have disrupted or distorted the order of genes along chromosomes, making it difficult to use those genes as genome-wide markers for plant genome comparisons. Results: Using the localized LASTZ/MULTIZ analysis pipeline, we aligned 15 genomes, including cucumber and other related angiosperm plants, and identified a set of genomic segments that are short in length, stable in structure, uniform in distribution and highly conserved across all 15 plants. Compared with protein-coding genes, these conserved segments were more suitable for use as genomic markers for detecting collinear segments among distantly divergent plants. Guided by this set of identified collinear genomic segments, we inferred 94,486 orthologous protein-coding gene pairs (OPPs) between cucumber and 14 other angiosperm species, which were used as proxies for transferring functional terms to cucumber genes from the annotations of the other 14 genomes. In total, 10,885 protein-coding genes were assigned Gene Ontology (GO) terms which was nearly 1,300 more than results collected in Uniprot-proteomic database. Our results showed that annotation accuracy would been improved compared with other existing approaches. Conclusions: In this study, we provided an alternative resource for the functional annotation of predicted cucumber protein-coding genes, which we expect will be beneficial for the cucumber's biological study, accessible from http://cmb.bnu.edu.cn/functional_annotation. Meanwhile, using the cucumber reference genome as a case study, we presented an efficient strategy for transferring gene functional information from previously well-characterized protein-coding genes in model species to newly sequenced or "non-model" plant species.